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(-) Description

Title :  CRYSTAL STRUCTURE OF THE N-(1-D-CARBOXYLETHYL)-L-NORVALINE DEHYDROGENASE FROM ARTHROBACTER SP. STRAIN 1C
 
Authors :  K. L. Britton, Y. Asano, D. W. Rice
Date :  05 Jun 98  (Deposition) - 13 Jan 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  (D, L) Stereospecific Opine Dehydrogenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. L. Britton, Y. Asano, D. W. Rice
Crystal Structure And Active Site Location Of N-(1-D-Carboxylethyl)-L-Norvaline Dehydrogenase.
Nat. Struct. Biol. V. 5 593 1998
PubMed-ID: 9665174  |  Reference-DOI: 10.1038/854
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - N-(1-D-CARBOXYLETHYL)-L-NORVALINE DEHYDROGENASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PODH1
    Expression System Taxid: 562
    Gene: ODH
    Organism Scientific: ARTHROBACTER SP.
    Organism Taxid: 79670
    Strain: 1C

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1BG6)

(-) Sites  (0, 0)

(no "Site" information available for 1BG6)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1BG6)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:108 -Pro A:109
2Leu A:164 -Pro A:165

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1BG6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1BG6)

(-) Exons   (0, 0)

(no "Exon" information available for 1BG6)

(-) 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:349
 aligned with ODH_ARTSC | Q44297 from UniProtKB/Swiss-Prot  Length:359

    Alignment length:356
                                    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       313       323       333       343       353      
            ODH_ARTSC     4 SKTYAVLGLGNGGHAFAAYLALKGQSVLAWDIDAQRIKEIQDRGAIIAEGPGLAGTAHPDLLTSDIGLAVKDADVILIVVPAIHHASIAANIASYISEGQLIILNPGATGGALEFRKILRENGAPEVTIGETSSMLFTCRSERPGQVTVNAIKGAMDFACLPAAKAGWALEQIGSVLPQYVAVENVLHTSLTNVNAVMHPLPTLLNAARCESGTPFQYYLEGITPSVGSLAEKVDAERIAIAKAFDLNVPSVCEWYKESYGQSPATIYEAVQGNPAYRGIAGPINLNTRYFFEDVSTGLVPLSELGRAVNVPTPLIDAVLDLISSLIDTDFRKEGRTLEKLGLSGLTAAGIRSAVE 359
               SCOP domains d1bg6a2 A:4-187 N-(1-D-carboxylethyl)-L-norvaline dehydrogenase                                                                                                                         d1bg6a1 A:188-359 N-(1-D-carboxylethyl)-L-norvaline dehydrogenase                                                                                                            SCOP domains
               CATH domains 1bg6A01 A:4-195 NAD(P)-binding Rossmann-like Domain                                                                                                                                             1bg6A02 A:196-348 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenas       e; domain 2                                                                       ----------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhh...eeeee...hhhhhhhhhh..eeee.....eee...eee..hhhhh....eeee...hhhhhhhhhhhhhh.....eeee......hhhhhhhhhhh......eeeee....eeee.....eeeeeee...eeeeee.hhhhhhhhhhh......eee...hhhhhh..hhhhh.hhhhhhhhhhhh......hhhhh..hhhhhhhhhhhhhhhhhhhhh......hhhh.-------...hhhhhh..hhh...........hhhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhhh....hhhh.............hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bg6 A   4 SKTYAVLGLGNGGHAFAAYLALKGQSVLAWDIDAQRIKEIQDRGAIIAEGPGLAGTAHPDLLTSDIGLAVKDADVILIVVPAIHHASIAANIASYISEGQLIILNPGATGGALEFRKILRENGAPEVTIGETSSMLFTCRSERPGQVTVNAIKGAMDFACLPAAKAGWALEQIGSVLPQYVAVENVLHTSLTNVNAVMHPLPTLLNAARCESGTPFQYYLEGITPSVGSLAEKVDAERIAIAKAFDLNVPSVCEWY-------PATIYEAVQGNPAYRGIAGPINLNTRYFFEDVSTGLVPLSELGRAVNVPTPLIDAVLDLISSLIDTDFRKEGRTLEKLGLSGLTAAGIRSAVE 359
                                    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     |   -   |   273       283       293       303       313       323       333       343       353      
                                                                                                                                                                                                                                                                                         259     267
   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  (2, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BG6)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (ODH_ARTSC | Q44297)
molecular function
    GO:0008677    2-dehydropantoate 2-reductase activity    Catalysis of the reaction: (R)-pantoate + NADP(+) = 2-dehydropantoate + H(+) + NADPH.
    GO:0050662    coenzyme binding    Interacting selectively and non-covalently with a coenzyme, any of various nonprotein organic cofactors that are required, in addition to an enzyme and a substrate, for an enzymatic reaction to proceed.
    GO:0047129    opine dehydrogenase activity    Catalysis of the reaction: (2S)-2-[(R)-1-carboxyethylamino]pentanoate + H(2)O + NAD(+) = L-2-aminopentanoate + H(+) + NADH + pyruvate.
    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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  Cis Peptide Bonds
    Asn A:108 - Pro A:109   [ RasMol ]  
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