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(-) Description

Title :  MALATE DEHYDROGENASE FROM AQUASPIRILLUM ARCTICUM
 
Authors :  S. Y. Kim, K. Y. Hwang, S. -H. Kim, Y. S. Han, Y. Cho
Date :  02 Feb 99  (Deposition) - 09 Jul 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Dehydrogenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Y. Kim, K. Y. Hwang, S. H. Kim, H. C. Sung, Y. S. Han, Y. Cho
Structural Basis For Cold Adaptation. Sequence, Biochemical Properties, And Crystal Structure Of Malate Dehydrogenase From A Psychrophile Aquaspirillium Arcticum.
J. Biol. Chem. V. 274 11761 1999
PubMed-ID: 10206992  |  Reference-DOI: 10.1074/JBC.274.17.11761

(-) Compounds

Molecule 1 - PROTEIN (MALATE DEHYDROGENASE)
    Chains: A
    Organism Scientific: AQUASPIRILLUM ARCTICUM
    Organism Taxid: 87645

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2OAA1Ligand/IonOXALOACETATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2OAA2Ligand/IonOXALOACETATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:161 , ARG A:165 , HIS A:190 , SER A:191 , GLY A:227 , LYS A:228 , ARG A:229 , GLY A:230 , SER A:241 , NAD A:334 , HOH A:356 , HOH A:359BINDING SITE FOR RESIDUE OAA A 350
2AC2SOFTWARETHR A:11 , GLY A:12 , GLY A:15 , GLN A:16 , ILE A:17 , GLU A:43 , ILE A:44 , VAL A:90 , GLY A:91 , ALA A:92 , GLN A:115 , VAL A:132 , GLY A:133 , ASN A:134 , MET A:158 , HIS A:190 , OAA A:350 , HOH A:367 , HOH A:381BINDING SITE FOR RESIDUE NAD A 334

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1B8U)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asn A:134 -Pro A:135

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1B8U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1B8U)

(-) Exons   (0, 0)

(no "Exon" information available for 1B8U)

(-) 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:327
 aligned with MDH_AQUAR | Q9ZF99 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:327
                                    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       
            MDH_AQUAR     3 KTPMRVAVTGAAGQICYSLLFRIANGDMLGKDQPVILQLLEIPNEKAQKALQGVMMEIDDCAFPLLAGMTAHADPMTAFKDADVALLVGARPRGPGMERKDLLEANAQIFTVQGKAIDAVASRNIKVLVVGNPANTNAYIAMKSAPSLPAKNFTAMLRLDHNRALSQIAAKTGKPVSSIEKLFVWGNHSPTMYADYRYAQIDGASVKDMINDDAWNRDTFLPTVGKRGAAIIDARGVSSAASAANAAIDHIHDWVLGTAGKWTTMGIPSDGSYGIPEGVIFGFPVTTENGEYKIVQGLSIDAFSQERINVTLNELLEEQNGVQHLLG 329
               SCOP domains d1b8ua1 A:3-158 Malate dehydrogenase                                                                                                                        d1b8ua2 A:159-329 Malate dehydrogenase                                                                                                                                      SCOP domains
               CATH domains 1b8uA01 A:3-157 NAD(P)-binding Rossmann-like Domain                                                                                                        1b8uA02 A:158-329 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....hhhhhhhhhhh..........eeeeee....hhhhhhhhhhhhhhhhh....eeeeeee..hhhh.....eeee...........hhhhhhhhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhh......hhheee..hhhhhhhhhhhhhhh...hhh....eee.......eee..........hhhhh..hhhhhh.hhhhhh.hhhhhhhhh....hhhhhhhhhhhhhhhhh......eeeeee...hhh.....eeeeeeeee..eeee.......hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b8u A   3 KTPMRVAVTGAAGQICYSLLFRIANGDMLGKDQPVILQLLEIPNEKAQKALQGVMMEIDDCAFPLLAGMTAHADPMTAFKDADVALLVGARPRGPGMERKDLLEANAQIFTVQGKAIDAVASRNIKVLVVGNPANTNAYIAMKSAPSLPAKNFTAMLRLDHNRALSQIAAKTGKPVSSIEKLFVWGNHSPTMYADYRYAQIDGASVKDMINDDAWNRDTFLPTVGKRGAAIIDARGVSSAASAANAAIDHIHDWVLGTAGKWTTMGIPSDGSYGIPEGVIFGFPVTTENGEYKIVQGLSIDAFSQERINVTLNELLEEQNGVQHLLG 329
                                    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
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1B8U)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (MDH_AQUAR | Q9ZF99)
molecular function
    GO:0030060    L-malate dehydrogenase activity    Catalysis of the reaction: (S)-malate + NAD+ = oxaloacetate + NADH + H+.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016615    malate dehydrogenase activity    Catalysis of the reversible conversion of pyruvate or oxaloacetate to malate.
    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:0016616    oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0019752    carboxylic acid metabolic process    The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
    GO:0006108    malate metabolic process    The chemical reactions and pathways involving malate, the anion of hydroxybutanedioic acid, a chiral hydroxydicarboxylic acid. The (+) enantiomer is an important intermediate in metabolism as a component of both the TCA cycle and the glyoxylate cycle.
    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.
    GO:0006099    tricarboxylic acid cycle    A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.

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        MDH_AQUAR | Q9ZF99: 1b8p 1b8v

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