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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE ZINC PROTEASE FROM BORDETELLA PERTUSSIS TOHAMA I
 
Authors :  C. Chang, G. Chhor, J. Bearden, A. Joachimiak, Midwest Center For St Genomics (Mcsg)
Date :  29 Jul 09  (Deposition) - 18 Aug 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Putative Zinc Protease, Bordetella Pertussis Tohama I, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Protease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Chang, G. Chhor, J. Bearden, A. Joachimiak
Crystal Structure Of Putative Zinc Protease From Bordetella Pertussis Tohama I
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE ZINC PROTEASE
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)MAGIC
    Expression System Taxid: 562
    Expression System Vector: PMCSG19
    Fragment: SEQUENCE DATABASE RESIDUES 258-451
    Gene: BP2497
    Organism Scientific: BORDETELLA PERTUSSIS
    Organism Taxid: 520

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 28)

Asymmetric/Biological Unit (3, 28)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2EDO3Ligand/Ion1,2-ETHANEDIOL
3MSE24Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:259 , ASP A:307 , THR A:308 , HOH A:456 , HOH A:503 , SER D:380 , LYS D:381 , HOH D:454BINDING SITE FOR RESIDUE EDO A 501
2AC2SOFTWAREVAL C:263BINDING SITE FOR RESIDUE EDO C 501
3AC3SOFTWARETHR D:303 , ASP D:307 , ARG D:377 , LYS D:381 , HOH D:469 , HOH D:476BINDING SITE FOR RESIDUE ACT D 501
4AC4SOFTWAREGLY F:407 , ARG F:410BINDING SITE FOR RESIDUE EDO F 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3IH6)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Asp A:335 -Pro A:336
2Asp B:335 -Pro B:336
3Asp C:335 -Pro C:336
4Asp D:335 -Pro D:336
5Asp E:335 -Pro E:336
6Asp F:335 -Pro F:336

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3IH6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3IH6)

(-) Exons   (0, 0)

(no "Exon" information available for 3IH6)

(-) 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:180
 aligned with Q7VVY4_BORPE | Q7VVY4 from UniProtKB/TrEMBL  Length:916

    Alignment length:193
                                   264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444   
         Q7VVY4_BORPE   255 PPEYTVEPVQDGERSVTLRRAGGTPLVAAMYHLPAAGSPDFVGLDLAATILADTPSSRLYHALVPTKLASGVFGFTMDQLDPGLAMFGAQLQPGMDQDKALQTLTATLESLSSKPFSQEELERARSKWLTAWQQTYADPEKVGVALSEAIASGDWRLFFLQRDRVREAKLDDVQRAAVAYLVRSNRTEGRYIP 447
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..-------------....eeeeeee.......hhhhhhhhhhhhhh...hhhhhhhh......eeeeeee......eeeeeee.....hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhheeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ih6 A 255 SNAYTVEP-------------GGTPLVAAmYHLPAAGSPDFVGLDLAATILADTPSSRLYHALVPTKLASGVFGFTmDQLDPGLAmFGAQLQPGmDQDKALQTLTATLESLSSKPFSQEELERARSKWLTAWQQTYADPEKVGVALSEAIASGDWRLFFLQRDRVREAKLDDVQRAAVAYLVRSNRTEGRYIP 447
                                   | -         - |     284       294       304       314       324      |334     | 344    |  354       364       374       384       394       404       414       424       434       444   
                                 262           276     284-MSE                                        331-MSE  340-MSE  349-MSE                                                                                              


Chain B from PDB  Type:PROTEIN  Length:180
 aligned with Q7VVY4_BORPE | Q7VVY4 from UniProtKB/TrEMBL  Length:916

    Alignment length:194
                                   264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444    
         Q7VVY4_BORPE   255 PPEYTVEPVQDGERSVTLRRAGGTPLVAAMYHLPAAGSPDFVGLDLAATILADTPSSRLYHALVPTKLASGVFGFTMDQLDPGLAMFGAQLQPGMDQDKALQTLTATLESLSSKPFSQEELERARSKWLTAWQQTYADPEKVGVALSEAIASGDWRLFFLQRDRVREAKLDDVQRAAVAYLVRSNRTEGRYIPT 448
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...--------------..eeeeeee.....hhhhhhhhhhhhhhhh...hhhhhhhh......eeeeeee......eeeeeee.....hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ih6 B 255 SNAYTVEPV--------------TPLVAAmYHLPAAGSPDFVGLDLAATILADTPSSRLYHALVPTKLASGVFGFTmDQLDPGLAmFGAQLQPGmDQDKALQTLTATLESLSSKPFSQEELERARSKWLTAWQQTYADPEKVGVALSEAIASGDWRLFFLQRDRVREAKLDDVQRAAVAYLVRSNRTEGRYIPT 448
                                    |-         -   |   284       294       304       314       324      |334     | 344    |  354       364       374       384       394       404       414       424       434       444    
                                  263            278     |                                            331-MSE  340-MSE  349-MSE                                                                                               
                                                       284-MSE                                                                                                                                                                


Chain C from PDB  Type:PROTEIN  Length:181
 aligned with Q7VVY4_BORPE | Q7VVY4 from UniProtKB/TrEMBL  Length:916

    Alignment length:194
                                   264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444    
         Q7VVY4_BORPE   255 PPEYTVEPVQDGERSVTLRRAGGTPLVAAMYHLPAAGSPDFVGLDLAATILADTPSSRLYHALVPTKLASGVFGFTMDQLDPGLAMFGAQLQPGMDQDKALQTLTATLESLSSKPFSQEELERARSKWLTAWQQTYADPEKVGVALSEAIASGDWRLFFLQRDRVREAKLDDVQRAAVAYLVRSNRTEGRYIPT 448
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...-------------...eeeeeee......hhhhhhhhhhhhhhh...hhhhhhhh......eeeeeee......eeeeeee.....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ih6 C 255 SNAYTVEPV-------------GTPLVAAmYHLPAAGSPDFVGLDLAATILADTPSSRLYHALVPTKLASGVFGFTmDQLDPGLAmFGAQLQPGmDQDKALQTLTATLESLSSKPFSQEELERARSKWLTAWQQTYADPEKVGVALSEAIASGDWRLFFLQRDRVREAKLDDVQRAAVAYLVRSNRTEGRYIPT 448
                                    |-         -  |    284       294       304       314       324      |334     | 344    |  354       364       374       384       394       404       414       424       434       444    
                                  263           277      |                                            331-MSE  340-MSE  349-MSE                                                                                               
                                                       284-MSE                                                                                                                                                                


Chain D from PDB  Type:PROTEIN  Length:181
 aligned with Q7VVY4_BORPE | Q7VVY4 from UniProtKB/TrEMBL  Length:916

    Alignment length:195
                                   264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444     
         Q7VVY4_BORPE   255 PPEYTVEPVQDGERSVTLRRAGGTPLVAAMYHLPAAGSPDFVGLDLAATILADTPSSRLYHALVPTKLASGVFGFTMDQLDPGLAMFGAQLQPGMDQDKALQTLTATLESLSSKPFSQEELERARSKWLTAWQQTYADPEKVGVALSEAIASGDWRLFFLQRDRVREAKLDDVQRAAVAYLVRSNRTEGRYIPTE 449
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...--------------..eeeeeee.......hhhhhhhhhhhhhh...hhhhhhhh......eeeeeee......eeeeeee.....hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ih6 D 255 SNAYTVEPV--------------TPLVAAmYHLPAAGSPDFVGLDLAATILADTPSSRLYHALVPTKLASGVFGFTmDQLDPGLAmFGAQLQPGmDQDKALQTLTATLESLSSKPFSQEELERARSKWLTAWQQTYADPEKVGVALSEAIASGDWRLFFLQRDRVREAKLDDVQRAAVAYLVRSNRTEGRYIPTE 449
                                    |-         -   |   284       294       304       314       324      |334     | 344    |  354       364       374       384       394       404       414       424       434       444     
                                  263            278     |                                            331-MSE  340-MSE  349-MSE                                                                                                
                                                       284-MSE                                                                                                                                                                 


Chain E from PDB  Type:PROTEIN  Length:182
 aligned with Q7VVY4_BORPE | Q7VVY4 from UniProtKB/TrEMBL  Length:916

    Alignment length:194
                                   264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444    
         Q7VVY4_BORPE   255 PPEYTVEPVQDGERSVTLRRAGGTPLVAAMYHLPAAGSPDFVGLDLAATILADTPSSRLYHALVPTKLASGVFGFTMDQLDPGLAMFGAQLQPGMDQDKALQTLTATLESLSSKPFSQEELERARSKWLTAWQQTYADPEKVGVALSEAIASGDWRLFFLQRDRVREAKLDDVQRAAVAYLVRSNRTEGRYIPT 448
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...------------....eeeeeee......hhhhhhhhhhhhhhh...hhhhhhhh......eeeeeee......eeeeeee.....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ih6 E 255 SNAYTVEPV------------GGTPLVAAmYHLPAAGSPDFVGLDLAATILADTPSSRLYHALVPTKLASGVFGFTmDQLDPGLAmFGAQLQPGmDQDKALQTLTATLESLSSKPFSQEELERARSKWLTAWQQTYADPEKVGVALSEAIASGDWRLFFLQRDRVREAKLDDVQRAAVAYLVRSNRTEGRYIPT 448
                                    |-         - |     284       294       304       314       324      |334     | 344    |  354       364       374       384       394       404       414       424       434       444    
                                  263          276     284-MSE                                        331-MSE  340-MSE  349-MSE                                                                                               


Chain F from PDB  Type:PROTEIN  Length:181
 aligned with Q7VVY4_BORPE | Q7VVY4 from UniProtKB/TrEMBL  Length:916

    Alignment length:194
                                   264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444    
         Q7VVY4_BORPE   255 PPEYTVEPVQDGERSVTLRRAGGTPLVAAMYHLPAAGSPDFVGLDLAATILADTPSSRLYHALVPTKLASGVFGFTMDQLDPGLAMFGAQLQPGMDQDKALQTLTATLESLSSKPFSQEELERARSKWLTAWQQTYADPEKVGVALSEAIASGDWRLFFLQRDRVREAKLDDVQRAAVAYLVRSNRTEGRYIPT 448
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...-------------...eeeeeee.......hhhhhhhhhhhhhh...hhhhhhhh......eeeeeee......eeeeeee.....hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ih6 F 255 SNAYTVEPV-------------GTPLVAAmYHLPAAGSPDFVGLDLAATILADTPSSRLYHALVPTKLASGVFGFTmDQLDPGLAmFGAQLQPGmDQDKALQTLTATLESLSSKPFSQEELERARSKWLTAWQQTYADPEKVGVALSEAIASGDWRLFFLQRDRVREAKLDDVQRAAVAYLVRSNRTEGRYIPT 448
                                    |-         -  |    284       294       304       314       324      |334     | 344    |  354       364       374       384       394       404       414       424       434       444    
                                  263           277      |                                            331-MSE  340-MSE  349-MSE                                                                                               
                                                       284-MSE
   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 3IH6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3IH6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3IH6)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (Q7VVY4_BORPE | Q7VVY4)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004222    metalloendopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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 Related Entries

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