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(-) Description

Title :  CRYSTAL STRUCTURE OF 3-ISOPROPYLMALATE DEHYDRATASE (LEUD) FROM METHHANOCALDOCOCCUS JANNASCHII DSM2661 (MJ1271)
 
Authors :  J. Jeyakanthan, D. R. Gayathri, D. Velmurugan, Y. Agari, A. Ebihara, S. Kuramitsu, A. Shinkai, Y. Shiro, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  18 Apr 07  (Deposition) - 22 Apr 08  (Release) - 07 Apr 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  A  (1x)
Keywords :  Beta Barrel, Amino-Acid Biosynthesis, Leucine Biosynthesis, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Jeyakanthan, R. M. Drevland, D. R. Gayathri, D. Velmurugan, A. Shinkai, S. Kuramitsu, S. Yokoyama, D. E. Graham
Substrate Specificity Determinants Of The Methanogen Homoaconitase Enzyme: Structure And Function Of The Small Subunit
Biochemistry V. 49 2687 2010
PubMed-ID: 20170198  |  Reference-DOI: 10.1021/BI901766Z

(-) Compounds

Molecule 1 - HOMOACONITASE SMALL SUBUNIT
    Chains: A
    EC Number: 4.2.1.114
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL-21 CONDON PLUS (DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AKSE
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 243232
    Strain: DSM 2661
    Synonym: ISOPROPYLMALATE ISOMERASE 1, ALPHA-IPM ISOMERASE 1, IPMI 1

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
2ZN1Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
2ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:13 , HIS A:36 , ASN A:60 , CYS A:63 , HOH A:493BINDING SITE FOR RESIDUE ZN A 171
2AC2SOFTWAREASN A:97 , GLU A:143 , ILE A:146 , HOH A:406 , HOH A:481BINDING SITE FOR RESIDUE PEG A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PKP)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2PKP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PKP)

(-) Exons   (0, 0)

(no "Exon" information available for 2PKP)

(-) 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:167
 aligned with HACB_METJA | Q58667 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:167
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       
           HACB_METJA     1 MIIKGRAHKFGDDVDTDAIIPGPYLRTTDPYELASHCMAGIDENFPKKVKEGDVIVAGENFGCGSSREQAVIAIKYCGIKAVIAKSFARIFYRNAINVGLIPIIANTDEIKDGDIVEIDLDKEEIVITNKNKTIKCETPKGLEREILAAGGLVNYLKKRKLIQSKKG 167
               SCOP domains d2pkpa_ A: automated matches                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------Aconitase_C-2pkpA01 A:26-108                                                       ----------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhh..hhhhhhh........hhhhhh....eeee.........hhhhhhhhhh....eeee...hhhhhhhhhhh..eeee.hhhhh....eeeee....eeee.hhheeee....hhhhhhhhhh.hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pkp A   1 MIIKGRAHKFGDDVDTDAIIPGPYLRTTDPYELASHCMAGIDENFPKKVKEGDVIVAGENFGCGSSREQAVIAIKYCGIKAVIAKSFARIFYRNAINVGLIPIIANTDEIKDGDIVEIDLDKEEIVITNKNKTIKCETPKGLEREILAAGGLVNYLKKRKLIQSKKG 167
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
   Legend:   → Mismatch (orange background)
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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  (1, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2PKP)

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (HACB_METJA | Q58667)
molecular function
    GO:0004409    homoaconitate hydratase activity    Catalysis of the reaction: (-)-homoisocitrate = cis-homoaconitate + H(2)O.
    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:0019298    coenzyme B biosynthetic process    The chemical reactions and pathways resulting in the formation of coenzyme B (7-mercaptoheptanoylthreonine phosphate), a coenzyme involved in the utilization of methane by methanogenic prokaryotes.
    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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