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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF LICMS IN COMPLEXED WITH PYRUVATE AND ACETYL-COA
 
Authors :  P. Zhang, J. Ma
Date :  11 Dec 07  (Deposition) - 11 Nov 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Tim Barrel, Licmsn, Substrate Specificity, Acyltransferase, Amino-Acid Biosynthesis, Branched-Chain Amino Acid Biosynthesis, Leucine Biosynthesis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Ma, P. Zhang, Z. Zhang, M. Zha, H. Xu, G. Zhao, J. Ding
Molecular Basis Of The Substrate Specificity And The Catalytic Mechanism Of Citramalate Synthase From Leptospira Interrogans
Biochem. J. V. 415 45 2008
PubMed-ID: 18498255  |  Reference-DOI: 10.1042/BJ20080242
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CITRAMALATE SYNTHASE FROM LEPTOSPIRA INTERROGANS
    Chains: A
    EC Number: 2.3.3.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-325
    Gene: CIMA
    Organism Scientific: LEPTOSPIRA INTERROGANS
    Organism Taxid: 173
    Strain: 56601

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1ACO1Ligand/IonACETYL COENZYME *A
2PYR1Ligand/IonPYRUVIC ACID
3ZN1Ligand/IonZINC ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1ACO2Ligand/IonACETYL COENZYME *A
2PYR2Ligand/IonPYRUVIC ACID
3ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:17 , HIS A:207 , HIS A:209 , ASN A:243 , HOH A:1087BINDING SITE FOR RESIDUE ZN A 1003
2AC2SOFTWAREARG A:16 , GLN A:20 , SER A:51 , ARG A:53 , LEU A:81 , GLU A:146 , ALA A:299 , HOH A:1086BINDING SITE FOR RESIDUE ACO A 1004
3AC3SOFTWAREARG A:16 , ASP A:17 , TYR A:144 , PRO A:177 , THR A:179 , HIS A:207 , HIS A:209 , HOH A:1087BINDING SITE FOR RESIDUE PYR A 1005

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3BLI)

(-) 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:311
 aligned with Q8F3Q1_LEPIN | Q8F3Q1 from UniProtKB/TrEMBL  Length:516

    Alignment length:319
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316         
         Q8F3Q1_LEPIN     7 RLEILDVTLRDGEQTRGVSFSTSEKLNIAKFLLQKLNVDRVEIASARVSKGELETVQKIMEWAATEQLTERIEILGFVDGNKTVDWIKDSGAKVLNLLTKGSLHHLEKQLGKTPKEFFTDVSFVIEYAIKSGLKINVYLEDWSNGFRNSPDYVKSLVEHLSKEHIERIFLPDTLGVLSPEETFQGVDSLIQKYPDIHFEFHGHNDYDLSVANSLQAIRAGVKGLHASINGLGERAGNTPLEALVTTIHDKSNSKTNINEIAITEASRLVEVFSGKRISANRPIVGEDVFTQTAGVHADGDKKGNLYANPILPERFGRKR 325
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..............hhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhhhh.hhh.eeeeee...hhhhhhhhhhh..eeeeeee.hhhhhhhhh..hhhhhhhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhh....eeee......hhhhhhhhhhhhh..eeeehhhhh.......hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh.....................--------.......hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bli A   7 RLEILDVTLRDGEQTRGVSFSTSEKLNIAKFLLQKLNVDRVEIASARVSKGELETVQKIMEWAATEQLTERIEILGFVDGNKTVDWIKDSGAKVLNLLTKGSLHHLEKQLGKTPKEFFTDVSFVIEYAIKSGLKINVYLEDWSNGFRNSPDYVKSLVEHLSKEHIERIFLPDTLGVLSPEETFQGVDSLIQKYPDIHFEFHGHNDYDLSVANSLQAIRAGVKGLHASINGLGERAGNTPLEALVTTIHDKSNSKTNINEIAITEASRLVEVFSGKRISANRPIVGEDVFTQTAGV--------NLYANPILPERFGRKR 325
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296    |    -   |   316         
                                                                                                                                                                                                                                                                                                                                301      310
   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  (0, 0)

(no "SCOP Domain" information available for 3BLI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q8F3Q1_LEPIN | Q8F3Q1)
molecular function
    GO:0003852    2-isopropylmalate synthase activity    Catalysis of the reaction: 3-methyl-2-oxobutanoate + acetyl-CoA + H(2)O = (2S)-2-isopropylmalate + CoA + 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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0046912    transferase activity, transferring acyl groups, acyl groups converted into alkyl on transfer    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor), with the acyl group being converted into alkyl on transfer.
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: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: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.

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        Q8F3Q1_LEPIN | Q8F3Q1: 3ble 3blf 3f6g 3f6h

(-) Related Entries Specified in the PDB File

3ble 3blf