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(-) Description

Title :  CRYSTAL STRUCTURE OF THE REGULATORY DOMAIN OF LICMS IN COMPLEXED WITH ISOLEUCINE - TYPE II
 
Authors :  P. Zhang, J. Ma, G. Zhao, J. Ding
Date :  06 Nov 08  (Deposition) - 21 Apr 09  (Release) - 23 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Licmsc, Allosteric Regulation, Feedback Inhibition, Selectivity, Specificity, Transferase, Acyltransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Zhang, J. Ma, Z. Zhang, M. Zha, H. Xu, G. Zhao, J. Ding
Molecular Basis Of The Inhibitor Selectivity And Insights Into The Feedback Inhibition Mechanism Of Citramalate Synthase From Leptospira Interrogans
Biochem. J. V. 421 133 2009
PubMed-ID: 19351325  |  Reference-DOI: 10.1042/BJ20090336
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALPHA-ISOPROPYLMALATE SYNTHASE
    Chains: B, A
    EC Number: 2.3.1.182
    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: REGULATORY DOMAIN, UNP RESIDUES 390-516
    Gene: CIMA
    Organism Scientific: LEPTOSPIRA INTERROGANS
    Organism Taxid: 173
    Strain: 56601
    Synonym: CITRAMALATE SYNTHASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
1ILE2Mod. Amino AcidISOLEUCINE
2SO48Ligand/IonSULFATE ION
3ZN2Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH B:104 , HIS B:400 , HIS B:408BINDING SITE FOR RESIDUE ZN B 358
02AC2SOFTWAREHOH A:27 , GLY A:428 , GLY A:429 , TYR A:430 , ASP A:431 , THR B:464 , ASP B:465 , ALA B:466 , VAL B:468 , PRO B:493 , ASP B:494 , GLN B:495BINDING SITE FOR RESIDUE ILE B 1
03AC3SOFTWAREHOH B:10 , TYR B:415 , GLN B:416 , LYS B:418 , LEU B:444BINDING SITE FOR RESIDUE SO4 B 1004
04AC4SOFTWAREHOH B:3 , HOH B:129 , ARG B:471 , LYS B:487 , MET B:489BINDING SITE FOR RESIDUE SO4 B 1005
05AC5SOFTWAREVAL B:491 , HIS B:501 , LYS B:505BINDING SITE FOR RESIDUE SO4 B 1006
06AC6SOFTWAREHOH A:40 , HIS A:492 , HOH B:53 , ILE B:403BINDING SITE FOR RESIDUE SO4 B 1007
07AC7SOFTWAREHOH A:143 , HIS A:400 , HIS A:408BINDING SITE FOR RESIDUE ZN A 359
08AC8SOFTWAREHOH A:6 , LYS A:463 , THR A:464 , ASP A:465 , ALA A:466 , PRO A:493 , ASP A:494 , GLN A:495 , GLY B:428 , TYR B:430 , ASP B:431 , TYR B:454BINDING SITE FOR RESIDUE ILE A 1
09AC9SOFTWAREHOH A:22 , HOH A:81 , LYS A:450 , LEU A:451 , LYS B:463 , THR B:464BINDING SITE FOR RESIDUE SO4 A 1001
10BC1SOFTWAREGLY A:402 , ILE A:403 , GLY A:404 , ILE A:405 , HIS B:492BINDING SITE FOR RESIDUE SO4 A 1002
11BC2SOFTWAREHOH A:115 , GLY A:490 , VAL A:491 , HIS A:501 , LYS A:505BINDING SITE FOR RESIDUE SO4 A 1003
12BC3SOFTWAREHOH A:112 , PRO A:459 , PRO A:460 , THR B:485BINDING SITE FOR RESIDUE SO4 A 1008

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3F6G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3F6G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3F6G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3F6G)

(-) Exons   (0, 0)

(no "Exon" information available for 3F6G)

(-) Sequences/Alignments

Asymmetric/Biological 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:121
 aligned with Q8F3Q1_LEPIN | Q8F3Q1 from UniProtKB/TrEMBL  Length:516

    Alignment length:123
                                   399       409       419       429       439       449       459       469       479       489       499       509   
         Q8F3Q1_LEPIN   390 KVLTIKSCNIHSGIGIRPHAQIELEYQGKIHKEISEGDGGYDAFMNALTKITNRLGISIPKLIDYEVRIPPGGKTDALVETRITWNKSLDLEEDQTFKTMGVHPDQTVAAVHATEKMLNQILQ 512
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee....eeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhhhh....eeeeeeee..........eeeeeeee..--.hhh.eeeeeeee.hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f6g A 390 KVLTIKSCNIHSGIGIRPHAQIELEYQGKIHKEISEGDGGYDAFMNALTKITNRLGISIPKLIDYEVRIPPGGKTDALVETRITWNKS--LEEDQTFKTMGVHPDQTVAAVHATEKMLNQILQ 512
                                   399       409       419       429       439       449       459       469       | -|      489       499       509   
                                                                                                                 477  |                                
                                                                                                                    480                                


Chain B from PDB  Type:PROTEIN  Length:115
 aligned with Q8F3Q1_LEPIN | Q8F3Q1 from UniProtKB/TrEMBL  Length:516

    Alignment length:123
                                   399       409       419       429       439       449       459       469       479       489       499       509   
         Q8F3Q1_LEPIN   390 KVLTIKSCNIHSGIGIRPHAQIELEYQGKIHKEISEGDGGYDAFMNALTKITNRLGISIPKLIDYEVRIPPGGKTDALVETRITWNKSLDLEEDQTFKTMGVHPDQTVAAVHATEKMLNQILQ 512
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee......eeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhhhh....eeeeeeee..........eeeeeeee.--------.eeeeeee.hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f6g B 390 KVLTIKSCNIHSGIGIRPHAQIELEYQGKIHKEISEGDGGYDAFMNALTKITNRLGISIPKLIDYEVRIPPGGKTDALVETRITWNK--------TFKTMGVHPDQTVAAVHATEKMLNQILQ 512
                                   399       409       419       429       439       449       459       469      |  -     | 489       499       509   
                                                                                                                476      485
   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 3F6G)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3F6G)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3F6G)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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 3bli 3f6h

(-) Related Entries Specified in the PDB File

3ble 3blf 3bli 3f6h