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(-) Description

Title :  CRYSTAL STRUCTURE OF BACILLUS STEAROTHERMOPHILUS GLYCEROL DEHYDROGENASE
 
Authors :  S. N. Ruzheinikov, J. Burke, S. Sedelnikova, P. J. Baker, R. Taylor, P. A. Bullough, N. M. Muir, M. G. Gore, D. W. Rice
Date :  03 Aug 01  (Deposition) - 03 Oct 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (8x)
Biol. Unit 2:  A  (2x)
Keywords :  Oxidoreductase, Nad, Glycerol Metabolism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. N. Ruzheinikov, J. Burke, S. Sedelnikova, P. J. Baker, R. Taylor, P. A. Bullough, N. M. Muir, M. G. Gore, D. W. Rice
Glycerol Dehydrogenase. Structure, Specificity, And Mechanism Of A Family Iii Polyol Dehydrogenase.
Structure V. 9 789 2001
PubMed-ID: 11566129  |  Reference-DOI: 10.1016/S0969-2126(01)00645-1
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLYCEROL DEHYDROGENASE
    Chains: A
    EC Number: 1.1.1.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKK233-2
    Expression System Strain: JM103
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GLDA OR GLD
    Mutation: YES
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (8x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:123 , ASP A:173 , HIS A:256 , HIS A:274 , HOH A:373 , HOH A:374BINDING SITE FOR RESIDUE ZN A 371
2AC2SOFTWAREGLU A:268 , HIS A:271BINDING SITE FOR RESIDUE ZN A 372

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADH_IRON_1PS00913 Iron-containing alcohol dehydrogenases signature 1.GLDA_GEOSE152-180  1A:152-180
2ADH_IRON_2PS00060 Iron-containing alcohol dehydrogenases signature 2.GLDA_GEOSE243-263  1A:243-263
Biological Unit 1 (2, 16)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADH_IRON_1PS00913 Iron-containing alcohol dehydrogenases signature 1.GLDA_GEOSE152-180  8A:152-180
2ADH_IRON_2PS00060 Iron-containing alcohol dehydrogenases signature 2.GLDA_GEOSE243-263  8A:243-263
Biological Unit 2 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADH_IRON_1PS00913 Iron-containing alcohol dehydrogenases signature 1.GLDA_GEOSE152-180  2A:152-180
2ADH_IRON_2PS00060 Iron-containing alcohol dehydrogenases signature 2.GLDA_GEOSE243-263  2A:243-263

(-) Exons   (0, 0)

(no "Exon" information available for 1JPU)

(-) 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:361
 aligned with GLDA_GEOSE | P32816 from UniProtKB/Swiss-Prot  Length:370

    Alignment length:366
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362      
           GLDA_GEOSE     3 AERVFISPAKYVQGKNVITKIANYLEGIGNKTVVIADEIVWKIAGHTIVNELKKGNIAAEEVVFSGEASRNEVERIANIARKAEAAIVIGVGGGKTLDTAKAVADELDAYIVIVPTAASTDAPTSALSVIYSDDGVFESYRFYKKNPDLVLVDTKIIANAPPRLLASGIADALATWVEARSVIKSGGKTMAGGIPTIAAEAIAEKCEQTLFKYGKLAYESVKAKVVTPALEAVVEANTLLSGLGFESGGLAAAHAIHNGFTALEGEIHHLTHGEKVAFGTLVQLALEEHSQQEIERYIELYLSLDLPVTLEDIKLKDASREDILKVAKAATAEGETIHNAFNVTADDVADAIFAADQYAKAYKEKH 368
               SCOP domains d1jpua_ A: Glycerol dehydrogenase                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains -------1jpuA01 A:10-161  [code=3.40.50.1970, no name defined]                                                                                                  1jpuA02 A:162-368 Dehydroquinate synthase-like - alpha domain                                                                                                                                                   CATH domains
               Pfam domains -------Fe-ADH-1jpuA01 A:10-350                                                                                                                                                                                                                                                                                                                              ------------------ Pfam domains
         Sec.struct. author .........eeeee.hhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhh.eeeeee...........ee.-----......ee......eeeeehhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..............hhhhhhhhhhhhh...hhhhhh...hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------ADH_IRON_1  PDB: A:152-180   --------------------------------------------------------------ADH_IRON_2           --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jpu A   3 AERVFISPAKYVQGKNVITKIANYLEGIGNKTVVIADEIVWKIAGHTIVNELKKGNIAAEEVVFSGEASRNEVERIANIARKAEAAIVIGVGGGKTLDTAKAVADELDAYIVIVPTAASTDAPTSALSV-----GVFESYRFYKKNPDLVLVDTKIIANAPPRLLASGIADALATWVEARSVIKSGGKTMAGGIPTIAAEAIAEKCEQTLFKYGKLAYESVKAKVVTPALEAVVEANTLLSGLGFESGGLAAAHAIHNGFTALEGEIHHLTHGEKVAFGTLVQLALEEHSQQEIERYIELYLCLDLPVTLEDIKLKDASREDILKVAKAATAEGETIHNAFNVTADDVADAIFAADQYAKAYKEKH 368
                                    12        22        32        42        52        62        72        82        92       102       112       122        |-    |  142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362      
                                                                                                                                                          131   137
   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: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: DHQS (27)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (GLDA_GEOSE | P32816)
molecular function
    GO:0008888    glycerol dehydrogenase [NAD+] activity    Catalysis of the reaction: glycerol + NAD(+) = glycerone + H(+) + NADH.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0019588    anaerobic glycerol catabolic process    The anaerobic chemical reactions and pathways resulting in the breakdown of glycerol, yielding energy in the form of ATP.
    GO:0006071    glycerol metabolic process    The chemical reactions and pathways involving glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.
    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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  1jpu
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  GLDA_GEOSE | P32816
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  1.1.1.6
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 Related Entries

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

UniProtKB/Swiss-Prot
        GLDA_GEOSE | P32816: 1jq5 1jqa

(-) Related Entries Specified in the PDB File

1jq5 THE SAME PROTEIN IN COMPLEX WITH NAD
1jqa THE SAME PROTEIN IN COMPLEX WITH GLYCEROL