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(-) Description

Title :  CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENASE FROM PSEUDOMONAS SP. LB400
 
Authors :  M. Huelsmeyer, H. -J. Hecht, K. Niefind, B. Hofer, K. N. Timmis, D. Schom
Date :  10 May 97  (Deposition) - 12 Nov 97  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Nad-Dependent Oxidoreductase, Short-Chain Alcohol Dehydrogenase, Pcb Degradation, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Hulsmeyer, H. J. Hecht, K. Niefind, B. Hofer, L. D. Eltis, K. N. Timmis, D. Schomburg
Crystal Structure Of Cis-Biphenyl-2, 3-Dihydrodiol-2, 3-Dehydrogenase From A Pcb Degrader At 2. 0 A Resolution.
Protein Sci. V. 7 1286 1998
PubMed-ID: 9655331
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENASE
    Cellular Location: CYTOPLASM
    Chains: A
    Organism Scientific: PSEUDOMONAS SP.
    Organism Taxid: 306
    Strain: LB400
    Variant: PLEBD4

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:12 , SER A:15 , GLY A:16 , LEU A:17 , ASP A:36 , LYS A:37 , ARG A:41 , GLY A:58 , ASP A:59 , VAL A:60 , ASN A:86 , TYR A:119 , THR A:140 , ILE A:141 , SER A:142 , TYR A:155 , LYS A:159 , SER A:184 , GLY A:185 , GLY A:186 , ILE A:187 , SER A:189 , ASP A:190 , LEU A:191 , HOH A:516 , HOH A:544 , HOH A:597 , HOH A:607BINDING SITE FOR RESIDUE NAD A 300
2CATUNKNOWNSER A:142 , TYR A:155 , LYS A:159THE CATALYTIC TRIAD IS BUILT BY SER 142 - TYR 155 - LYS 159.

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala A:174 -Pro A:175

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADH_SHORTPS00061 Short-chain dehydrogenases/reductases family signature.BPHB_PARXL142-170  1A:142-170
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADH_SHORTPS00061 Short-chain dehydrogenases/reductases family signature.BPHB_PARXL142-170  4A:142-170

(-) Exons   (0, 0)

(no "Exon" information available for 1BDB)

(-) 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:267
 aligned with BPHB_PARXL | P47227 from UniProtKB/Swiss-Prot  Length:277

    Alignment length:276
                                    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      
           BPHB_PARXL     1 MKLKGEAVLITGGASGLGRALVDRFVAEGAKVAVLDKSAERLAELETDHGDNVLGIVGDVRSLEDQKQAASRCVARFGKIDTLIPNAGIWDYSTALVDLPEESLDAAFDEVFHINVKGYIHAVKACLPALVASRGNVIFTISNAGFYPNGGGPLYTAAKHAIVGLVRELAFELAPYVRVNGVGSGGINSDLRGPSSLGMGSKAISTVPLADMLKSVLPIGRMPEVEEYTGAYVFFATRGDAAPATGALLNYDGGLGVRGFFSGAGGNDLLEQLNIH 276
               SCOP domains d1bdba_ A: Cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase                                                                                                                                                                                                                            SCOP domains
               CATH domains 1bdbA00 A:1-276 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee....hhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhheeeee.....hhhhhhhhhhhhhhh....eee...........hhh.....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..eeeee..hhh.......hhhhhhhhhhhhhhhhhhhhh....eeeeeee..........hhh.---------.hhhhhhh.........hhhh.hhhhhhh.hhhh......eeee...hhh...........hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: A:142-170    ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1bdb A   1 MKLKGEAVLITGGASGLGRALVDRFVAEGAKVAVLDKSAERLAELETDHGDNVLGIVGDVRSLEDQKQAASRCVARFGKIDTLIPNAGIWDYSTALVDLPEESLDAAFDEVFHINVKGYIHAVKACLPALVASRGNVIFTISNAGFYPNGGGPLYTAAKHAIVGLVRELAFELAPYVRVNGVGSGGINSDLRGPSSLG---------PLADMLKSVLPIGRMPEVEEYTGAYVFFATRGDAAPATGALLNYDGGLGVRGFFSGAGGNDLLEQLNIH 276
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       | -       210       220       230       240       250       260       270      
                                                                                                                                                                                                                               198       208
   Legend:   → Mismatch (orange background)
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  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  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BDB)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (BPHB_PARXL | P47227)
molecular function
    GO:0018509    cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase activity    Catalysis of the reaction: cis-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD+ = biphenyl-2,3-diol + NADH + H+.
    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:0016628    oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces NAD or NADP.
biological process
    GO:0019439    aromatic compound catabolic process    The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
    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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