Structure of Escherichia coli YhdH, a putative quinone oxidoreductase.
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.
Sulzenbacher
Gerlind
G
AFMB, UMR 6098, CNRS and Universités Aix-Marseille I and II, 31 Chemin J. Aiguier, F-13402 Marseille 20, France.
Roig-Zamboni
Véronique
V
Pagot
Fabienne
F
Grisel
Sacha
S
Salomoni
Aurelia
A
Valencia
Christel
C
Campanacci
Valérie
V
Vincentelli
Renaud
R
Tegoni
Mariella
M
Eklund
Hans
H
Cambillau
Christian
C
D000595:Amino Acid Sequence; D001120:Arginine / Q000737:chemistry; D001216:Asparagine / Q000737:chemistry; D001224:Aspartic Acid / Q000737:chemistry; D020134:Catalytic Domain; D003001:Cloning, Molecular; D018360:Crystallography, X-Ray; D019281:Dimerization; D042967:Electron Transport Complex I / Q000737:chemistry*; D004926:Escherichia coli / Q000201:enzymology*; D029968:Escherichia coli Proteins / Q000737:chemistry*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D011808:Quinone Reductases / Q000737:chemistry*; D017386:Sequence Homology, Amino Acid; D016963:Thermus thermophilus / Q000201:enzymology
D029968:Escherichia coli Proteins; D001224:Aspartic Acid; D001216:Asparagine; D001120:Arginine; D011808:Quinone Reductases; C498064:YhdH protein, E coli; D042967:Electron Transport Complex I