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(-) Description

Title :  CRYSTAL STRUCTURE OF LEUCINE DEHYDROGENASE FROM A PSYCHROPHILIC BACTERIUM SPOROSARCINA PSYCHROPHILA.
 
Authors :  Y. Zhao, T. Wakamatsu, K. Doi, H. Sakuraba, T. Ohshima
Date :  14 Mar 12  (Deposition) - 06 Feb 13  (Release) - 06 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (4x)
Keywords :  Rossmann Fold, Leucine Dehydrogense, Nad/Leucine Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Zhao, T. Wakamatsu, K. Doi, H. Sakuraba, T. Ohshima
A Psychrophilic Leucine Dehydrogenase From Sporosarcina Psychrophila: Purification, Characterization, Gene Sequencing And Crystal Structure Analysis
J. Mol. Catal. , B Enzym. V. 83 65 2012
PubMed: search  |  Reference-DOI: 10.1016/J.MOLCATB.2012.06.018

(-) Compounds

Molecule 1 - LEUCINE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.4.1.9
    Organism Scientific: SPOROSARCINA PSYCHROPHILA
    Organism Taxid: 1476
    Strain: DSM 3
    Synonym: LEUDH

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (4x): AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3VPX)

(-) Sites  (0, 0)

(no "Site" information available for 3VPX)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3VPX)

(-) 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:356
 aligned with I0IJU1_SPOPS | I0IJU1 from UniProtKB/TrEMBL  Length:364

    Alignment length:363
                                    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       280       290       300       310       320       330       340       350       360   
         I0IJU1_SPOPS     1 MEIFKYMEHQDYEQLVICQDKASGLKAIIAIHDTTLGPALGGTRMWTYASEEEAIEDALRLARGMTYKNAAAGLNLGGGKTVIIGNPKTDKNDEMFRAFGRYIEGLNGRYITAEDVGTTEADMDLINLETDYVTGTSAGAGSSGNPSPVTAYGIYYGMKAAAKEAFGDDSLAGKTVAVQGVGNVAYALCEYLHEEGAKLIITDINEEAVQRAVDAFGATAVGINEIYSQEADIFAPCALGAIINDETIPQLKAKVIAGSANNQLKETRHGDLIHEMGIVYAPDYVINSGGVINVADELDGYNRERALKRVEGIYDVIGKIFAISKRDNIPTYVAADRMAEERIARVANTRSTFLQNEKSVLSR 363
               SCOP domains d3vpxa1 A:1-133 automated matches                                                                                                    -----------d3vpxa2 A:145-363 automated matches                                                                                                                                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh...eeeeeee....eeeeeeeee.....ee..eeee...hhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee.......hhhhhhhhhhhhhh....ee.......hhhhhhhhh..........-------.hhhhhhhhhhhhhhhhhhhhh......eeeeeee..hhhhhhhhhhhhhh.eee.....hhhhhhhhhhhhh...............eeee.........hhhhhh...ee.........hhhhhhhhh....ee.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vpx A   1 MEIFKYMEHQDYEQLVICQDKASGLKAIIAIHDTTLGPALGGTRMWTYASEEEAIEDALRLARGMTYKNAAAGLNLGGGKTVIIGNPKTDKNDEMFRAFGRYIEGLNGRYITAEDVGTTEADMDLINLETDYVTGTS-------NPSPVTAYGIYYGMKAAAKEAFGDDSLAGKTVAVQGVGNVAYALCEYLHEEGAKLIITDINEEAVQRAVDAFGATAVGINEIYSQEADIFAPCALGAIINDETIPQLKAKVIAGSANNQLKETRHGDLIHEMGIVYAPDYVINSGGVINVADELDGYNRERALKRVEGIYDVIGKIFAISKRDNIPTYVAADRMAEERIARVANTRSTFLQNEKSVLSR 363
                                    10        20        30        40        50        60        70        80        90       100       110       120       130      |  -    |  150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360   
                                                                                                                                                                  137     145                                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:359
 aligned with I0IJU1_SPOPS | I0IJU1 from UniProtKB/TrEMBL  Length:364

    Alignment length:363
                                    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       280       290       300       310       320       330       340       350       360   
         I0IJU1_SPOPS     1 MEIFKYMEHQDYEQLVICQDKASGLKAIIAIHDTTLGPALGGTRMWTYASEEEAIEDALRLARGMTYKNAAAGLNLGGGKTVIIGNPKTDKNDEMFRAFGRYIEGLNGRYITAEDVGTTEADMDLINLETDYVTGTSAGAGSSGNPSPVTAYGIYYGMKAAAKEAFGDDSLAGKTVAVQGVGNVAYALCEYLHEEGAKLIITDINEEAVQRAVDAFGATAVGINEIYSQEADIFAPCALGAIINDETIPQLKAKVIAGSANNQLKETRHGDLIHEMGIVYAPDYVINSGGVINVADELDGYNRERALKRVEGIYDVIGKIFAISKRDNIPTYVAADRMAEERIARVANTRSTFLQNEKSVLSR 363
               SCOP domains d3vpxb1 B:1-133 automated matches                                                                                                    -----------d3vpxb2 B:145-363 automated matches                                                                                                                                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh...eeeeeee....eeeeeeeee.....ee..eeee...hhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee.......hhhhhhhhhhhhhhh...ee.......hhhhhhhhh.............----.hhhhhhhhhhhhhhhhh..........eeeeeee..hhhhhhhhhhhhhh.eeee....hhhhhhhhhhhhh...............eeee..................ee.........hhhhhhhhhhh..ee.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vpx B   1 MEIFKYMEHQDYEQLVICQDKASGLKAIIAIHDTTLGPALGGTRMWTYASEEEAIEDALRLARGMTYKNAAAGLNLGGGKTVIIGNPKTDKNDEMFRAFGRYIEGLNGRYITAEDVGTTEADMDLINLETDYVTGTSAGA----NPSPVTAYGIYYGMKAAAKEAFGDDSLAGKTVAVQGVGNVAYALCEYLHEEGAKLIITDINEEAVQRAVDAFGATAVGINEIYSQEADIFAPCALGAIINDETIPQLKAKVIAGSANNQLKETRHGDLIHEMGIVYAPDYVINSGGVINVADELDGYNRERALKRVEGIYDVIGKIFAISKRDNIPTYVAADRMAEERIARVANTRSTFLQNEKSVLSR 363
                                    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       280       290       300       310       320       330       340       350       360   
                                                                                                                                                                     140  145
   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, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (I0IJU1_SPOPS | I0IJU1)
molecular function
    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:0016639    oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-NH2 group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
biological process
    GO:0006520    cellular amino acid metabolic process    The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
    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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 Related Entries

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