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(-) Description

Title :  CRYSTAL STRUCTURE OF 3-ISOPROPYLMALATE DEHYDROGENASE (TM0556) FROM THERMOTOGA MARITIMA AT 1.90 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  20 Jul 04  (Deposition) - 21 Sep 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Tm0556, 3-Isopropylmalate Dehydrogenase, Structural Genomics, Jcsg, Psi, Protein Structure Initiative, Joint Center For Structural Genomics, Dehydrogenase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of 3-Isopropylmalate Dehydrogenase (Tm0556) From Thermotoga Maritima At 1. 90 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 3-ISOPROPYLMALATE DEHYDROGENASE
    Chains: A
    EC Number: 1.1.1.85
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: LEUB, TM0556
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: BETA-IPM DEHYDROGENASE, IMDH, 3-IPM-DH

 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
1CL1Ligand/IonCHLORIDE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:139 , VAL A:140 , MET A:240BINDING SITE FOR RESIDUE CL A 355

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gln A:144 -Pro A:145

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IDH_IMDHPS00470 Isocitrate and isopropylmalate dehydrogenases signature.LEU3_THEMA239-258  1A:239-258
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IDH_IMDHPS00470 Isocitrate and isopropylmalate dehydrogenases signature.LEU3_THEMA239-258  2A:239-258

(-) Exons   (0, 0)

(no "Exon" information available for 1VLC)

(-) 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:362
 aligned with LEU3_THEMA | Q9WZ26 from UniProtKB/Swiss-Prot  Length:354

    Alignment length:362
                                    1                                                                                                                                                                                                                                                                                                                                                                 
                                    |2        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       332       342       352  
           LEU3_THEMA     - --------MKIAVLPGDGIGPEVVREALKVLEVVEKKTGKTFEKVFGHIGGDAIDRFGEPLPEETKKICLEADAIFLGSVGGPKWDDLPPEKRPEIGGLLALRKMLNLYANIRPIKVYRSLVHVSPLKEKVIGSGVDLVTVRELSYGVYYGQPRGLDEEKGFDTMIYDRKTVERIARTAFEIAKNRRKKVTSVDKANVLYSSMLWRKVVNEVAREYPDVELTHIYVDNAAMQLILKPSQFDVILTTNMFGDILSDESAALPGSLGLLPSASFGDKNLYEPAGGSAPDIAGKNIANPIAQILSLAMMLEHSFGMVEEARKIERAVELVIEEGYRTRDIAEDPEKAVSTSQMGDLICKKLEEIW 354
               SCOP domains d1vlca_ A: 3-isopropylmalate dehydrogenase, IPMDH                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1vlcA00 A:-7-354 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhh.eeeeee...hhhhhhhhh...hhhhhhhhhhh.eeeeee..hhhhh......hhhhhhhhhhhhhh...eeeeeee.hhhhhhhh..hhhhhh...eeeeeee..hhhhheeeeee....eeee...hhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhh....hhhh.eeeee...eeeee...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.hhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IDH_IMDH            ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vlc A  -7 KIHHHHHHMKIAVLPGDGIGPEVVREALKVLEVVEKKTGKTFEKVFGHIGGDAIDRFGEPLPEETKKICLEADAIFLGSVGGPKWDDLPPEKRPEIGGLLALRKMLNLYANIRPIKVYRSLVHVSPLKEKVIGSGVDLVTVRELSYGVYYGQPRGLDEEKGFDTMIYDRKTVERIARTAFEIAKNRRKKVTSVDKANVLYSSMLWRKVVNEVAREYPDVELTHIYVDNAAMQLILKPSQFDVILTTNMFGDILSDESAALPGSLGLLPSASFGDKNLYEPAGGSAPDIAGKNIANPIAQILSLAMMLEHSFGMVEEARKIERAVELVIEEGYRTRDIAEDPEKAVSTSQMGDLICKKLEEIW 354
                                     2        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       332       342       352
   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 1VLC)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (LEU3_THEMA | Q9WZ26)
molecular function
    GO:0003862    3-isopropylmalate dehydrogenase activity    Catalysis of the reaction: 3-carboxy-2-hydroxy-4-methylpentanoate + NAD+ = 3-carboxy-4-methyl-2-oxopentanoate + NADH + H+.
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0009082    branched-chain amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine.
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0009098    leucine biosynthetic process    The chemical reactions and pathways resulting in the formation of leucine, 2-amino-4-methylpentanoic acid.
    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.
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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