1O89

Crystal structure of E. COLI K-12 yhdH

Summary for 1O89

• Entry DOI: 10.2210/pdb1o89/pdb
• Related: 1O8C
• Descriptor: YHDH (2 entities in total)
• Functional Keywords: structural genomics, unknown function, possible nadph-dependent quinone oxidoreductase
• Biological source: ESCHERICHIA COLI
• Cellular location: Cytoplasm (Potential): P26646
• Total number of polymer chains: 1
• Total formula weight: 37294.47

Authors

Sulzenbacher, G.,Roig-Zamboni, V.,Pagot, F.,Grisel, S.,Salamoni, A.,Valencia, C.,Bignon, C.,Vincentelli, R.,Tegoni, M.,Cambillau, C. (deposition date: 2002-11-26, release date: 2004-02-26, Last modification date: 2024-05-01)

Primary citation

Sulzenbacher, G.,Roig-Zamboni, V.,Pagot, F.,Grisel, S.,Salamoni, A.,Valencia, C.,Campanacci, V.,Vincentelli, R.,Tegoni, M.,Eklund, H.,Cambillau, C.
Structure of the Escherichia Coli Yhdh, a Putative Quinone Oxidoreductase
Acta Crystallogr.,Sect.D, 60:1855-, 2004

PubMed 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.

PubMed: 15388933
DOI: 10.1107/S0907444904020220

Experimental method

X-RAY DIFFRACTION (2.25 Å)