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(-) Description

Title :  STRUCTURE OF THE FULLY OXIDIZED DI-HEME CYTOCHROME C PEROXIDASE FROM R. CAPSULATUS
 
Authors :  L. De Smet, S. N. Savvides, E. Van Horen, G. Pettigrew, J. J. Van Beeumen
Date :  14 Jun 05  (Deposition) - 29 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Biol. Unit 3:  A,B,C,D  (1x)
Keywords :  Cytochrome C Peroxidase, Heme Groups, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. De Smet, S. N. Savvides, E. Van Horen, G. Pettigrew, J. J. Van Beeumen
Structural And Mutagenesis Studies On The Cytochrome C Peroxidase From Rhodobacter Capsulatus Provide New Insights Into Structure-Function Relationships Of Bacterial Di-Heme Peroxidases
J. Biol. Chem. V. 281 4371 2006
PubMed-ID: 16314410  |  Reference-DOI: 10.1074/JBC.M509582200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME C PEROXIDASE
    Chains: A, B, C, D
    EC Number: 1.11.1.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: RHODOBACTER CAPSULATUS
    Organism Taxid: 1061

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 
Biological Unit 3 (1x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 20)

Asymmetric Unit (3, 20)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2HEC8Ligand/IonHEME C
3ZN8Ligand/IonZINC ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2HEC4Ligand/IonHEME C
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2HEC4Ligand/IonHEME C
3ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 8)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2HEC8Ligand/IonHEME C
3ZN-1Ligand/IonZINC ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:82 , THR A:259 , PRO A:261 , HOH A:1029 , HOH A:1030BINDING SITE FOR RESIDUE CA A 401
02AC2SOFTWAREASN B:82 , THR B:259 , PRO B:261BINDING SITE FOR RESIDUE CA B 501
03AC3SOFTWAREASN C:82 , THR C:259 , PRO C:261BINDING SITE FOR RESIDUE CA C 601
04AC4SOFTWAREASN D:82 , THR D:259 , PRO D:261BINDING SITE FOR RESIDUE CA D 701
05AC5SOFTWAREHIS A:264BINDING SITE FOR RESIDUE ZN A 402
06AC6SOFTWAREHIS B:264BINDING SITE FOR RESIDUE ZN B 502
07AC7SOFTWAREGLU B:160 , GLU B:163 , HEC B:401BINDING SITE FOR RESIDUE ZN B 503
08AC8SOFTWAREASP B:243 , ASP B:244 , GLU B:245BINDING SITE FOR RESIDUE ZN B 504
09AC9SOFTWAREHIS C:264BINDING SITE FOR RESIDUE ZN C 602
10BC1SOFTWAREHIS D:264BINDING SITE FOR RESIDUE ZN D 702
11BC2SOFTWAREARG A:272 , ASP A:289 , ASP A:293 , ARG C:272 , ASP C:289 , ASP C:293BINDING SITE FOR RESIDUE ZN A 801
12BC3SOFTWAREASP B:289 , ASP B:293 , ASP D:187BINDING SITE FOR RESIDUE ZN B 802
13BC4SOFTWAREPHE A:52 , CYS A:54 , CYS A:57 , HIS A:58 , SER A:71 , ILE A:72 , GLY A:73 , HIS A:74 , TRP A:76 , GLN A:77 , ARG A:81 , PRO A:84 , ASN A:92 , GLN A:95 , TRP A:97 , VAL A:159 , GLU A:163 , ARG A:249 , HOH A:1034BINDING SITE FOR RESIDUE HEC A 802
14BC5SOFTWARETRP A:97 , GLY A:199 , CYS A:200 , CYS A:203 , HIS A:204 , TYR A:215 , GLY A:218 , VAL A:219 , PHE A:248 , ARG A:249 , ALA A:250 , ILE A:256 , TYR A:262 , PHE A:263 , HIS A:264 , MET A:278 , ALA A:279 , LEU A:283BINDING SITE FOR RESIDUE HEC A 803
15BC6SOFTWAREPHE B:52 , CYS B:54 , CYS B:57 , HIS B:58 , SER B:71 , ILE B:72 , GLY B:73 , HIS B:74 , TRP B:76 , GLN B:77 , ARG B:81 , PRO B:84 , ASN B:92 , GLN B:95 , TRP B:97 , VAL B:159 , GLU B:163 , ARG B:249 , ZN B:503BINDING SITE FOR RESIDUE HEC B 401
16BC7SOFTWARETRP B:97 , GLY B:199 , CYS B:200 , CYS B:203 , HIS B:204 , GLY B:218 , VAL B:219 , PHE B:248 , ARG B:249 , ALA B:250 , ILE B:256 , TYR B:262 , PHE B:263 , HIS B:264 , MET B:278 , ALA B:279 , LEU B:283BINDING SITE FOR RESIDUE HEC B 402
17BC8SOFTWAREPHE C:52 , CYS C:54 , CYS C:57 , HIS C:58 , SER C:71 , ILE C:72 , GLY C:73 , HIS C:74 , TRP C:76 , GLN C:77 , ARG C:81 , PRO C:84 , ASN C:92 , GLN C:95 , TRP C:97 , VAL C:159 , GLU C:163 , ARG C:249BINDING SITE FOR RESIDUE HEC C 401
18BC9SOFTWARETRP C:97 , GLY C:199 , CYS C:200 , CYS C:203 , HIS C:204 , GLY C:218 , VAL C:219 , PHE C:248 , ARG C:249 , ALA C:250 , ILE C:256 , TYR C:262 , PHE C:263 , HIS C:264 , MET C:278 , ALA C:279 , LEU C:283BINDING SITE FOR RESIDUE HEC C 402
19CC1SOFTWAREPHE D:52 , CYS D:54 , CYS D:57 , HIS D:58 , SER D:71 , ILE D:72 , GLY D:73 , HIS D:74 , TRP D:76 , GLN D:77 , ARG D:81 , PRO D:84 , ASN D:92 , GLN D:95 , TRP D:97 , VAL D:159 , GLU D:163 , ARG D:249BINDING SITE FOR RESIDUE HEC D 401
20CC2SOFTWARETRP D:97 , GLY D:199 , CYS D:200 , CYS D:203 , HIS D:204 , GLY D:218 , VAL D:219 , PHE D:248 , ARG D:249 , ALA D:250 , ILE D:256 , TYR D:262 , PHE D:263 , HIS D:264 , MET D:278 , ALA D:279 , LEU D:283BINDING SITE FOR RESIDUE HEC D 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ala A:260 -Pro A:261
2Ala B:260 -Pro B:261
3Ala C:260 -Pro C:261
4Ala D:260 -Pro D:261

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1ZZH)

(-) 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:297
                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d1zzha1 A:4-169 automated matches                                                                                                                     d1zzha2 A:170-326 automated matches                                                                                                                 SCOP domains
               CATH domains 1zzhA01        1zzhA02 A:19-167,A:306-326 Cytochrome c                                                                                              1zzhA01 A:4-18,A:168-305 Cytochrome c                                                                                           1zzhA02 Cytochrome c  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh............hhhhhhhhhhhhhhhhh.....hhhhhh.............................hhhhh.....eeehhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh......hhhhhhhhh.....hhhhhhhhhhhhhhhhhhh..........ee.eeeee....eeeee.....eeee.....hhhhh..........hhhhhhhhhhh.......hhhhhhhhhhhhhhhh.....eee............... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zzh A   4 ALREEAKGLFEVIPMQAPVTRDKIDLGAMLFFDPRMSKSGVFSCQSCHNVGLGGVDGLETSIGHGWQKGPRNAPTALNAVFNVAQFWDGRAPDLAAQAMNNTPENLVATVQSMPGYVEAFAKAFPGQKDPISFDNFALAVEAFEATLITPNSKFDQWLMGADGAMSADEKAGLKLFIDTGCAACHNGINIGGNGYYPFGVVEKPGRFAVTATADDEYVFRAGPLRNIALTAPYFHSGKVWDLREAVSVMANSQLGATLDDTQVDQITAFLGTLTGEQPEVVHPILPVRSAQTPRPEH 326
                                    13       |30        40        50        60        70        80        90       100       119       129       139       149       159       169       179       189       199       209       219   ||  239       249       259       269       279       289       299       309       319       
                                            21|                                                                            108|                                                                                                      223|                                                                                            
                                             29                                                                             118                                                                                                       234                                                                                            


Chain B from PDB  Type:PROTEIN  Length:308
                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d1zzhb1 B:4-169 automated matches                                                                                                                        d1zzhb2 B:170-326 automated matches                                                                                                                         SCOP domains
               CATH domains 1zzhB01        1zzhB02 B:19-167,B:306-326 Cytochrome c                                                                                                 1zzhB01 B:4-18,B:168-305 Cytochrome c                                                                                                   1zzhB02 Cytochrome c  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh............hhhhhhhhhhhhhhhhhhhh.....hhhhhh.............................hhhhh.....eeehhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh......hhhhhhhh......hhhhhhhhhhhhhhhhhhh..........ee.eeeee............eeeee.....eeee.....hhhhh..........hhhhhhhhhhh.......hhhhhhhhhhhhhhhh....................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zzh B   4 ALREEAKGLFEVIPMQAPQNTVTRDKIDLGAMLFFDPRMSKSGVFSCQSCHNVGLGGVDGLETSIGHGWQKGPRNAPTALNAVFNVAQFWDGRAPDLAAQAMNNTPENLVATVQSMPGYVEAFAKAFPGQKDPISFDNFALAVEAFEATLITPNSKFDQWLMGADGAMSADEKAGLKLFIDTGCAACHNGINIGGNGYYPFGVVEKPGAEVLPDKGRFAVTATADDEYVFRAGPLRNIALTAPYFHSGKVWDLREAVSVMANSQLGATLDDTQVDQITAFLGTLTGEQPEVVHPILPVRSAQTPRPEH 326
                                    13        27        37        47        57        67        77        87        97       107||     126       136       146       156       166       176       186       196       206       216       226  ||   238       248       258       268       278       288       298       308       318        
                                             22|                                                                              108|                                                                                                            229|                                                                                              
                                              27                                                                               118                                                                                                             232                                                                                              


Chain C from PDB  Type:PROTEIN  Length:307
                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains d1zzhc1 C:4-169 automated matches                                                                                                                        d1zzhc2 C:170-326 automated matches                                                                                                                        SCOP domains
               CATH domains 1zzhC01        1zzhC02 C:19-167,C:306-326 Cytochrome c                                                                                                 1zzhC01 C:4-18,C:168-305 Cytochrome c                                                                                                  1zzhC02 Cytochrome c  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh............hhhhhhhhhhhhhhhhhhhh.....hhhhhh.............................hhhhh.....eeehhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh......hhhhhhhh......hhhhhhhhhhhhhhhhhhh..........ee.eeeee...........eeeee.....eeee.....hhhhh..........hhhhhhhhhhh.......hhhhhhhhhhhhhhhh....................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zzh C   4 ALREEAKGLFEVIPMQAPQNTVTRDKIDLGAMLFFDPRMSKSGVFSCQSCHNVGLGGVDGLETSIGHGWQKGPRNAPTALNAVFNVAQFWDGRAPDLAAQAMNNTPENLVATVQSMPGYVEAFAKAFPGQKDPISFDNFALAVEAFEATLITPNSKFDQWLMGADGAMSADEKAGLKLFIDTGCAACHNGINIGGNGYYPFGVVEKPGAEVLPAGRFAVTATADDEYVFRAGPLRNIALTAPYFHSGKVWDLREAVSVMANSQLGATLDDTQVDQITAFLGTLTGEQPEVVHPILPVRSAQTPRPEH 326
                                    13        27        37        47        57        67        77        87        97       107||     126       136       146       156       166       176       186       196       206       216       226   ||  239       249       259       269       279       289       299       309       319       
                                             22|                                                                              108|                                                                                                             230|                                                                                            
                                              27                                                                               118                                                                                                              234                                                                                            


Chain D from PDB  Type:PROTEIN  Length:298
                                                                                                                                                                                                                                                                                                                                          
               SCOP domains d1zzhd1 D:4-169 automated matches                                                                                                                      d1zzhd2 D:170-326 automated matches                                                                                                                 SCOP domains
               CATH domains 1zzhD01        1zzhD02 D:19-167,D:306-326 Cytochrome c                                                                                               1zzhD01 D:4-18,D:168-305 Cytochrome c                                                                                           1zzhD02 Cytochrome c  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh.............hhhhhhhhhhhhhhhhh.....hhhhhh.............................hhhhh.....eeehhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh......hhhhhhhh......hhhhhhhhhhhhhhhhhhh..........ee.eeeee....eeeee.....eeee.....hhhhh..........hhhhhhhhhhh.......hhhhhhhhhhhhhhhh.....eee............... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zzh D   4 ALREEAKGLFEVIPMQAPQVTRDKIDLGAMLFFDPRMSKSGVFSCQSCHNVGLGGVDGLETSIGHGWQKGPRNAPTALNAVFNVAQFWDGRAPDLAAQAMNNTPENLVATVQSMPGYVEAFAKAFPGQKDPISFDNFALAVEAFEATLITPNSKFDQWLMGADGAMSADEKAGLKLFIDTGCAACHNGINIGGNGYYPFGVVEKPGRFAVTATADDEYVFRAGPLRNIALTAPYFHSGKVWDLREAVSVMANSQLGATLDDTQVDQITAFLGTLTGEQPEVVHPILPVRSAQTPRPEH 326
                                    13        29        39        49        59        69        79        89        99       118       128       138       148       158       168       178       188       198       208       218    || 238       248       258       268       278       288       298       308       318        
                                             22|                                                                            108|                                                                                                      223|                                                                                            
                                              29                                                                             118                                                                                                       234
   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, 8)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Fold: Cytochrome c (308)
(-)
Superfamily: Cytochrome c (308)
(-)
Family: automated matches (31)
(-)
Protein domain: automated matches (31)
(-)
Rhodobacter capsulatus [TaxId: 1061] (1)
1ad1zzha1A:4-169
1bd1zzha2A:170-326
1cd1zzhb1B:4-169
1dd1zzhb2B:170-326
1ed1zzhc1C:4-169
1fd1zzhc2C:170-326
1gd1zzhd1D:4-169
1hd1zzhd2D:170-326

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)
(-)
Architecture: Orthogonal Bundle (10391)
(-)
Topology: Cytochrome Bc1 Complex; Chain D, domain 2 (279)
(-)
Homologous Superfamily: Cytochrome c (279)
(-)
Rhodobacter capsulatus. Organism_taxid: 1061. (3)
1a1zzhA01A:4-18,A:168-305
1b1zzhD01D:4-18,D:168-305
1c1zzhC01C:4-18,C:168-305
1d1zzhB01B:4-18,B:168-305
1e1zzhA02A:19-167,A:306-326
1f1zzhD02D:19-167,D:306-326
1g1zzhB02B:19-167,B:306-326
1h1zzhC02C:19-167,C:306-326

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1ZZH)

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  Cis Peptide Bonds
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  1zzh
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