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(-) Description

Title :  CRYSTAL STRUCTURE OF NAD DEPENDENT D-3-HYDROXYBUTYLATE DEHYDROGENASE
 
Authors :  K. Ito, Y. Nakajima, E. Ichihara, K. Ogawa, T. Yoshimoto
Date :  06 Jul 04  (Deposition) - 06 Sep 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Nad, Nadh, Short Chain Dehydrogenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Ito, Y. Nakajima, E. Ichihara, K. Ogawa, N. Katayama, K. Nakashima, T. Yoshimoto
D-3-Hydroxybutyrate Dehydrogenase From Pseudomonas Fragi: Molecular Cloning Of The Enzyme Gene And Crystal Structure Of The Enzyme
J. Mol. Biol. V. 355 722 2006
PubMed-ID: 16325199  |  Reference-DOI: 10.1016/J.JMB.2005.10.072

(-) Compounds

Molecule 1 - D(-)-3-HYDROXYBUTYRATE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.1.1.30
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKK233-3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PSEUDOMONAS FRAGI
    Organism Taxid: 296

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1CAC2Ligand/IonCACODYLATE ION
2MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1CAC4Ligand/IonCACODYLATE ION
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:38 , HIS A:128 , HOH A:1305 , HOH A:1314BINDING SITE FOR RESIDUE MG A 1301
2AC2SOFTWAREGLN A:94 , SER A:142 , TYR A:155 , GLY A:186 , TRP A:257 , HOH A:1346 , HOH A:1410BINDING SITE FOR RESIDUE CAC A 1302
3AC3SOFTWAREASP B:38 , HIS B:128 , HOH B:2304 , HOH B:2306BINDING SITE FOR RESIDUE MG B 2301
4AC4SOFTWAREGLN B:94 , SER B:142 , TYR B:155 , PRO B:185 , GLY B:186 , HOH B:2335BINDING SITE FOR RESIDUE CAC B 2302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1WMB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WMB)

(-) Sequences/Alignments

Asymmetric 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:260
 aligned with Q5KST5_PSEFR | Q5KST5 from UniProtKB/TrEMBL  Length:260

    Alignment length:260
                                    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
         Q5KST5_PSEFR     1 MLKGKVAVVTGSTSGIGLGIATALAAQGADIVLNGFGDAAEIEKVRAGLAAQHGVKVLYDGADLSKGEAVRGLVDNAVRQMGRIDILVNNAGIQHTALIEDFPTEKWDAILALNLSAVFHGTAAALPHMKKQGFGRIINIASAHGLVASANKSAYVAAKHGVVGFTKVTALETAGQGITANAICPGWVRTPLVEKQISALAEKNGVDQETAARELLSEKQPSLQFVTPEQLGGTAVFLASDAAAQITGTTVSVDGGWTAR 260
               SCOP domains d1wmba1 A:1-260 D(-)-3-hydroxybutyrate dehydrogenase                                                                                                                                                                                                                 SCOP domains
               CATH domains 1wmbA00 A:1-260 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee....hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhh.hhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wmb A   1 MLKGKVAVVTGSTSGIGLGIATALAAQGADIVLNGFGDAAEIEKVRAGLAAQHGVKVLYDGADLSKGEAVRGLVDNAVRQMGRIDILVNNAGIQHTALIEDFPTEKWDAILALNLSAVFHGTAAALPHMKKQGFGRIINIASAHGLVASANKSAYVAAKHGVVGFTKVTALETAGQGITANAICPGWVRTPLVEKQISALAEKNGVDQETAARELLSEKQPSLQFVTPEQLGGTAVFLASDAAAQITGTTVSVDGGWTAR 260
                                    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


Chain B from PDB  Type:PROTEIN  Length:260
 aligned with Q5KST5_PSEFR | Q5KST5 from UniProtKB/TrEMBL  Length:260

    Alignment length:260
                                    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
         Q5KST5_PSEFR     1 MLKGKVAVVTGSTSGIGLGIATALAAQGADIVLNGFGDAAEIEKVRAGLAAQHGVKVLYDGADLSKGEAVRGLVDNAVRQMGRIDILVNNAGIQHTALIEDFPTEKWDAILALNLSAVFHGTAAALPHMKKQGFGRIINIASAHGLVASANKSAYVAAKHGVVGFTKVTALETAGQGITANAICPGWVRTPLVEKQISALAEKNGVDQETAARELLSEKQPSLQFVTPEQLGGTAVFLASDAAAQITGTTVSVDGGWTAR 260
               SCOP domains d1wmbb_ B: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1wmbB00 B:1-260 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                  CATH domains
           Pfam domains (1) ----adh_short-1wmbB01 B:5-174                                                                                                                                                 -------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----adh_short-1wmbB02 B:5-174                                                                                                                                                 -------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .....eeee....hhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhh.hhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wmb B   1 MLKGKVAVVTGSTSGIGLGIATALAAQGADIVLNGFGDAAEIEKVRAGLAAQHGVKVLYDGADLSKGEAVRGLVDNAVRQMGRIDILVNNAGIQHTALIEDFPTEKWDAILALNLSAVFHGTAAALPHMKKQGFGRIINIASAHGLVASANKSAYVAAKHGVVGFTKVTALETAGQGITANAICPGWVRTPLVEKQISALAEKNGVDQETAARELLSEKQPSLQFVTPEQLGGTAVFLASDAAAQITGTTVSVDGGWTAR 260
                                    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
   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  (2, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q5KST5_PSEFR | Q5KST5)
molecular function
    GO:0003858    3-hydroxybutyrate dehydrogenase activity    Catalysis of the reaction: (R)-3-hydroxybutanoate + NAD(+) = acetoacetate + H(+) + 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.
biological process
    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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