Systemic acidemia impairs cardiac function in critically Ill patients.

BACKGROUND: Acidemia, is associated with reduced cardiac function in animals, but no studies showing an effect of acidemia on cardiac function in humans are reported. In the present study, we examined the effect of acidemia on cardiac function assessed with transpulmonary thermodilution technique with integrated pulse contour analysis (Pulse Contour Cardiac Output, PiCCO™) in a large cohort of critically ill patients. METHODS: This was a prospective multicenter observational cross-sectional study of 297 patients from 6 intensive care units in London, England selected from all patients admitted consecutively between May 2018 and March 2019. Measurements of lowest plasma pH and concurrent assessment of cardiac function were obtained. FINDINGS: There was a significant difference between two pH categories (pH ≤ 7.28 vs. pH > 7.28) for the following variables of cardiac function: SVI (difference in means 32.7; 95% CI: 21 to 45 mL/m2; p < 0.001); GEF (18; 95% CI: 11 to 26%; p < 0.001), dPmax (-331; 95% CI: -510 to -153 mmHg/s; p = 0.001), CFI (0.7; 95% CI: 0.2 to 1.3 1/min; p = 0.01) and CPI (0.09; 95% CI: 0.03 to 0.15 W/m2; p < 0.001). However, there was no significant difference in CI (0.13; 95% CI: -0.20 to 0.47 L/min/m2; p = 0.12) between the pH categories. Also, a significant relationship was found between the quantitative pH and the following variables: SVI (132; 95% CI: 77 to 188 mL/m2; p < 0.001), GEF (74.7; 95% CI: 37.1 to 112.4%; p < 0.001), dPmax (-1587; 95% CI: -2361 to -815 mmHg/s; p < 0.001), CFI (3.5; 95% CI: 0.9 to 6.1 /min; p = 0.009), CPI (0.62; 95% CI: 0.36 to 0.88 W/m2; p < 0.001) and CI (regression coefficient 1.96; 95% CI:0.45 to 3.47 L/min/m2; p = 0.01). INTERPRETATION: Acidemia is associated with impaired cardiac function in seriously ill patients hospitalized in the intensive care unit supporting the potential value of early diagnosis and improvement of arterial pH in these patients. FUNDING: The study was partially supported by unrestricted funds from the UCLA School of Medicine.

Referrer and service provider beliefs and attitudes towards rehabilitation in the home; factors related to utilisation of Early Supported Discharge.

PURPOSE: To investigate the attitudes and beliefs held by referrers and service providers of an Australian Early Supported Discharge (ESD) service called "Rehabilitation in the Home" (RITH); with particular consideration of factors that may influence referral to RITH. METHODS: A cross-sectional online survey based on the Theory of Planned Behaviour was undertaken. RESULTS: There were 113 respondents; 90 referrers and 23 service providers. Referrers and RITH staff had a moderately favourable attitude towards RITH. The majority of referrers, and, to a greater degree, RITH staff members, understood and appreciated the advantages ascribed to ESD. However, views varied with regard to some of the factors upon which the decision to refer to RITH rests. Two-fifths of referrers did not think that RITH provided hospital equivalent therapy intensity and over one-fifth of referrers had concerns about the capability of the RITH service to provide specialist stroke rehabilitation. Opinion of RITH staff was also varied on these topics. CONCLUSIONS: This study provides evidence that there was a level of uncertainty amongst referrers and RITH service providers regarding issues directly and indirectly related to patient eligibility and RITH service capability. This uncertainty needs to be explored in future research. IMPLICATIONS FOR REHABILITATION: Differences in views held by referrers and ESD service providers were identified in this study that could lead to inconsistencies in patient selection for, and under-utilization of, ESD services. Improved communication between referrers and ESD service providers, for instance attendance of RITH staff at inpatient team meetings, could ameliorate some of these misconceptions. On-going education of referrers about service capability is essential to ensure timely transfer of appropriate clients to ESD services.

Urea transport in bacteria: acid acclimation by gastric Helicobacter spp.

Urea transporters in bacteria are relatively rare. There are three classes, the ABC transporters such as those expressed by cyanobacteria and Corynebacterium glutamicum, the Yut protein expressed by Yersinia spp and the UreI expressed by gastric Helicobacter spp. This review focuses largely on the UreI proton-gated channel that is part of the acid acclimation mechanism essential for gastric colonization by the latter. UreI is a six-transmembrane polytopic integral membrane protein, N and C termini periplasmic, and is expressed in all gastric Helicobacter spp that have been studied but also in Helicobacter hepaticus and Streptococcus salivarius. The first two are proton-gated, the latter is pH insensitive. Site-directed mutagenesis and chimeric constructs have identified histidines and dicarboxylic amino acids in the second periplasmic loop of H. pylori and the first loop of H. hepaticus UreI and the C terminus of both as involved in a hydrogen-bonding dependence of proton gating, with the membrane domain in these but not in the UreI of S. salivarius responding to the periplasmic conformational changes. UreI and urease are essential for gastric colonization and urease associates with UreI during acid exposure, facilitating activation of the UreA and UreB apoenzyme complex by Ni2+ insertion by the UreF-UreH and UreE-UreG assembly proteins. Transcriptome analysis of acid responses of H. pylori also identified a cytoplasmic and periplasmic carbonic anhydrase as responding specifically to changes in periplasmic pH and these have been shown to be essential also for acid acclimation. The finding also of upregulation of the two-component histidine kinase HP0165 and its response element HP0166, illustrates the complexity of the acid acclimation processes involved in gastric colonization by this pathogen.

Detection and localization of H+-K+-ATPase isoforms in human kidney.

An H+-K+-ATPase contributes to hydrogen secretion and potassium reabsorption by the rat and rabbit collecting ducts. Transport of these ions appears to be accomplished by one or both of two isoforms of the H+-K+-ATPase, HKalpha(1) and HKalpha(2,) because both isoforms are found in the collecting ducts and transport of hydrogen and potassium is attenuated by exposure to inhibitors of these transport proteins. To evaluate whether an H+-K+-ATPase is present in the human kidney, immunohistochemical studies were performed using normal human renal tissue probed with antibodies directed against epitopes of three of the known isoforms of the H+-K+-ATPase , HKalpha(1), HKalpha(2), and HKalpha(4), and the V-type H+-ATPase. Cortical and medullary tissue probed with antibodies against HKalpha(1) showed cytoplasmic staining of intercalated cells that was less intense than that observed in the parietal cells of normal rat stomach stained with the same antibody. Also, weak immunoreactivity was detected in principal cells of the human collecting ducts. Cortical and medullary tissue probed with antibodies directed against HKalpha(4) revealed weak, diffuse staining of intercalated cells of the collecting ducts and occasional light staining of principal cells. Cortical and medullary tissue probed with antibodies directed against the H+-ATPase revealed staining of intercalated cells of the collecting ducts and some cells of the proximal convoluted tubules. By contrast, no discernible staining was noted with the use of the antibody against HKalpha(2). These data indicate that HKalpha(1) and HKalpha(4) are present in the collecting ducts of the human kidney. In this location, these isoforms might contribute to hydrogen and potassium transport by the kidney.

Use of base in the treatment of severe acidemic states.

Severe acidemia (blood pH < 7.1 to 7.2) suppresses myocardial contractility, predisposes to cardiac arrhythmias, causes venoconstriction, and can decrease total peripheral vascular resistance and blood pressure, reduce hepatic blood flow, and impair oxygen delivery. These alterations in organ function can contribute to increased morbidity and mortality. Although it seemed logical to administer sodium bicarbonate to attenuate acidemia and therefore lessen the impact on cardiac function, the routine use of bicarbonate in the treatment of the most common causes of severe acidemia, diabetic ketoacidosis, lactic acidosis, and cardiac arrest, has been an issue of great controversy. Studies of animals and patients with these disorders have reported conflicting data on the benefits of bicarbonate, showing both beneficial and detrimental effects. Alternative alkalinizing agents, tris-hydroxymethyl aminomethane and Carbicarb, have shown some promise in studies of animals and humans, and reevaluation of these buffers in the treatment of severe acidemic states seems warranted. The potential value of base therapy in the treatment of severe acidemia remains an important issue, and further studies are required to determine which patients should be administered base therapy and what base should be used.

HEMO equilibrated Kt/V goals are difficult to achieve in large male patients.

The long-term outcome of chronic hemodialysis patients is influenced by the adequacy of dialysis treatment. A major objective of the ongoing US HEMO Study is to determine if a higher target value of treatment as measured by the equilibrated Kt/V (eKt/V), a calculation of dialysis adequacy developed for the study, of 1.45 results in a better outcome than the presently accepted target value for eKt/V of 1.05 (approximately equal to spKt/V of 1.2). eKt/V corrects for urea rebound and gives a better estimate of actual treatment received. To examine the feasibility of achieving the higher eKt/V in large hemodialysis patients, a retrospective analysis of 389 monthly eKt/V values from 65 men on chronic hemodialysis of larger than average size dialyzed at high blood and dialysate flows (QB 400, QD 800 ml/min) with large dialyzers (1.8-2.2 m2) for longer than 4 hours three times weekly was performed. A total of 278 treatments considered optimal by a blood water urea clearance estimate were included in the final analyses. The mean body weight and Chertow water volume were 84.3+/-16.5 kgm and 50.0+/-6.7 L, respectively. The mean sp Kt/V was 1.29+/-0.17. The mean eKt/V was 1.16+/-0.14 and was inversely correlated with weight and water volume (p < 0.0001). Despite the large dialyzers and high blood and dialysate flow rates, no patient weighing more than 80 kgm or with body water volume exceeding 46 liters achieved an eKt/V of 1.45. This study suggests that creative dialyses will be required to achieve the HEMO "high arm" target in large patients.

Approach to patients with acid-base disorders.

Disorders of acid-base balance are commonly encountered in clinical practice and can have a substantial impact on the prognosis of the patient. Moreover, identification of a particular acid-base disturbance can provide a clue to an underlying disorder. Proper evaluation and treatment of acid-base disorders requires a systematic and analytic approach including: (1) assess the accuracy of the acid-base values using the Henderson equation or Henderson-Hasselbalch equation, (2) obtain a complete history and physical examination, (3) calculate the serum anion gap, (4) identify the primary acid-base disturbance and determine whether a simple or mixed disturbance is present, (5) examine serum electrolytes and additional laboratory data, and (6) measure urine pH and urine electrolytes and calculate the urine anion and osmolal gaps. Strict adherence to these principles will enable the clinician to diagnose the acid-base disturbance in the majority of cases. To illustrate these principles, 5 cases of patients with acid-base disturbances are analyzed.

Disturbances of acid-base balance and bone disease in end-stage renal disease.

Bone disease in patients with chronic renal failure (CRF) is thought to be the consequence primarily of the interplay of several factors, including the serum levels of parathyroid hormone (PTH), vitamin D, calcium, and phosphorus, and exposure to bone toxins such as aluminum or amyloid. Recently the metabolic acidosis noted with CRF has been implicated as an additional factor contributing to the genesis of bone disease. Although metabolic acidosis might be the dominant factor in the cause of bone disease in some instances, more commonly this acid-base disturbance interacts with other factors contributing to the development of bone disease. The following article summarizes the data in support of an important role for metabolic acidosis in the genesis of bone disease in patients with CRF and presents our recommendations for treatment of uremic acidosis to prevent or treat the bone disease.

Successful utilization of ECMO to treat an adult burn patient with ARDS.

We present an interesting case of the first adult reported in the United States to suffer from thermal burns, adult respiratory distress syndrome (ARDS) and to be treated with extracorporeal membrane oxygenation (ECMO) who survived. Our patient is a 26 year old male who sustained thermal burns (12% TBSA) to his face and anterior trunk and broncoscopically demonstrable inhalation injury. He was transported to our regional burn center for burn wound care and ventilatory support. The patient was treated with silver sulfadiazine 1% to his wounds which healed per primam. Because of low oxygen saturation he required increasing FIO2. The following parameters: FIO2= 1, PEEP = 17, minute ventilation of 15.1 1, peak airway pressure of 45 and mean of 27, along with chest X-rays corroborated the severity of ARDS. The patient failed volume control ventilation. A trial of pressure ventilation was attempted but the patient only reached O2 saturation in the low 80s. At this point, the decision was made to transfer the patient to a hospital capable of ECMO treatment. The patient was subsequently treated with veno venous ECMO. Six weeks later the patient was discharged from the hospital off all ventilatory support.

The Na(+)-K(+)-ATPase beta 1 subunit is associated with the HK alpha 2 protein in the rat kidney.

The Na-K-ATPase beta 1 subunit acts as the beta subunit for the HK alpha 2 protein in the rat kidney. The colonic H(+)-K(+)-ATPase is a member of the P-type ATPases, and has been shown to contribute to potassium transport by the mammalian kidney and colon. The P-type ATPases often consist of an alpha subunit that contains the catalytic site and a beta subunit that participates in regulation of enzyme activity and targeting of the enzyme to the plasma membrane. The cDNA of the alpha subunit (HK alpha 2) has been cloned and the HK alpha 2 protein has been isolated from the rat kidney and colon. However, a unique beta subunit for the colonic H(+)-K(+)-ATPase has not been described. To determine if one of the known beta subunits present in the kidney might act as the beta subunit for the colonic H(+)-K(+)-ATPase, microsomes enriched in the colonic H(+)-K(+)-ATPase were isolated using an HK alpha 2-specific antibody (AS 31.7) and the Minimac magnetic separation system. Immunoblots of rat kidney microsomal protein isolated with antibody AS 31.7 were probed with antibodies directed against the gastric HK beta subunit, Na(+)-K(+)-ATPase alpha 1, and Na(+)-K(+)-ATPase beta 1 subunits. A band of the appropriate size was detected with Na(+)-K(+)-ATPase beta 1-specific antibodies, but not those directed against HK beta 1. These data suggest that Na(+)-K(+)-ATPase beta 1 could be the beta subunit for the colonic H(+)-K(+)-ATPase in the kidney.

Trilaminar skin coverage combined with cultured epithelial autografts--a new technique for treating the elderly patient with burn injuries.

Additional morbidity may be associated with standard split-thickness skin graft donor sites in elderly (65 years or older) patients with burn injuries. In an attempt to minimize the area of the donor sites and maximize autografts, we describe a new technique that uses trilaminar harvesting of skin grafts with dermolipectomy closure, and permanent coverage of the autograft layers achieved with cultured epithelial autografts in an elderly burn victim. An 80-year-old man was admitted with a 15% total body surface area burn to the bilateral lower extremities and buttocks. All meshed split-thickness skin grafts (12) applied showed excellent take, and it was reported that the cultured epithelial autograft take was approximately 90%. All dermolipectomy sites healed without infection. Our procedure proved to be a useful technique in the permanent closure of full- and partial-thickness burns in an elderly patient admitted to the burn unit.

Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism.

DNA polymerase beta (pol beta) fills single nucleotide (nt) gaps in DNA produced by the base excision repair pathway of mammalian cells. Crystal structures have been determined representing intermediates in the 1 nt gap-filling reaction of pol beta: the binary complex with a gapped DNA substrate (2.4 A resolution), the ternary complex including ddCTP (2.2 A), and the binary product complex containing only nicked DNA (2.6 A). Upon binding ddCTP to the binary gap complex, the thumb subdomain rotates into the closed conformation to contact the otherwise solvent-exposed ddCTP-template base pair. Thumb movement triggers further conformational changes which poise catalytic residue Asp192, dNTP, and template for nucleotidyl transfer, effectively assembling the active site. In the product nicked DNA complex, the thumb returns to the open conformation as in the gapped binary DNA complex, facilitating dissociation of the product. These findings suggest that pol beta may enhance fidelity by an induced fit mechanism in which correct base pairing between template and incoming dNTP induces alignment of catalytic groups for catalysis (via thumb closure), but incorrect base pairing will not. The structures also reveal that pol beta binds both gapped and nicked DNA with a 90 degrees kink occurring precisely at the 5'-phosphodiester linkage of the templating residue. If the DNA were not kinked in this way, contact between the thumb and dNTP-template base pair, presumably important for the checking mechanism, would be impossible, especially when the gap is but a single nucleotide. Such a 90 degrees kink may be a mechanistic feature employed by any polymerase involved in filling gaps to completion.

Effect of hypokalemia on the abundance of HK alpha 1 and HK alpha 2 protein in the rat kidney.

An H(+)-K(+)-adenosinetriphosphatase (H(+)-K(+)-ATPase) contributes to potassium reabsorption by the collecting ducts of the rat kidney. mRNAs for two isoforms of the H(+)-K(+)-ATPase, HK alpha 1 and HK alpha 2, have been found in the rat kidney. To evaluate whether the HK alpha 1 and HK alpha 2 proteins are present in the rat kidney, microsomes enriched in HK alpha 1 or HK alpha 2 were isolated using the MiniMac magnetic separation system with antibodies directed against either HK alpha 1 (HK 12.18) or HK alpha 2 (AS 31.7). Immunoblots of rat kidney microsomal protein isolated with HK 12.18 revealed a band approximately 94 kDa in size that comigrated with the G1 fraction of the stomach. Immunoblots of rat kidney microsomal protein isolated with AS 31.7 revealed a band slightly greater than 94 kDa that comigrated with a band obtained from rat colonic microsomal protein. To examine the effect of perturbations in potassium metabolism, the abundance of the HK alpha 1 and HK alpha 2 isoforms was compared in rats fed a normal or potassium-deficient diet. A low-potassium diet increased the abundance of HK alpha 2, whereas that of HK alpha 1 was not altered. These data suggest that HK alpha 2 might be the isoform responsible for potassium conservation by the kidney.

Concomitant laparoscopic cholecystectomy and splenectomy for surgical management of hereditary spherocytosis.

Laparoscopic splenectomy is rapidly becoming a common treatment modality in the surgical management of hematological processes involving the spleen. Hereditary spherocytosis is the most common red blood cell membrane disorder, and its diagnosis is often associated with hemolytic crisis and premature cholelithiasis. This condition has not been successfully treated laparoscopically until recently, and to our knowledge, the technique of concomitant laparoscopic splenectomy and cholecystectomy described here is the first reported in U.S. literature. Our patients, a 16-year-old 5-foot 3-inch-tall 90 pound emaciated albino, presented with cholelithiasis, splenomegaly, and anemia. Because of persistent anemia and gastrointestinal symptoms, the patient underwent laparoscopic cholecystectomy and splenectomy. The cholecystectomy was performed in a standard laparoscopic fashion. An additional 12-mm trocar was utilized for takedown of the spleen. The umbilical incision was extended to 4.5 cm, and the spleen was extracted manually. Total operative time was 12 hours. Examination demonstrated a 15 x 10 x 5-cm spleen, which weighed 350 grams. The gallbladder microscopically showed cholecystitis and had several stones. In conclusion, we present a combined laparoscopic cholecystectomy and splenectomy for hereditary spherocytosis associated with splenomegaly, cholelithiasis, and cholecystitis.

pH-dependent conformational changes in Escherichia coli dihydrofolate reductase revealed by Raman difference spectroscopy.

The catalytic site of all dihydrofolate reductases contains an invariant carboxylic acid, equivalent to Asp-27 in Escherichia coli dihydrofolate reductase (ecDHFR). It has been found that various kinetic and ligand binding properties of ecDHFR show a pH profile with a pKa of about 6.5. The group responsible for this pKa is often assumed to be carboxyl group of Asp-27. To determine the ionization state of this carboxyl and its pKa, we have employed a novel method, based on Raman difference spectroscopy, to obtain its vibrational spectrum in situ. The method is general for the study of protein carboxyl groups, which are often significantly implicated in protein function and structure; this study establishes the method's limits and problems. The Raman difference spectrum between wild-type ecDHFR and the Asp-27 to serine mutant (D27S) in the pH range 5.6-9.0 has been taken. No protonation of the carboxyl group was detected, implying that its pKa is probably less than 5.0. We did, however, detect a pH dependence in the intensity of Raman bands in the difference spectrum with a pKa of 6.3, indicating that the apo enzyme undergoes a pH-dependent conformational change. Because the carboxyl group of Asp-27 at the active site is the only ionizable group in the binding site, other groups, away from the catalytic site, must be responsible for the pH behavior of ecDHFR.

Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: crystallographic evidence.

The reaction catalyzed by Escherichia coli dihydrofolate reductase (ecDHFR) cycles through five detectable kinetic intermediates: holoenzyme, Michaelis complex, ternary product complex, tetrahydrofolate (THF) binary complex, and THF.NADPH complex. Isomorphous crystal structures analogous to these five intermediates and to the transition state (as represented by the methotrexate-NADPH complex) have been used to assemble a 2.1 A resolution movie depicting loop and subdomain movements during the catalytic cycle (see Supporting Information). The structures suggest that the M20 loop is predominantly closed over the reactants in the holoenzyme, Michaelis, and transition state complexes. But, during the remainder of the cycle, when nicotinamide is not bound, the loop occludes (protrudes into) the nicotinamide-ribose binding pocket. Upon changing from the closed to the occluded conformation, the central portion of the loop rearranges from beta-sheet to 3(10) helix. The change may occur by way of an irregularly structured open loop conformation, which could transiently admit a water molecule into position to protonate N5 of dihydrofolate. From the Michaelis to the transition state analogue complex, rotation between two halves of ecDHFR, the adenosine binding subdomain and loop subdomain, closes the (p-aminobenzoyl)glutamate (pABG) binding crevice by approximately 0.5 A. Resulting enhancement of contacts with the pABG moiety may stabilize puckering at C6 of the pteridine ring in the transition state. The subdomain rotation is further adjusted by cofactor-induced movements (approximately 0.5 A) of helices B and C, producing a larger pABG cleft in the THF.NADPH analogue complex than in the THF analogue complex. Such movements may explain how THF release is assisted by NADPH binding. Subdomain rotation is not observed in vertebrate DHFR structures, but an analogous loop movement (residues 59-70) appears to similarly adjust the pABG cleft width, suggesting that these movements are important for catalysis. Loop movement, also unobserved in vertebrate DHFR structures, may preferentially weaken NADP+ vs NADPH binding in ecDHFR, an evolutionary adaptation to reduce product inhibition in the NADP+ rich environment of prokaryotes.

A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta.

When crystals of human DNA polymerase beta (pol beta) complexed with DNA [Pelletier, H., Sawaya, M. R., Wolfle, W., Wilson, S. H., & Kraut, J. (1996) Biochemistry 35, 12742-12761] are soaked in the presence of dATP and Mn2+, X-ray structural analysis shows that nucleotidyl transfer to the primer 3'-OH takes place directly in the crystals, even though the DNA is blunt-ended at the active site. Under similar crystal-soaking conditions, there is no evidence for a reaction when Mn2+ is replaced by Mg2+, which is thought to be the divalent metal ion utilized by most polymerases in vivo. These results suggest that one way Mn2+ may manifest its mutagenic effect on polymerases is by promoting greater reactivity than Mg2+ at the catalytic site, thereby allowing the nucleotidyl transfer reaction to take place with little or no regard to instructions from a template. Non-template-directed nucleotidyl transfer is also observed when pol beta-DNA cocrystals are soaked in the presence of dATP and Zn2+, but the reaction products differ in that the sugar moiety of the incorporated nucleotide appears distorted or otherwise cleaved, in agreement with reports that Zn2+ may act as a polymerase inhibitor rather than as a mutagen [Sirover, M. A., & Loeb, L. A. (1976) Science 194, 1434-1436]. Although no reaction is observed when crystals are soaked in the presence of dATP and other metal ions such as Ca2+, Co2+, Cr3+, or Ni2+, X-ray structural analyses show that these metal ions coordinate the triphosphate moiety of the nucleotide in a manner that differs from that observed with Mg2+. In addition, all metal ions tested, with the exception of Mg2+, promote a change in the side-chain position of aspartic acid 192, which is one of three highly conserved active-site carboxylate residues. Soaking experiments with nucleotides other than dATP (namely, dCTP, dGTP, dTTP, ATP, ddATP, ddCTP, AZT-TP, and dATP alpha S) reveal a non-base-specific binding site on pol beta for the triphosphate and sugar moieties of a nucleotide, suggesting a possible mechanism for nucleotide selectivity whereby triphosphate-sugar binding precedes a check for correct base pairing with the template.

Crystal structures of human DNA polymerase beta complexed with DNA: implications for catalytic mechanism, processivity, and fidelity.

Mammalian DNA polymerase beta (pol beta) is a small (39 kDa) DNA gap-filling enzyme that comprises an amino-terminal 8-kDa domain and a carboxy-terminal 31-kDa domain. In the work reported here, crystal structures of human pol beta complexed with blunt-ended segments of DNA show that, although the crystals belong to a different space group, the DNA is nevertheless bound in the pol beta binding channel in the same way as the DNA in previously reported structures of rat pol beta complexed with a template-primer and ddCTP [Pelletier, H., Sawaya, M. R., Kumar, A., Wilson, S. H., & Kraut, J. (1994) Science 264, 1891-1903]. The 8-kDa domain is in one of three previously observed positions relative to the 31-kDa domain, suggesting that the 8-kDa domain may assume only a small number of stable conformations. The thumb subdomain is in a more open position in the human pol beta-DNA binary complex than it is in the rat pol beta-DNA-ddCTP ternary complex, and a closing thumb upon nucleotide binding could represent the rate-limiting conformational change that has been observed in pre-steady-state kinetic studies. Intermolecular contacts between the DNA and the 8-kDa domain of a symmetry-related pol beta molecule reveal a plausible binding site on the 8-kDa domain for the downstream oligonucleotide of a gapped-DNA substrate; in addition to a lysine-rich binding pocket that accommodates a 5'-PO4 end group, the 8-kDa domain also contains a newly discovered helix-hairpin-helix (HhH) motif that binds to DNA in the same way as does a structurally and sequentially homologous HhH motif in the 31-kDa domain. DNA binding by both HhH motifs is facilitated by a metal ion. In that HhH motifs have been identified in other DNA repair enzymes and DNA polymerases, the HhH-DNA interactions observed in pol beta may be applicable to a broad range of DNA binding proteins. The sequence similarity between the HhH motif of endonuclease III from Escherichia coli and the HhH motif of the 8-kDa domain of pol beta is particularly striking in that all of the conserved residues are clustered in one short sequence segment, LPGVGXK, where LPGV corresponds to a type II beta-turn (the hairpin turn), and GXK corresponds to a part of the HhH motif that is proposed to be critical for DNA binding and catalysis for both enzymes. These results suggest that endonuclease III and the 8-kDa domain of pol beta may employ a similar mode of DNA binding and may have similar catalytic mechanisms for their respective DNA lyase activities. A model for productive binding of pol beta to a gapped-DNA substrate requires a 90 degrees bend in the single-stranded template, which could enhance nucleotide selectivity during DNA repair or replication.