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(-) Description

Title :  CRYSTAL STRUCTURE OF PHOSPHOGLYCERATE DEHYDROGENASE FROM PYROCOCCUS HORIKOSHII OT3
 
Authors :  M. Sugahara, N. Kunishima, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  06 Jan 05  (Deposition) - 17 Jan 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Phosphoglycerate Dehydrogenase, Pyrococcus Horikoshii, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Sugahara, N. Kunishima
Crystal Structure Of Phosphoglycerate Dehydrogenase From Pyrococcus Horikoshii Ot3
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PHOSPHOGLYCERATE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.1.1.95
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 70601
    Strain: OT3

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:100 , GLY A:146 , PHE A:147 , GLY A:148 , ARG A:149 , ILE A:150 , TYR A:168 , ASP A:169 , PRO A:170 , TYR A:171 , VAL A:201 , PRO A:202 , SER A:206 , THR A:207 , THR A:228 , SER A:229 , ARG A:230 , ASP A:254 , HIS A:278 , GLY A:280 , ALA A:281 , HOH A:1006 , HOH A:1007 , HOH A:1020 , HOH A:1024 , HOH A:1025 , HOH A:1041 , HOH A:1047 , HOH A:1076 , HOH A:1113BINDING SITE FOR RESIDUE NAD A 1001
2AC2SOFTWAREVAL B:100 , PHE B:147 , GLY B:148 , ARG B:149 , ILE B:150 , TYR B:168 , ASP B:169 , PRO B:170 , TYR B:171 , HIS B:200 , VAL B:201 , PRO B:202 , SER B:206 , THR B:207 , THR B:228 , SER B:229 , ASP B:254 , HIS B:278 , GLY B:280 , ALA B:281 , HOH B:2008 , HOH B:2013 , HOH B:2035 , HOH B:2084 , HOH B:2097 , HOH B:2099 , HOH B:2113 , HOH B:2159 , HOH B:2218BINDING SITE FOR RESIDUE NAD B 2001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WWK)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Lys A:50 -Pro A:51
2Glu A:259 -Pro A:260
3Lys B:50 -Pro B:51
4Glu B:259 -Pro B:260

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WWK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1WWK)

(-) Exons   (0, 0)

(no "Exon" information available for 1WWK)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:304
 aligned with O50095_PYRHO | O50095 from UniProtKB/TrEMBL  Length:307

    Alignment length:304
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303    
         O50095_PYRHO     4 MKVLVAAPLHEKAIQVLKDAGLEVIYEEYPDEDRLVELVKDVEAIIVRSKPKVTRRVIESAPKLKVIARAGVGLDNIDVEAAKEKGIEVVNAPAASSRSVAELAVGLMFSVARKIAFADRKMREGVWAKKEAMGIELEGKTIGIIGFGRIGYQVAKIANALGMNILLYDPYPNEERAKEVNGKFVDLETLLKESDVVTIHVPLVESTYHLINEERLKLMKKTAILINTSRGPVVDTNALVKALKEGWIAGAGLDVFEEEPLPKDHPLTKFDNVVLTPHIGASTVEAQERAGVEVAEKVVKILKG 307
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1wwkA01 A:1-91,A:283-304 NAD(P)-binding Rossmann-like Domain                               1wwkA02 A:92-282 NAD(P)-binding Rossmann-like Domain                                                                                                                                           1wwkA01                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....hhhhhhhhhhh..eeee....hhhhhhhhh....eeee......hhhhhh......eeee........hhhhhhhhh.eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................eeeee..hhhhhhhhhhhhhh..eeeee....hhhhhhhh..ee.hhhhhhhhh.eeee............hhhhhhhh....eeee..hhhhhhhhhhhhhhhh....eeee...........hhhhhh..eee.......hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wwk A   1 MKVLVAAPLHEKAIQVLKDAGLEVIYEEYPDEDRLVELVKDVEAIIVRSKPKVTRRVIESAPKLKVIARAGVGLDNIDVEAAKEKGIEVVNAPAASSRSVAELAVGLMFSVARKIAFADRKMREGVWAKKEAMGIELEGKTIGIIGFGRIGYQVAKIANALGMNILLYDPYPNEERAKEVNGKFVDLETLLKESDVVTIHVPLVESTYHLINEERLKLMKKTAILINTSRGPVVDTNALVKALKEGWIAGAGLDVFEEEPLPKDHPLTKFDNVVLTPHIGASTVEAQERAGVEVAEKVVKILKG 304
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300    


Chain B from PDB  Type:PROTEIN  Length:302
 aligned with O50095_PYRHO | O50095 from UniProtKB/TrEMBL  Length:307

    Alignment length:302
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303  
         O50095_PYRHO     4 MKVLVAAPLHEKAIQVLKDAGLEVIYEEYPDEDRLVELVKDVEAIIVRSKPKVTRRVIESAPKLKVIARAGVGLDNIDVEAAKEKGIEVVNAPAASSRSVAELAVGLMFSVARKIAFADRKMREGVWAKKEAMGIELEGKTIGIIGFGRIGYQVAKIANALGMNILLYDPYPNEERAKEVNGKFVDLETLLKESDVVTIHVPLVESTYHLINEERLKLMKKTAILINTSRGPVVDTNALVKALKEGWIAGAGLDVFEEEPLPKDHPLTKFDNVVLTPHIGASTVEAQERAGVEVAEKVVKIL 305
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --2-Hacid_dh-1wwkB01 B:3-302                                                                                                                                                                                                                                                                                   Pfam domains (1)
           Pfam domains (2) --2-Hacid_dh-1wwkB02 B:3-302                                                                                                                                                                                                                                                                                   Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------------2-Hacid_dh_C-1wwkB03 B:105-280                                                                                                                                                  ---------------------- Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------------------------------------------2-Hacid_dh_C-1wwkB04 B:105-280                                                                                                                                                  ---------------------- Pfam domains (4)
         Sec.struct. author .eeee....hhhhhhhhhhh..eeee....hhhhhhhhh....eeee......hhhhhhhh....eeee........hhhhhhhhh.eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................eeeee..hhhhhhhhhhhhhh..eeeee....hhhhhhhh.eee.hhhhhhhhh.eeee....hhhhh...hhhhhhhh....eeee..hhhhhhhhhhhhhhhhh...eeee...........hhhhhh..eee.......hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wwk B   1 MKVLVAAPLHEKAIQVLKDAGLEVIYEEYPDEDRLVELVKDVEAIIVRSKPKVTRRVIESAPKLKVIARAGVGLDNIDVEAAKEKGIEVVNAPAASSRSVAELAVGLMFSVARKIAFADRKMREGVWAKKEAMGIELEGKTIGIIGFGRIGYQVAKIANALGMNILLYDPYPNEERAKEVNGKFVDLETLLKESDVVTIHVPLVESTYHLINEERLKLMKKTAILINTSRGPVVDTNALVKALKEGWIAGAGLDVFEEEPLPKDHPLTKFDNVVLTPHIGASTVEAQERAGVEVAEKVVKIL 302
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 1WWK)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: Form_Glyc_dh (56)
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (O50095_PYRHO | O50095)
molecular function
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016616    oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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