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(-) Description

Title :  CRYSTAL STRUCTURE OF RIPC FROM YERSINIA PESTIS
 
Authors :  R. Torres, C. W. Goulding
Date :  02 Feb 11  (Deposition) - 11 Jan 12  (Release) - 28 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  A,B,C  (2x)
Keywords :  Beta Barrel, Citrate Lyase Beta Subunit, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Torres, N. Chim, B. Sankaran, C. Pujol, J. B. Bliska, C. W. Goulding
Structural Insights Into Ripc, A Putative Citrate Lyase Bet Subunit From A Yersinia Pestis Virulence Operon
Acta Crystallogr. , Sect. F V. 68 2 2012
PubMed-ID: 22232161  |  Reference-DOI: 10.1107/S1744309111048056

(-) Compounds

Molecule 1 - CITRATE LYASE
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CITE2, Y2383, YPO1928, YP_1670
    Organism Scientific: YERSINIA PESTIS
    Organism Taxid: 632
    Synonym: PUTATIVE CITRATE LYASE BETA CHAIN, SIMILAR TO CITE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): ABC
Biological Unit 2 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric Unit (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 24)
No.NameCountTypeFull Name
1MSE24Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3QLL)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3QLL)

(-) 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:215
 aligned with Q9ZC38_YERPE | Q9ZC38 from UniProtKB/TrEMBL  Length:280

    Alignment length:236
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234      
         Q9ZC38_YERPE     5 DTYQTRSWLFTPATRSDRFAKAAENGADVAIIDLEDSVSQADKEQARQKAISYLSSRPATSLPLALRINGLDTRAGIEDIHALLECGSLPDYLVLPKTESAAHLQILDRLMMFAGSDTRLIGIIESVRGLNAVESIAAATPKLAGLIFGAADMAADIGAASTWEPLALARARLVSACAMNGIPAIDAPFFDVHDVSGLQSETLRASDFGFSAKAAIHPAQISTINTLFTPTAAEIR 240
               SCOP domains d3qlla_ A: auto          mated matches                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.eeeeee...----------...eeeee.....hhhhhhhhhhhhhh---------..eeee.....hhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhh...--..eeeeee.hhhhhhhhhhhhh....eeeeeehhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...eee.......hhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhh..hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qll A   5 DTYQTRSWLFTPATR----------GADVAIIDLEDSVSQADKEQARQKAIS---------LPLALRINGLDTRAGIEDIHALLECGSLPDYLVLPKTESAAHLQILDRLmmFA--DTRLIGIIESVRGLNAVESIAAATPKLAGLIFGAADmAADIGAASTWEPLALARARLVSACAmNGIPAIDAPFFDVHDVSGLQSETLRASDFGFSAKAAIHPAQISTINTLFTPTAAEIR 240
                                    14    |    -     |  34        44        54 |       - |      74        84        94       104       114|| |  |124       134       144       154  |    164       174       184       194       204       214       224       234      
                                         19         30                        56        66                                              115-MSE |                                 157-MSE                   183-MSE                                                     
                                                                                                                                         116-MSE|                                                                                                                       
                                                                                                                                           118  |                                                                                                                       
                                                                                                                                              121                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:215
 aligned with Q9ZC38_YERPE | Q9ZC38 from UniProtKB/TrEMBL  Length:280

    Alignment length:236
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234      
         Q9ZC38_YERPE     5 DTYQTRSWLFTPATRSDRFAKAAENGADVAIIDLEDSVSQADKEQARQKAISYLSSRPATSLPLALRINGLDTRAGIEDIHALLECGSLPDYLVLPKTESAAHLQILDRLMMFAGSDTRLIGIIESVRGLNAVESIAAATPKLAGLIFGAADMAADIGAASTWEPLALARARLVSACAMNGIPAIDAPFFDVHDVSGLQSETLRASDFGFSAKAAIHPAQISTINTLFTPTAAEIR 240
               SCOP domains d3qllb_ B: auto          mated matches                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.eeeeee...----------...eeeee.....hhhhhhhhhhhhhh---------..eeee.....hhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhh.--..eeeeee.hhhhhhhhhhhhh....eeeeeehhhhhhhhhh....hhhhhhhhhhhhhhhhhh...eee.......hhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhh..hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qll B   5 DTYQTRSWLFTPATR----------GADVAIIDLEDSVSQADKEQARQKAIS---------LPLALRINGLDTRAGIEDIHALLECGSLPDYLVLPKTESAAHLQILDRLmmFA--DTRLIGIIESVRGLNAVESIAAATPKLAGLIFGAADmAADIGAASTWEPLALARARLVSACAmNGIPAIDAPFFDVHDVSGLQSETLRASDFGFSAKAAIHPAQISTINTLFTPTAAEIR 240
                                    14    |    -     |  34        44        54 |       - |      74        84        94       104       114|| |  |124       134       144       154  |    164       174       184       194       204       214       224       234      
                                         19         30                        56        66                                              115-MSE |                                 157-MSE                   183-MSE                                                     
                                                                                                                                         116-MSE|                                                                                                                       
                                                                                                                                           118  |                                                                                                                       
                                                                                                                                              121                                                                                                                       


Chain C from PDB  Type:PROTEIN  Length:215
 aligned with Q9ZC38_YERPE | Q9ZC38 from UniProtKB/TrEMBL  Length:280

    Alignment length:236
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234      
         Q9ZC38_YERPE     5 DTYQTRSWLFTPATRSDRFAKAAENGADVAIIDLEDSVSQADKEQARQKAISYLSSRPATSLPLALRINGLDTRAGIEDIHALLECGSLPDYLVLPKTESAAHLQILDRLMMFAGSDTRLIGIIESVRGLNAVESIAAATPKLAGLIFGAADMAADIGAASTWEPLALARARLVSACAMNGIPAIDAPFFDVHDVSGLQSETLRASDFGFSAKAAIHPAQISTINTLFTPTAAEIR 240
               SCOP domains d3qllc_ C: auto          mated matches                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee...----------...eeeee........hhhhhhhhhhh---------..eeee.....hhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhh...--..eeeeee.hhhhhhhhhhhhh....eeeeeehhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...eee.......hhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhh..hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qll C   5 DTYQTRSWLFTPATR----------GADVAIIDLEDSVSQADKEQARQKAIS---------LPLALRINGLDTRAGIEDIHALLECGSLPDYLVLPKTESAAHLQILDRLmmFA--DTRLIGIIESVRGLNAVESIAAATPKLAGLIFGAADmAADIGAASTWEPLALARARLVSACAmNGIPAIDAPFFDVHDVSGLQSETLRASDFGFSAKAAIHPAQISTINTLFTPTAAEIR 240
                                    14    |    -     |  34        44        54 |       - |      74        84        94       104       114|| |  |124       134       144       154  |    164       174       184       194       204       214       224       234      
                                         19         30                        56        66                                              115-MSE |                                 157-MSE                   183-MSE                                                     
                                                                                                                                         116-MSE|                                                                                                                       
                                                                                                                                           118  |                                                                                                                       
                                                                                                                                              121
   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, 3)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q9ZC38_YERPE | Q9ZC38)
molecular function
    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: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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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