Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 3 de 3
Filter
Add more filters










Database
Language
Publication year range
1.
Acta Crystallogr D Biol Crystallogr ; 60(Pt 10): 1855-62, 2004 Oct.
Article in English | MEDLINE | ID: mdl-15388933

ABSTRACT

As part of a structural genomics project on bacterial gene products of unknown function, the crystal structures of YhdH, a putative quinone oxidoreductase, and its complex with NADP have been determined at 2.25 and 2.6 A resolution, respectively. The overall fold of YhdH is very similar to that of alcohol dehydrogenases and quinone reductases despite its low sequence identity. The absence of any Zn ion indicates that YdhH is a putative quinone oxidoreductase. YhdH forms a homodimer, with each subunit composed of two domains: a catalytic domain and a coenzyme-binding domain. NADP is bound in a deep cleft formed between the two domains. Large conformational changes occur upon NADP binding, with the two domains closing up to each other and narrowing the NADP-binding cleft. Comparisons of the YdhH active site with those of the quinone oxidoreductases from Escherichia coli and Thermus thermophilus made it possible to identify essential conserved residues as being Asn41, Asp43, Asp64 and Arg318. The active-site size is very narrow and unless an induced fit occurs is accessible only to reagents the size of benzoquinone.


Subject(s)
Electron Transport Complex I/chemistry , Escherichia coli Proteins/chemistry , Escherichia coli/enzymology , Quinone Reductases/chemistry , Amino Acid Sequence , Arginine/chemistry , Asparagine/chemistry , Aspartic Acid/chemistry , Catalytic Domain , Cloning, Molecular , Crystallography, X-Ray , Dimerization , Models, Molecular , Molecular Sequence Data , Protein Conformation , Protein Folding , Protein Structure, Tertiary , Sequence Homology, Amino Acid , Thermus thermophilus/enzymology
2.
J Mol Biol ; 337(2): 273-83, 2004 Mar 19.
Article in English | MEDLINE | ID: mdl-15003446

ABSTRACT

In the course of a structural genomics program aiming at solving the structures of Escherichia coli open reading frame products of unknown function, we have determined the structure of YadB at 1.5A using molecular replacement. The YadB protein is 298 amino acid residues long and displays 34% sequence identity with E.coli glutamyl-tRNA synthetase (GluRS). It is much shorter than GluRS, which contains 468 residues, and lacks the complete domain interacting with the tRNA anticodon loop. As E.coli GluRS, YadB possesses a Zn2+ located in the putative tRNA acceptor stem-binding domain. The YadB cluster uses cysteine residues as the first three zinc ligands, but has a weaker tyrosine ligand at the fourth position. It shares with canonical amino acid RNA synthetases a major functional feature, namely activation of the amino acid (here glutamate). It differs, however, from GluRSs by the fact that the activation step is tRNA-independent and that it does not catalyze attachment of the activated glutamate to E.coli tRNAGlu, but to another, as yet unknown tRNA. These results suggest thus a novel function, distinct from that of GluRSs, for the yadB gene family.


Subject(s)
Amino Acyl-tRNA Synthetases/genetics , Amino Acyl-tRNA Synthetases/metabolism , Escherichia coli Proteins/genetics , Escherichia coli Proteins/metabolism , Escherichia coli/enzymology , Escherichia coli/genetics , Adenosine Monophosphate/metabolism , Adenosine Triphosphate/metabolism , Amino Acid Sequence , Amino Acyl-tRNA Synthetases/chemistry , Carrier Proteins/metabolism , Crystallography, X-Ray , Escherichia coli Proteins/chemistry , Genes, Bacterial , Glutamate-tRNA Ligase/chemistry , Glutamate-tRNA Ligase/genetics , Glutamate-tRNA Ligase/metabolism , Glutamic Acid/metabolism , Kinetics , Ligands , Models, Molecular , Molecular Sequence Data , Neoplasm Proteins/metabolism , Nuclear Proteins/metabolism , Protein Conformation , RNA, Transfer, Glu/metabolism , Sequence Homology, Amino Acid , Thermus thermophilus/enzymology , Thermus thermophilus/genetics , Zinc/metabolism
3.
Acta Crystallogr D Biol Crystallogr ; 58(Pt 12): 2109-15, 2002 Dec.
Article in English | MEDLINE | ID: mdl-12454472

ABSTRACT

The first results of a medium-scale structural genomics program clearly demonstrate the value of using a medium-throughput crystallization approach based on a two-step procedure: a large screening step employing robotics, followed by manual or automated optimization of the crystallization conditions. The structural genomics program was based on cloning in the Gateway vectors pDEST17, introducing a long 21-residue tail at the N-terminus. So far, this tail has not appeared to hamper crystallization. In ten months, 25 proteins were subjected to crystallization; 13 yielded crystals, of which ten led to usable data sets and five to structures. Furthermore, the results using a robot dispensing 50-200 nl drops indicate that smaller protein samples can be used for crystallization. These still partial results might indicate present and future directions for those who have to make crucial choices concerning their crystallization platform in structural genomics programs.


Subject(s)
Crystallization/methods , Crystallization/instrumentation , Escherichia coli Proteins/biosynthesis , Escherichia coli Proteins/chemistry , Escherichia coli Proteins/isolation & purification , Light , Robotics , Scattering, Radiation
SELECTION OF CITATIONS
SEARCH DETAIL
...