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(-) Description

Title :  CRYSTAL STRUCTURE OF D-3-HYDROXYBUTYRATE DEHYDROGENASE FROM ALCALIGENES FAECALIS COMPLEXED WITH NAD+ AND AN INHIBITOR METHYLMALONATE
 
Authors :  H. Kanazawa, M. Tsunoda, M. M. Hoque, K. Suzuki, T. Yamamoto, A. Takenak
Date :  12 Mar 13  (Deposition) - 12 Mar 14  (Release) - 12 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.37
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Rossmann Fold, Oxidreductase, Nad+ Binding Methylmalonate Binding, Mitochondria, Oxidoreductase, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Kanazawa, M. Tsunoda, M. M. Hoque, K. Suzuki, T. Yamamoto, A. Takenaka
X-Ray Diffraction Of D-3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis Complexed With Nad+ And Methylmalonate
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - D-3-HYDROXYBUTYRATE DEHYDROGENASE
    Chains: A
    EC Number: 1.1.1.30
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ALCALIGENES FAECALIS
    Organism Taxid: 511

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric Unit (4, 6)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2DXX1Ligand/IonMETHYLMALONIC ACID
3NA3Ligand/IonSODIUM ION
4NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2DXX4Ligand/IonMETHYLMALONIC ACID
3NA-1Ligand/IonSODIUM ION
4NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:11 , THR A:13 , SER A:14 , GLY A:15 , ILE A:16 , ASN A:34 , PHE A:36 , ALA A:62 , ASP A:63 , LEU A:64 , ASN A:90 , GLY A:92 , LEU A:113 , ILE A:140 , ALA A:141 , SER A:142 , TYR A:155 , LYS A:159 , PRO A:185 , GLY A:186 , TRP A:187 , VAL A:188 , THR A:190 , PRO A:191 , LEU A:192 , VAL A:193 , DXX A:302 , HOH A:412 , HOH A:432 , HOH A:534 , HOH A:564 , HOH A:570 , HOH A:583BINDING SITE FOR RESIDUE NAD A 301
2AC2SOFTWAREGLN A:94 , SER A:142 , HIS A:144 , LYS A:152 , TYR A:155 , TRP A:187 , LEU A:192 , GLN A:196 , TRP A:257 , NAD A:301BINDING SITE FOR RESIDUE DXX A 302
3AC3SOFTWARESER A:149 , VAL A:150 , LYS A:219BINDING SITE FOR RESIDUE CL A 303
4AC4SOFTWAREVAL A:147 , ARG A:260 , HOH A:476 , HOH A:705BINDING SITE FOR RESIDUE NA A 304
5AC5SOFTWARELEU A:64 , SER A:65 , ALA A:112 , SER A:116 , ALA A:117 , HOH A:447 , HOH A:454BINDING SITE FOR RESIDUE NA A 305
6AC6SOFTWAREGLY A:4 , LYS A:6 , ASP A:85 , HOH A:640BINDING SITE FOR RESIDUE NA A 306

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3W8D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3W8D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3W8D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3W8D)

(-) Exons   (0, 0)

(no "Exon" information available for 3W8D)

(-) 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 D0VWQ0_ALCFA | D0VWQ0 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
         D0VWQ0_ALCFA     1 MLKGKKAVVTGSTSGIGLAMATELAKAGADVVINGFGQPEDIERERSTLESKFGVKAYYLNADLSDAQATRDFIAKAAEALGGLDILVNNAGIQHTAPIEEFPVDKWNAIIALNLSAVFHGTAAALPIMQKQGWGRIINIASAHGLVASVNKSAYVAAKHGVVGLTKVTALENAGKGITCNAICPGWVRTPLVEKQIEAISQQKGIDIEAAARELLAEKQPSLQFVTPEQLGGAAVFLSSAAADQMTGTTLSLDGGWTAR 260
               SCOP domains d3w8da_ A: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee....hhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w8d A   1 MLKGKKAVVTGSTSGIGLAMATELAKAGADVVINGFGQPEDIERERSTLESKFGVKAYYLNADLSDAQATRDFIAKAAEALGGLDILVNNAGIQHTAPIEEFPVDKWNAIIALNLSAVFHGTAAALPIMQKQGWGRIINIASAHGLVASVNKSAYVAAKHGVVGLTKVTALENAGKGITCNAICPGWVRTPLVEKQIEAISQQKGIDIEAAARELLAEKQPSLQFVTPEQLGGAAVFLSSAAADQMTGTTLSLDGGWTAR 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  (1, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3W8D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3W8D)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (D0VWQ0_ALCFA | D0VWQ0)
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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  1.1.1.30
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        D0VWQ0_ALCFA | D0VWQ0: 2yz7 3vdq 3vdr 3w8e 3w8f 5b4t 5b4u 5b4v

(-) Related Entries Specified in the PDB File

2yz7 THE SAME PROTEIN IN NATIVE FORM.
3vdq THE SAME PROTEIN COMPLEXED WITH NAD+ AND ACETATE.
3vdr THE SAME PROTEIN COMPLEXED WITH NAD+ AND D-3- HYDOROXYBUTYRATE.
3w8e THE SAME PROTEIN COMPLEXED WITH NAD+ AND MALONATE.
3w8f THE SAME PROTEIN COMPLEXED WITH NAD+ AND D-3- HYDROXYBUTYRATE, AND HIGH RESOLUTION.