title: Crystal structures of type IIIH NAD-dependent D-3-phosphoglycerate dehydrogenase from two thermophiles.
abstract: In the L-Serine biosynthesis, D-3-phosphoglycerate dehydrogenase (PGDH) catalyzes the inter-conversion of D-3-phosphoglycerate to phosphohydroxypyruvate. PGDH belongs to 2-hydroxyacid dehydrogenases family. We have determined the crystal structures of PGDH from Sulfolobus tokodaii (StPGDH) and Pyrococcus horikoshii (PhPGDH) using X-ray diffraction to resolution of 1.77Å and 1.95Å, respectively. The PGDH protomer from both species exhibits identical structures, consisting of substrate binding domain and nucleotide binding domain. The residues and water molecules interacting with the NAD are identified. The catalytic triad residues Glu-His-Arg are highly conserved. The residues involved in the dimer interface and the structural features responsible for thermostability are evaluated. Overall, structures of PGDHs with two domains and histidine at the active site are categorized as type IIIH and such PGDHs structures having this type are reported for the first time.
authors: Department of Studies in Physics, University of Mysore, Mysore 570 006, India.
authors: S M
authors: SM
authors: Kumar
authors: Department of Studies in Microbiology, University of Mysore, Mysore 570 006, India.
authors: K J
authors: KJ
authors: Pampa
authors: Department of Studies in Physics, University of Mysore, Mysore 570 006, India.
authors: M
authors: M
authors: Manjula
authors: Department of Studies in Computer Science, University of Mysore, Mysore 570 006, India.
authors: G
authors: G
authors: Hemantha Kumar
authors: Advanced Protein Crystallography Research Group, RIKEN SPring-8 Center, Harima Institute, Hyogo 679-5148, Japan.
authors: Naoki
authors: N
authors: Kunishima
authors: Department of Studies in Physics, University of Mysore, Mysore 570 006, India. Electronic address: lokanath@physics.uni-mysore.ac.in.
authors: N K
authors: NK
authors: Lokanath
mesh_terms: D019843:Archaeal Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D004795:Enzyme Stability; D008958:Models, Molecular; D009243:NAD / Q000378:metabolism; D050543:Phosphoglycerate Dehydrogenase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D011487:Protein Conformation; D055503:Protein Multimerization; D043902:Pyrococcus horikoshii / Q000201:enzymology*; D016944:Sulfolobus / Q000201:enzymology*
chemical_list: D019843:Archaeal Proteins; D009243:NAD; D050543:Phosphoglycerate Dehydrogenase
keywords: NAD(+); Nucleotide binding domain; PGDH; Substrate binding domain