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(-) Description

Title :  THIOL PEROXIDASE FROM CHROMOBACTERIUM VIOLACEUM
 
Authors :  J. Osipiuk, O. Kagan, A. Savchenko, A. M. Edwards, A. Joachimiak, Midwe For Structural Genomics (Mcsg)
Date :  25 Oct 09  (Deposition) - 03 Nov 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Structural Genomics, Apc40679, Thiol Peroxidase. , Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Oxidoreductase, Peroxidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Osipiuk, O. Kagan, A. Savchenko, A. M. Edwards, A. Joachimiak
X-Ray Crystal Structure Of Thiol Peroxidase From Chromobacterium Violaceum
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROBABLE THIOL PEROXIDASE
    Chains: A, B, C, D
    EC Number: 1.11.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B MODIFIED
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CV_3708
    Organism Scientific: CHROMOBACTERIUM VIOLACEUM
    Organism Taxid: 536
    Strain: ATCC 12472

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 15)

Asymmetric Unit (3, 15)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2MSE10Mod. Amino AcidSELENOMETHIONINE
3SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE5Mod. Amino AcidSELENOMETHIONINE
3SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE5Mod. Amino AcidSELENOMETHIONINE
3SO41Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG B:69 , HIS B:101 , HOH B:260BINDING SITE FOR RESIDUE SO4 B 301
2AC2SOFTWAREARG C:69 , HIS C:101 , HOH C:644BINDING SITE FOR RESIDUE SO4 C 302
3AC3SOFTWAREARG B:72 , LEU B:103 , PRO B:104 , ASN B:105 , ILE B:106BINDING SITE FOR RESIDUE CL B 303
4AC4SOFTWAREGLU D:59 , ASP D:60 , GLU D:61 , HIS D:62 , HOH D:496BINDING SITE FOR RESIDUE CL D 304
5AC5SOFTWAREARG C:72 , LEU C:103 , PRO C:104 , ASN C:105 , ILE C:106BINDING SITE FOR RESIDUE CL C 305

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Tyr A:128 -Pro A:129
2Tyr B:128 -Pro B:129
3Tyr C:128 -Pro C:129
4Tyr D:128 -Pro D:129

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KEB)

(-) 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:175
 aligned with Q7NRS2_CHRVO | Q7NRS2 from UniProtKB/TrEMBL  Length:220

    Alignment length:175
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171     
         Q7NRS2_CHRVO     2 EDFWVQYGDEMLPVIGDFPRKGDYLPSFMLVDDQKHDAALESFSHTPKLIVTLLSVDEDEHAGLLLLRETRRFLDSWPHLKLIVITVDSPSSLARARHEHGLPNIALLSTLRGRDFHKRYGVLITEYPLSGYTSPAIILADAANVVHYSERLANTRDFFDFDAIEKLLQEGEQQA 176
               SCOP domains d3keba_ A: automated matches                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee...............eeee....eee.hhhh...eeeee..........hhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhhh....eeee.....hhhhhh...............eeeee.....eeeeee........hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3keb A   2 EDFWVQYGDEmLPVIGDFPRKGDYLPSFmLVDDQKHDAALESFSHTPKLIVTLLSVDEDEHAGLLLLRETRRFLDSWPHLKLIVITVDSPSSLARARHEHGLPNIALLSTLRGRDFHKRYGVLITEYPLSGYTSPAIILADAANVVHYSERLANTRDFFDFDAIEKLLQEGEQQA 176
                                    11|       21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171     
                                     12-MSE            30-MSE                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:173
 aligned with Q7NRS2_CHRVO | Q7NRS2 from UniProtKB/TrEMBL  Length:220

    Alignment length:174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170    
         Q7NRS2_CHRVO     1 MEDFWVQYGDEMLPVIGDFPRKGDYLPSFMLVDDQKHDAALESFSHTPKLIVTLLSVDEDEHAGLLLLRETRRFLDSWPHLKLIVITVDSPSSLARARHEHGLPNIALLSTLRGRDFHKRYGVLITEYPLSGYTSPAIILADAANVVHYSERLANTRDFFDFDAIEKLLQEGEQ 174
               SCOP domains d3kebb_ B: automated matches                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee..eeee...............eeee....eee.hhh....eeeee..........hhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhhh....eeee...-hhhhhhh...............eeeee.....eeeeee........hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3keb B   1 mEDFWVQYGDEmLPVIGDFPRKGDYLPSFmLVDDQKHDAALESFSHTPKLIVTLLSVDEDEHAGLLLLRETRRFLDSWPHLKLIVITVDSPSSLARARHEHGLPNIALLSTLR-RDFHKRYGVLITEYPLSGYTSPAIILADAANVVHYSERLANTRDFFDFDAIEKLLQEGEQ 174
                            |       10 |      20        30        40        50        60        70        80        90       100       110  | |  120       130       140       150       160       170    
                            1-MSE     12-MSE            30-MSE                                                                            113 |                                                           
                                                                                                                                            115                                                           


Chain C from PDB  Type:PROTEIN  Length:173
 aligned with Q7NRS2_CHRVO | Q7NRS2 from UniProtKB/TrEMBL  Length:220

    Alignment length:174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170    
         Q7NRS2_CHRVO     1 MEDFWVQYGDEMLPVIGDFPRKGDYLPSFMLVDDQKHDAALESFSHTPKLIVTLLSVDEDEHAGLLLLRETRRFLDSWPHLKLIVITVDSPSSLARARHEHGLPNIALLSTLRGRDFHKRYGVLITEYPLSGYTSPAIILADAANVVHYSERLANTRDFFDFDAIEKLLQEGEQ 174
               SCOP domains d3kebc_ C: automated matches                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee..eeee...............eeee....eee.hhh....eeeee..........hhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhhh....eeee...-hhhhhhh...............eeeee.....eeeeee........hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3keb C   1 mEDFWVQYGDEmLPVIGDFPRKGDYLPSFmLVDDQKHDAALESFSHTPKLIVTLLSVDEDEHAGLLLLRETRRFLDSWPHLKLIVITVDSPSSLARARHEHGLPNIALLSTLR-RDFHKRYGVLITEYPLSGYTSPAIILADAANVVHYSERLANTRDFFDFDAIEKLLQEGEQ 174
                            |       10 |      20        30        40        50        60        70        80        90       100       110  | |  120       130       140       150       160       170    
                            1-MSE     12-MSE            30-MSE                                                                            113 |                                                           
                                                                                                                                            115                                                           


Chain D from PDB  Type:PROTEIN  Length:175
 aligned with Q7NRS2_CHRVO | Q7NRS2 from UniProtKB/TrEMBL  Length:220

    Alignment length:175
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171     
         Q7NRS2_CHRVO     2 EDFWVQYGDEMLPVIGDFPRKGDYLPSFMLVDDQKHDAALESFSHTPKLIVTLLSVDEDEHAGLLLLRETRRFLDSWPHLKLIVITVDSPSSLARARHEHGLPNIALLSTLRGRDFHKRYGVLITEYPLSGYTSPAIILADAANVVHYSERLANTRDFFDFDAIEKLLQEGEQQA 176
               SCOP domains d3kebd_ D: automated matches                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eeeee..............eeee....eee.hhhh...eeeee..........hhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhhh....eeee.hhhhhhhhhh...............eeeee.....eeeeee........hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3keb D   2 EDFWVQYGDEmLPVIGDFPRKGDYLPSFmLVDDQKHDAALESFSHTPKLIVTLLSVDEDEHAGLLLLRETRRFLDSWPHLKLIVITVDSPSSLARARHEHGLPNIALLSTLRGRDFHKRYGVLITEYPLSGYTSPAIILADAANVVHYSERLANTRDFFDFDAIEKLLQEGEQQA 176
                                    11|       21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171     
                                     12-MSE            30-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  (1, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q7NRS2_CHRVO | Q7NRS2)
molecular function
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0004601    peroxidase activity    Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
biological process
    GO:0098869    cellular oxidant detoxification    Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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