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(-) Description

Title :  CRYSTAL STRUCTURE OF CITRATE SYNTHASE FROM THERMUS THERMOPHILUS HB8
 
Authors :  E. Kanamori, T. Kouyama, Riken Structural Genomics/Proteomics In (Rsgi)
Date :  19 Mar 01  (Deposition) - 29 Jul 03  (Release) - 04 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Open Form, Synthase, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Kanamori, S. Kawaguchi, S. Kuramitsu, T. Kouyama, M. Murakami
Structural Comparison Between The Open And Closed Forms Of Citrate Synthase From Thermus Thermophilus Hb8
Biophys Physicobio. V. 12 47 2015
PubMed: search  |  Reference-DOI: 10.2142/BIOPHYSICO.12.0_47

(-) Compounds

Molecule 1 - CITRATE SYNTHASE
    Chains: A
    EC Number: 4.1.3.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-3A
    Expression System Strain: BL21(DE3)PLYSE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8

 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, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1CO31Ligand/IonCARBONATE ION
2GOL3Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1CO32Ligand/IonCARBONATE ION
2GOL6Ligand/IonGLYCEROL
3SO42Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:137 , LYS A:142 , HOH A:1394 , HOH A:1395BINDING SITE FOR RESIDUE SO4 A 600
2AC2SOFTWAREHIS A:184 , ASN A:187 , HIS A:219 , PHE A:333 , ARG A:337 , GOL A:400 , HOH A:1220 , HOH A:1428 , HOH A:1430 , HOH A:1465BINDING SITE FOR RESIDUE CO3 A 500
3AC3SOFTWAREHIS A:258 , ARG A:267 , ASP A:312 , PHE A:333 , CO3 A:500 , HOH A:1066 , HOH A:1169BINDING SITE FOR RESIDUE GOL A 400
4AC4SOFTWARETYR A:30 , LEU A:51 , HIS A:52 , GLY A:53 , ARG A:114 , LEU A:346 , GLU A:347 , GLU A:350 , GOL A:402 , HOH A:1161 , HOH A:1176BINDING SITE FOR RESIDUE GOL A 401
5AC5SOFTWARELEU A:51 , HIS A:52 , ARG A:114 , TYR A:118 , GOL A:401 , HOH A:1086 , HOH A:1091 , HOH A:1176 , HOH A:1291BINDING SITE FOR RESIDUE GOL A 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1IOM)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1IOM)

(-) 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:374
 aligned with Q5SIM6_THET8 | Q5SIM6 from UniProtKB/TrEMBL  Length:377

    Alignment length:374
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372    
         Q5SIM6_THET8     3 VARGLEGVLFTESRMCYIDGQQGKLYYYGIPIQELAEKSSFEETTFLLLHGRLPRRQELEEFSAALARRRALPAHLLESFKRYPVSAHPMSFLRTAVSEFGMLDPTEGDISREALYEKGLDLIAKFATIVAANKRLKEGKEPIPPREDLSHAANFLYMANGVEPSPEQARLMDAALILHAEHGFNASTFTAIAAFSTETDLYSAITAAVASLKGPRHGGANEAVMRMIQEIGTPERAREWVREKLAKKERIMGMGHRVYKAFDPRAGVLEKLARLVAEKHGHSKEYQILKIVEEEAGKVLNPRGIYPNVDFYSGVVYSDLGFSLEFFTPIFAVARISGWVGHILEYQELDNRLLRPGAKYVGELDVPYVPLEAR 376
               SCOP domains d1ioma_ A: Citrate synthase                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------1iomA01 A:13-220,A:323-356 Citrate Synthase, domain 1                                                                                                                                                           1iomA02 A:221-322 Cytochrome P450-Terp, domain 2                                                      1iomA01 A:13-220,A:323-356        -------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.........eeee....eeee..eehhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...hhhhhhhhh......hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhh...hhhhhhhhhhhhhhhh....hhhhhhhhhhhh...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...................hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iom A   3 VARGLEGVLFTESRMCYIDGQQGKLYYYGIPIQELAEKSSFEETTFLLLHGRLPRRQELEEFSAALARRRALPAHLLESFKRYPVSAHPMSFLRTAVSEFGMLDPTEGDISREALYEKGLDLIAKFATIVAANKRLKEGKEPIPPREDLSHAANFLYMANGVEPSPEQARLMDAALILHAEHGFNASTFTAIAAFSTETDLYSAITAAVASLKGPRHGGANEAVMRMIQEIGTPERAREWVREKLAKKERIMGMGHRVYKAFDPRAGVLEKLARLVAEKHGHSKEYQILKIVEEEAGKVLNPRGIYPNVDFYSGVVYSDLGFSLEFFTPIFAVARISGWVGHILEYQELDNRLLRPGAKYVGELDVPYVPLEAR 376
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372    


Chain A from PDB  Type:PROTEIN  Length:374
 aligned with Q9LCX9_THETH | Q9LCX9 from UniProtKB/TrEMBL  Length:377

    Alignment length:374
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372    
         Q9LCX9_THETH     3 VARGLEGVLFTESRMCYIDGQQGKLYYYGIPIQELAEKSSFEETTFLLLHGRLPRRQELEEFSAALARRRAMPAHLLESFKRYPVSAHPMSFLRTAVSEFGMLDPTEGDISREALYEKGLDLIAKFATIVAANKRLKEGKEPIPPREDLSHAANFLYMANGVEPSPEQARLMDAALILHAEHGFNASTFTAIAAFSTETDLYSAITAAVASLKGPRHGGANEAVMRMIQEIGTPERAREWVREKLAKKERIMGMGHRVYKAFDPRAGVLEKLARLVAEKHGHSKEYQILKIVEEEAGKVLNPRGIYPNVDFYSGVVYSDLGFSLEFFTPIFAVARISGWVGHILEYQELDNRLLRPGAKYVGELDVPYVPLEAR 376
               SCOP domains d1ioma_ A: Citrate synthase                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------1iomA01 A:13-220,A:323-356 Citrate Synthase, domain 1                                                                                                                                                           1iomA02 A:221-322 Cytochrome P450-Terp, domain 2                                                      1iomA01 A:13-220,A:323-356        -------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.........eeee....eeee..eehhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...hhhhhhhhh......hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhh...hhhhhhhhhhhhhhhh....hhhhhhhhhhhh...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...................hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iom A   3 VARGLEGVLFTESRMCYIDGQQGKLYYYGIPIQELAEKSSFEETTFLLLHGRLPRRQELEEFSAALARRRALPAHLLESFKRYPVSAHPMSFLRTAVSEFGMLDPTEGDISREALYEKGLDLIAKFATIVAANKRLKEGKEPIPPREDLSHAANFLYMANGVEPSPEQARLMDAALILHAEHGFNASTFTAIAAFSTETDLYSAITAAVASLKGPRHGGANEAVMRMIQEIGTPERAREWVREKLAKKERIMGMGHRVYKAFDPRAGVLEKLARLVAEKHGHSKEYQILKIVEEEAGKVLNPRGIYPNVDFYSGVVYSDLGFSLEFFTPIFAVARISGWVGHILEYQELDNRLLRPGAKYVGELDVPYVPLEAR 376
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372
   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, 1)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IOM)

(-) Gene Ontology  (3, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q9LCX9_THETH | Q9LCX9)
molecular function
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain A   (Q5SIM6_THET8 | Q5SIM6)
molecular function
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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