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(-) Description

Title :  CRYSTAL STRUCTURE OF METHANOGEN 3-ISOPROPYLMALATE ISOMERASE SMALL SUBUNIT
 
Authors :  K. Y. Hwang, E. H. Lee
Date :  02 Jan 12  (Deposition) - 14 Nov 12  (Release) - 14 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Keywords :  Lyase, Leud, Cytosol (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. H. Lee, Y. W. Cho, K. Y. Hwang
Crystal Structure Of Leud From Methanococcus Jannaschii.
Biochem. Biophys. Res. Commun. V. 419 160 2012
PubMed-ID: 22326391  |  Reference-DOI: 10.1016/J.BBRC.2012.01.125

(-) Compounds

Molecule 1 - ISOPROPYLMALATE/CITRAMALATE ISOMERASE SMALL SUBUNIT
    Chains: A, B, C, D, E, F
    EC Number: 4.2.1.33, 4.2.1.35, 4.2.1.31
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: LEUD, MJ1277
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 243232
    Strain: DSM 2661
    Synonym: (R)-2-METHYLMALATE DEHYDRATASE, (R)-CITRAMALATE DEHYDRATASE, 3-ISOPROPYLMALATE DEHYDRATASE, ALPHA-ISOPROPYLMALATE DEHYDRATASE, CITRACONATE HYDRATASE, ISOPROPYLMALATE ISOMERASE, IPMI, MALEATE HYDRATASE, MALEASE

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB    
Biological Unit 2 (1x):   CD  
Biological Unit 3 (1x):     EF

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3VBA)

(-) Sites  (0, 0)

(no "Site" information available for 3VBA)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3VBA)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3VBA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VBA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VBA)

(-) Exons   (0, 0)

(no "Exon" information available for 3VBA)

(-) 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:169
 aligned with LEUD_METJA | Q58673 from UniProtKB/Swiss-Prot  Length:168

    Alignment length:169
                                                                                                                                                                                                 168 
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       | 
           LEUD_METJA     1 MRSIIKGRVWKFGNNVDTDAILPARYLVYTKPEELAQFVMTGADPDFPKKVKPGDIIVGGKNFGCGSSREHAPLGLKGAGISCVIAESFARIFYRNAINVGLPLIECKGISEKVNEGDELEVNLETGEIKNLTTGEVLKGQKLPEFMMEILEAGGLMPYLKKKMAESQ-   -
               SCOP domains d3vbaa_ A: automated matches                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.....hhhhhhhhhhh...hhhhhhhhh......hhhhhh....eeee..........hhhhhhhhhh...eeee...hhhhhhhhhhh...eee..hhhhhh....eeeee....eeee.....eee....hhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vba A   1 MRSIIKGRVWKFGNNVDTDAILPARYLVYTKPEELAQFVMTGADPDFPKKVKPGDIIVGGKNFGCGSSREHAPLGLKGAGISCVIAESFARIFYRNAINVGLPLIECKGISEKVNEGDELEVNLETGEIKNLTTGEVLKGQKLPEFMMEILEAGGLMPYLKKKMAESQL 169
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160         


Chain B from PDB  Type:PROTEIN  Length:169
 aligned with LEUD_METJA | Q58673 from UniProtKB/Swiss-Prot  Length:168

    Alignment length:169
                                                                                                                                                                                                 168 
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       | 
           LEUD_METJA     1 MRSIIKGRVWKFGNNVDTDAILPARYLVYTKPEELAQFVMTGADPDFPKKVKPGDIIVGGKNFGCGSSREHAPLGLKGAGISCVIAESFARIFYRNAINVGLPLIECKGISEKVNEGDELEVNLETGEIKNLTTGEVLKGQKLPEFMMEILEAGGLMPYLKKKMAESQ-   -
               SCOP domains d3vbab_ B: automated matches                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.....hhhhhhhhhhh...hhhhhhhhh......hhhhhh....eeee..........hhhhhhhhhh...eeee...hhhhhhhhhhh...eee..hhhhhh....eeeee....eeee.....eee....hhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vba B   1 MRSIIKGRVWKFGNNVDTDAILPARYLVYTKPEELAQFVMTGADPDFPKKVKPGDIIVGGKNFGCGSSREHAPLGLKGAGISCVIAESFARIFYRNAINVGLPLIECKGISEKVNEGDELEVNLETGEIKNLTTGEVLKGQKLPEFMMEILEAGGLMPYLKKKMAESQL 169
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160         


Chain C from PDB  Type:PROTEIN  Length:166
 aligned with LEUD_METJA | Q58673 from UniProtKB/Swiss-Prot  Length:168

    Alignment length:166
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160      
           LEUD_METJA     1 MRSIIKGRVWKFGNNVDTDAILPARYLVYTKPEELAQFVMTGADPDFPKKVKPGDIIVGGKNFGCGSSREHAPLGLKGAGISCVIAESFARIFYRNAINVGLPLIECKGISEKVNEGDELEVNLETGEIKNLTTGEVLKGQKLPEFMMEILEAGGLMPYLKKKMAE 166
               SCOP domains d3vbac_ C: automated matches                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.....hhhhhhhhhhh...hhhhhhhhh......hhhhhh....eeee..........hhhhhhhhhh...eeee...hhhhhhhhhhhh..eee..hhhhhh....eeeee....eeee.....eee....hhhhhhhhhh.hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vba C   1 MRSIIKGRVWKFGNNVDTDAILPARYLVYTKPEELAQFVMTGADPDFPKKVKPGDIIVGGKNFGCGSSREHAPLGLKGAGISCVIAESFARIFYRNAINVGLPLIECKGISEKVNEGDELEVNLETGEIKNLTTGEVLKGQKLPEFMMEILEAGGLMPYLKKKMAE 166
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160      


Chain D from PDB  Type:PROTEIN  Length:163
 aligned with LEUD_METJA | Q58673 from UniProtKB/Swiss-Prot  Length:168

    Alignment length:163
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160   
           LEUD_METJA     1 MRSIIKGRVWKFGNNVDTDAILPARYLVYTKPEELAQFVMTGADPDFPKKVKPGDIIVGGKNFGCGSSREHAPLGLKGAGISCVIAESFARIFYRNAINVGLPLIECKGISEKVNEGDELEVNLETGEIKNLTTGEVLKGQKLPEFMMEILEAGGLMPYLKKK 163
               SCOP domains d3vbad_ D: automated matches                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.....hhhhhhhhhhhhh.hhhhhhhhh......hhhhhh....eeee..........hhhhhhhhhh...eeee...hhhhhhhhhhhh..eee..hhhhhh....eeeee....eeee.....eee....hhhhhhhhhh.hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vba D   1 MRSIIKGRVWKFGNNVDTDAILPARYLVYTKPEELAQFVMTGADPDFPKKVKPGDIIVGGKNFGCGSSREHAPLGLKGAGISCVIAESFARIFYRNAINVGLPLIECKGISEKVNEGDELEVNLETGEIKNLTTGEVLKGQKLPEFMMEILEAGGLMPYLKKK 163
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160   


Chain E from PDB  Type:PROTEIN  Length:165
 aligned with LEUD_METJA | Q58673 from UniProtKB/Swiss-Prot  Length:168

    Alignment length:165
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160     
           LEUD_METJA     1 MRSIIKGRVWKFGNNVDTDAILPARYLVYTKPEELAQFVMTGADPDFPKKVKPGDIIVGGKNFGCGSSREHAPLGLKGAGISCVIAESFARIFYRNAINVGLPLIECKGISEKVNEGDELEVNLETGEIKNLTTGEVLKGQKLPEFMMEILEAGGLMPYLKKKMA 165
               SCOP domains d3vbae_ E: automated matches                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.....hhhhhhhhhhh...hhhhhhhhh......hhhhhh....eeee..........hhhhhhhhhh...eeee...hhhhhhhhhhhh..eee..hhhhhh....eeeee....eeee.....eee....hhhhhhhhhh.hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vba E   1 MRSIIKGRVWKFGNNVDTDAILPARYLVYTKPEELAQFVMTGADPDFPKKVKPGDIIVGGKNFGCGSSREHAPLGLKGAGISCVIAESFARIFYRNAINVGLPLIECKGISEKVNEGDELEVNLETGEIKNLTTGEVLKGQKLPEFMMEILEAGGLMPYLKKKMA 165
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160     


Chain F from PDB  Type:PROTEIN  Length:165
 aligned with LEUD_METJA | Q58673 from UniProtKB/Swiss-Prot  Length:168

    Alignment length:165
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160     
           LEUD_METJA     1 MRSIIKGRVWKFGNNVDTDAILPARYLVYTKPEELAQFVMTGADPDFPKKVKPGDIIVGGKNFGCGSSREHAPLGLKGAGISCVIAESFARIFYRNAINVGLPLIECKGISEKVNEGDELEVNLETGEIKNLTTGEVLKGQKLPEFMMEILEAGGLMPYLKKKMA 165
               SCOP domains d3vbaf_ F: automated matches                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.....hhhhhhhhhhh...hhhhhhhhh......hhhhh.....eeee..........hhhhhhhhhh...eeee...hhhhhhhhhhhh..eee..hhhhhh....eeeee....eeee.....eee....hhhhhhhhhh.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vba F   1 MRSIIKGRVWKFGNNVDTDAILPARYLVYTKPEELAQFVMTGADPDFPKKVKPGDIIVGGKNFGCGSSREHAPLGLKGAGISCVIAESFARIFYRNAINVGLPLIECKGISEKVNEGDELEVNLETGEIKNLTTGEVLKGQKLPEFMMEILEAGGLMPYLKKKMA 165
                                    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, 6)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VBA)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VBA)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (LEUD_METJA | Q58673)
molecular function
    GO:0047508    (R)-2-methylmalate dehydratase activity    Catalysis of the reaction: (R)-citramalate = 2-methylmaleate + H(2)O.
    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.
    GO:0050075    maleate hydratase activity    Catalysis of the reaction: (R)-malate = H(2)O + maleate.
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:0009097    isoleucine biosynthetic process    The chemical reactions and pathways resulting in the formation of isoleucine, (2R*,3R*)-2-amino-3-methylpentanoic acid.
    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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  3vba
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 Related Entries

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