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(-) Description

Title :  STRUCTURE OF 3-ISOPROPYLMALATE ISOMERASE SMALL SUBUNIT FROM PYROCOCCUS HORIKOSHII
 
Authors :  M. Yao, T. Kirita, N. Sakai, I. Tanaka
Date :  18 Dec 03  (Deposition) - 16 Nov 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.98
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A (4x),B (4x)
Biol. Unit 3:  A  (1x)
Biol. Unit 4:  B  (1x)
Keywords :  Beta Barrel, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Yasutake, M. Yao, N. Sakai, T. Kirita, I. Tanaka
Crystal Structure Of The Pyrococcus Horikoshii Isopropylmalate Isomerase Small Subunit Provides Insight Into The Dual Substrate Specificity Of The Enzyme
J. Mol. Biol. V. 344 325 2004
PubMed-ID: 15522288  |  Reference-DOI: 10.1016/J.JMB.2004.09.035

(-) Compounds

Molecule 1 - 3-ISOPROPYLMALATE DEHYDRATASE SMALL SUBUNIT
    Chains: A, B
    EC Number: 4.2.1.33
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-22B
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PH1724
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 70601
    Strain: OT3
    Synonym: 3-ISOPROPYLMALATE ISOMERASE SMALL SUBUNIT, ISOPROPYLMALATE ISOMERASE, ALPHA-IPM ISOMERASE, IPMI

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (4x): A (4x)B (4x)
Biological Unit 3 (1x): A 
Biological Unit 4 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1V7L)

(-) Sites  (0, 0)

(no "Site" information available for 1V7L)

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:161 -A:161
2B:161 -B:161

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V7L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V7L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V7L)

(-) Exons   (0, 0)

(no "Exon" information available for 1V7L)

(-) 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
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Chain A from PDB  Type:PROTEIN  Length:162
 aligned with LEUD_PYRHO | O59393 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
           LEUD_PYRHO     1 MITTGKVWKFGDDISTDEITPGRYNLTKDPKELAKIAFIEVRPDFARNVRPGDVVVAGKNFGIGSSRESAALALKALGIAGVIAESFGRIFYRNAINIGIPLLLGKTEGLKDGDLVTVNWETGEVRKGDEILMFEPLEDFLLEIVREGGILEYIRRRGDLCI 162
               SCOP domains d1v7la_ A: Isopropylmalate isomerase LeuD                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhh........hhhhhhhhh......hhhhhh....eee...........hhhhhhhhhhh..eeee...hhhhhhhhhhhh..eee..........eeeee....eeee..eeee.ee.hhhhhhhhhh.hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1v7l A   1 MITTGKVWKFGDDISTDEITPGRYNLTKDPKELAKIAFIEVRPDFARNVRPGDVVVAGKNFGIGSSRESAALALKALGIAGVIAESFGRIFYRNAINIGIPLLLGKTEGLKDGDLVTVNWETGEVRKGDEILMFEPLEDFLLEIVREGGILEYIRRRGDLCI 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  


Chain B from PDB  Type:PROTEIN  Length:163
 aligned with LEUD_PYRHO | O59393 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:163
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160   
           LEUD_PYRHO     1 MITTGKVWKFGDDISTDEITPGRYNLTKDPKELAKIAFIEVRPDFARNVRPGDVVVAGKNFGIGSSRESAALALKALGIAGVIAESFGRIFYRNAINIGIPLLLGKTEGLKDGDLVTVNWETGEVRKGDEILMFEPLEDFLLEIVREGGILEYIRRRGDLCIR 163
               SCOP domains d1v7lb_ B: Isopropylmalate isomerase LeuD                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------Aconitase_C-1v7lB01 B:11-107                                                                     -------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----------Aconitase_C-1v7lB02 B:11-107                                                                     -------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .eeeeeeee.....hhhhhh........hhhhhhhhh......hhhhhh....eee...........hhhhhhhhhh...eeee...hhhhhhhhhhhh..eee..........eeeee....eeee..eeee....hhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v7l B   1 MITTGKVWKFGDDISTDEITPGRYNLTKDPKELAKIAFIEVRPDFARNVRPGDVVVAGKNFGIGSSRESAALALKALGIAGVIAESFGRIFYRNAINIGIPLLLGKTEGLKDGDLVTVNWETGEVRKGDEILMFEPLEDFLLEIVREGGILEYIRRRGDLCIR 163
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
   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  (1, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1V7L)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Leu-IlvD (4)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (LEUD_PYRHO | O59393)
molecular function
    GO:0003861    3-isopropylmalate dehydratase activity    Catalysis of the reaction: 3-isopropylmalate = 2-isopropylmaleate + H2O.
    GO:0016836    hydro-lyase activity    Catalysis of the cleavage of a carbon-oxygen bond by elimination of water.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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  1v7l
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  4.2.1.33
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