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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DI-HAEM CYTOCHROME C PEROXIDASE FROM PSEUDOMONAS AERUGINOSA
 
Authors :  V. Fulop
Date :  24 Jul 01  (Deposition) - 24 Jul 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Oxidoreductase, Peroxidase, Heme, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. Fulop, C. J. Ridout, C. Greenwood, J. Hajdu
Crystal Structure Of The Di-Haemcytochrome C Peroxidase From Pseudomonas Aeruginosa
Structure V. 3 1225 1995
PubMed-ID: 8591033  |  Reference-DOI: 10.1016/S0969-2126(01)00258-1

(-) Compounds

Molecule 1 - CYTOCHROME C551 PEROXIDASE
    ChainsA
    EC Number1.11.1.5
    Organism ScientificPSEUDOMONAS AERUGINOSA
    Organism Taxid287
    StrainNTCC 6750
    SynonymCYTOCHROME C PEROXIDASE, CCP, DI-HAEM CYTOCHROME C PEROXIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2HEC2Ligand/IonHEME C
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2HEC4Ligand/IonHEME C

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:79 , THR A:256 , PRO A:258 , HOH A:2017 , HOH A:2018 , HOH A:2048 , HOH A:2049BINDING SITE FOR RESIDUE CA A 403
2AC2SOFTWARECYS A:51 , CYS A:54 , HIS A:55 , SER A:68 , VAL A:69 , GLY A:70 , HIS A:71 , GLN A:74 , ARG A:78 , SER A:80 , PRO A:81 , ALA A:86 , ASN A:89 , GLN A:92 , PHE A:93 , TRP A:94 , PRO A:108 , SER A:112 , GLU A:160 , ARG A:246 , HOH A:2071 , HOH A:2072 , HOH A:2073BINDING SITE FOR RESIDUE HEC A 401
3AC3SOFTWARETRP A:94 , GLY A:196 , CYS A:197 , CYS A:200 , HIS A:201 , PHE A:214 , GLY A:215 , LEU A:216 , ARG A:246 , TYR A:259 , PHE A:260 , HIS A:261 , MET A:275 , LEU A:280 , HOH A:2017 , HOH A:2042 , HOH A:2048BINDING SITE FOR RESIDUE HEC A 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1EB7)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala A:257 -Pro A:258

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (6, 6)

Asymmetric Unit (6, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_CCPR_PSEAE_001 *G81DCCPR_PSEAE  ---  ---AG58D
2UniProtVAR_CCPR_PSEAE_002 *G83DCCPR_PSEAE  ---  ---AG60D
3UniProtVAR_CCPR_PSEAE_003 *I152VCCPR_PSEAE  ---  ---AI129V
4UniProtVAR_CCPR_PSEAE_004 *P164ACCPR_PSEAE  ---  ---AP141A
5UniProtVAR_CCPR_PSEAE_005 *K198ICCPR_PSEAE  ---  ---AK175I
6UniProtVAR_CCPR_PSEAE_006 *L334WCCPR_PSEAE  ---  ---AL311W
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (6, 12)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_CCPR_PSEAE_001 *G81DCCPR_PSEAE  ---  ---AG58D
2UniProtVAR_CCPR_PSEAE_002 *G83DCCPR_PSEAE  ---  ---AG60D
3UniProtVAR_CCPR_PSEAE_003 *I152VCCPR_PSEAE  ---  ---AI129V
4UniProtVAR_CCPR_PSEAE_004 *P164ACCPR_PSEAE  ---  ---AP141A
5UniProtVAR_CCPR_PSEAE_005 *K198ICCPR_PSEAE  ---  ---AK175I
6UniProtVAR_CCPR_PSEAE_006 *L334WCCPR_PSEAE  ---  ---AL311W
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CCPR_PSEAE52-160
206-323
  2A:29-137
A:183-300
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CCPR_PSEAE52-160
206-323
  4A:29-137
A:183-300

(-) Exons   (0, 0)

(no "Exon" information available for 1EB7)

(-) 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:317
 aligned with CCPR_PSEAE | P14532 from UniProtKB/Swiss-Prot  Length:346

    Alignment length:323
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343   
           CCPR_PSEAE    24 DALHDQASALFKPIPEQVTELRGQPISEQQRELGKKLFFDPRLSRSHVLSCNTCHNVGTGGADNVPTSVGHGWQKGPRNSPTVFNAVFNAAQFWDGRAKDLGEQAKGPIQNSVEMHSTPQLVEQTLGSIPEYVDAFRKAFPKAGKPVSFDNMALAIEAYEATLVTPDSPFDLYLKGDDKALDAQQKKGLKAFMDSGCSACHNGINLGGQAYFPFGLVKKPDASVLPSGDKGRFAVTKTQSDEYVFRAAPLRNVALTAPYFHSGQVWELKDAVAIMGNAQLGKQLAPDDVENIVAFLHSLSGKQPRVEYPLLPASTETTPRPAE 346
               SCOP domains d1eb7a1 A:1-164 Di-heme cytochrome c peroxidase                                                                                                                     d1eb7a2 A:165-323 Di-heme cytochrome c peroxidase                                                                                                               SCOP domains
               CATH domains 1eb7A01         1eb7A02 A:17-164,A:303-323 Cytochrome c                                                                                                             1eb7A01 A:1-16,A:165-302 Cytochrome c                                                                                                     1eb7A02 Cytochrome c  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh........ee..ee.hhhhhhhhhhhhhhhhhh.....hhhhhh.............................hhhhh.....eee.hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh....hhhhhhhh......hhhhhhhhhhhhhhhhhhh..........ee.eeeee....------....eeeee.....eeee.....hhhhh..........hhhhhhhhhh........hhhhhhhhhhhhhh......................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------D-D--------------------------------------------------------------------V-----------A---------------------------------I---------------------------------------------------------------------------------------------------------------------------------------W------------ SAPs(SNPs)
                    PROSITE ----------------------------CYTC  PDB: A:29-137 UniProt: 52-160                                                                          ---------------------------------------------CYTC  PDB: A:183-300 UniProt: 206-323                                                                                 ----------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1eb7 A   1 DALHDQASALFKPIPEQVTELRGQPISEQQRELGKKLFFDPRLSRSHVLSCNTCHNVGTGGADNVPTSVGHGWQKGPRNSPTVFNAVFNAAQFWDGRAKDLGEQAKGPIQNSVEMHSTPQLVEQTLGSIPEYVDAFRKAFPKAGKPVSFDNMALAIEAYEATLVTPDSPFDLYLKGDDKALDAQQKKGLKAFMDSGCSACHNGINLGGQAYFPFGLVKKPDA------DKGRFAVTKTQSDEYVFRAAPLRNVALTAPYFHSGQVWELKDAVAIMGNAQLGKQLAPDDVENIVAFLHSLSGKQPRVEYPLLPASTETTPRPAE 323
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 |     230       240       250       260       270       280       290       300       310       320   
                                                                                                                                                                                                                                                       222    229                                                                                              

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1EB7)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (CCPR_PSEAE | P14532)
molecular function
    GO:0004130    cytochrome-c peroxidase activity    Catalysis of the reaction: 2 ferrocytochrome c + hydrogen peroxide = 2 ferricytochrome c + 2 H2O.
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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