2DBR

Crystal Structure of Glyoxylate Reductase (PH0597) from Pyrococcus horikoshii OT3, Complexed with NADP (P1)

Summary for 2DBR

• Entry DOI: 10.2210/pdb2dbr/pdb
• Related: 2DBQ 2DBZ
• Descriptor: Glyoxylate reductase, SULFATE ION, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, ... (4 entities in total)
• Functional Keywords: glyoxylate reductase, d-3-phosphoglycerate dehydrogenase, structural genomics, nppsfa, national project on protein structural and functional analyses, riken structural genomics/proteomics initiative, rsgi, oxidoreductase
• Biological source: Pyrococcus horikoshii
• Cellular location: Cytoplasm (By similarity): O58320
• Total number of polymer chains: 6
• Total formula weight: 233956.06

Authors

Yoshikawa, S.,Arai, R.,Kinoshita, Y.,Uchikubo-Kamo, T.,Akasaka, R.,Terada, T.,Shirouzu, M.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2005-12-16, release date: 2006-06-16, Last modification date: 2023-10-25)

Primary citation

Yoshikawa, S.,Arai, R.,Kinoshita, Y.,Uchikubo-Kamo, T.,Wakamatsu, T.,Akasaka, R.,Masui, R.,Terada, T.,Kuramitsu, S.,Shirouzu, M.,Yokoyama, S.
Structure of archaeal glyoxylate reductase from Pyrococcus horikoshii OT3 complexed with nicotinamide adenine dinucleotide phosphate.
Acta Crystallogr.,Sect.D, 63:357-365, 2007

PubMed Abstract: Glyoxylate reductase catalyzes the NAD(P)H-linked reduction of glyoxylate to glycolate. Here, the 1.7 A crystal structure of glyoxylate reductase from the hyperthermophilic archaeon Pyrococcus horikoshii OT3 complexed with nicotinamide adenine dinucleotide phosphate [NADP(H)] determined by the single-wavelength anomalous dispersion (SAD) method is reported. The monomeric structure comprises the two domains typical of NAD(P)-dependent dehydrogenases: the substrate-binding domain (SBD) and the nucleotide-binding domain (NBD). The crystal structure and analytical ultracentrifugation results revealed dimer formation. In the NADP(H)-binding site, the pyrophosphate moiety and the 2'-phosphoadenosine moiety are recognized by the glycine-rich loop (residues 157-162) and by loop residues 180-182, respectively. Furthermore, the present study revealed that P. horikoshii glyoxylate reductase contains aromatic clusters and has a larger number of ion pairs and a lower percentage of hydrophobic accessible surface area than its mesophilic homologues, suggesting its thermostability mechanism.

PubMed: 17327673
DOI: 10.1107/S0907444906055442

Experimental method

X-RAY DIFFRACTION (2.61 Å)