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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MJ0490 GENE PRODUCT, THE FAMILY OF LACTATE/MALATE DEHYDROGENASE, DIMERIC STRUCTURE
 
Authors :  B. I. Lee, C. Chang, S. -J. Cho, S. W. Suh
Date :  19 Jan 01  (Deposition) - 18 Apr 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Nucleotide Binding Domain, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. I. Lee, C. Chang, S. J. Cho, S. H. Eom, K. K. Kim, Y. G. Yu, S. W. Suh
Crystal Structure Of The Mj0490 Gene Product Of The Hyperthermophilic Archaebacterium Methanococcus Jannaschii, A Novel Member Of The Lactate/Malate Family Of Dehydrogenases.
J. Mol. Biol. V. 307 1351 2001
PubMed-ID: 11292347  |  Reference-DOI: 10.1006/JMBI.2001.4532
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - L-LACTATE/MALATE DEHYDROGENASE
    Chains: A
    EC Number: 1.1.1.27
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: C41(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MJ0490
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:7 , SER A:9 , GLY A:10 , ARG A:11 , VAL A:12 , ARG A:34 , HIS A:36 , SER A:37 , ASN A:68 , THR A:81 , GLY A:83 , VAL A:84 , ARG A:86 , ILE A:102 , TYR A:106 , ILE A:121 , THR A:122 , ASN A:123 , LEU A:146 , HIS A:178 , GLU A:219 , HOH A:1003 , HOH A:1007 , HOH A:1019 , HOH A:1046BINDING SITE FOR RESIDUE NAP A 748

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asn A:123 -Pro A:124

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1HYE)

(-) 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:307
 aligned with MDH_METJA | Q60176 from UniProtKB/Swiss-Prot  Length:313

    Alignment length:313
                                    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   
            MDH_METJA     1 MKVTIIGASGRVGSATALLLAKEPFMKDLVLIGREHSINKLEGLREDIYDALAGTRSDANIYVESDENLRIIDESDVVIITSGVPRKEGMSRMDLAKTNAKIVGKYAKKIAEICDTKIFVITNPVDVMTYKALVDSKFERNQVFGLGTHLDSLRFKVAIAKFFGVHIDEVRTRIIGEHGDSMVPLLSATSIGGIPIQKFERFKELPIDEIIEDVKTKGEQIIRLKGGSEFGPAAAILNVVRCIVNNEKRLLTLSAYVDGEFDGIRDVCIGVPVKIGRDGIEEVVSIELDKDEIIAFRKSAEIIKKYCEEVKNL 313
               SCOP domains d1hyea1 A:1-145 MJ0490, lactate/malate dehydrogenase                                                                                             d1hyea2 A:146-313 MJ0490, lactate/malate dehydrogenase                                                                                                                   SCOP domains
               CATH domains 1hyeA01 A:1-147 NAD(P)-binding Rossmann-like Domain                                                                                                1hyeA02 A:148-310 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                        --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhhhhhhh......eeeeee..hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhh.....eee..hhhhhhhhhhhhhhhhh.hhh.ee..eee.....eee.hhh.ee..ee.hhhhhhhhhhhhhhhhhhhhhh.....------.hhhhhhhhhhhhhhh...eeeeeeeeee......eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hye A   1 MKVTIIGASGRVGSATALLLAKEPFMKDLVLIGREHSINKLEGLREDIYDALAGTRSDANIYVESDENLRIIDESDVVIITSGVPRKEGMSRMDLAKTNAKIVGKYAKKIAEICDTKIFVITNPVDVMTYKALVDSKFERNQVFGLGTHLDSLRFKVAIAKFFGVHIDEVRTRIIGEHGDSMVPLLSATSIGGIPIQKFERFKELPIDEIIEDVKTKGEQIIR------FGPAAAILNVVRCIVNNEKRLLTLSAYVDGEFDGIRDVCIGVPVKIGRDGIEEVVSIELDKDEIIAFRKSAEIIKKYCEEVKNL 313
                                    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   
                                                                                                                                                                                                                                                        223    230
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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: 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 1HYE)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (MDH_METJA | Q60176)
molecular function
    GO:0004459    L-lactate dehydrogenase activity    Catalysis of the reaction: (S)-lactate + NAD+ = pyruvate + 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: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: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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  1hye
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 Related Entries

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

UniProtKB/Swiss-Prot
        MDH_METJA | Q60176: 1hyg

(-) Related Entries Specified in the PDB File

1hyg 1HYG CONTAINS THE SAME PROTEIN AS TETRAMER.