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(-) Description

Title :  ENGINEERING ASCORBATE PEROXIDASE ACTIVITY INTO CYTOCHROME C PEROXIDASE
 
Authors :  T. L. Poulos, Y. T. Meharenna, P. Oertel
Date :  05 Aug 08  (Deposition) - 21 Oct 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Cytochrome C Peroxidase (Ccp), Ascorbate Peroxidase (Apx), Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. T. Meharenna, P. Oertel, B. Bhaskar, T. L. Poulos
Engineering Ascorbate Peroxidase Activity Into Cytochrome C Peroxidase.
Biochemistry V. 47 10324 2008
PubMed-ID: 18771292  |  Reference-DOI: 10.1021/BI8007565
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME C PEROXIDASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PT7-7
    Expression System Strain: BL21(DE3)STAR
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 68-361, SEE REMARK 999
    Gene: CCP1, CCP, CPO, YKR066C
    Mutation: YES
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: CCP

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:37 , ARG A:41 , TRP A:44 , PRO A:138 , ASP A:139 , ALA A:140 , LEU A:164 , MET A:165 , ALA A:167 , HIS A:168 , GLY A:171 , LYS A:172 , THR A:173 , HIS A:174 , ARG A:177 , SER A:178 , LEU A:225 , THR A:227 , HOH A:1054 , HOH A:1126 , HOH A:1215 , HOH A:1370BINDING SITE FOR RESIDUE HEM A 296

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3E2N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3E2N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_CCPR_YEAST_001 *T120ICCPR_YEAST  ---  ---AT46I
2UniProtVAR_CCPR_YEAST_002 *D219GCCPR_YEAST  ---  ---AD145G
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEROXIDASE_2PS00436 Peroxidases active site signature.CCPR_YEAST110-121  1A:36-47
2PEROXIDASE_1PS00435 Peroxidases proximal heme-ligand signature.CCPR_YEAST234-244  1A:160-170

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YKR066C1YKR066C.1XI:566840-5657551086CCPR_YEAST1-3613611A:6-287 (gaps)289

(-) 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:282
 aligned with CCPR_YEAST | P00431 from UniProtKB/Swiss-Prot  Length:361

    Alignment length:289
                                    82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352         
           CCPR_YEAST    73 HVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKHDNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQGPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKTHLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQDPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361
               SCOP domains d3e2na_ A: Cytochrome c perox       idase, CCP                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 3e2nA01 A:6-137,A:259-287  [c       ode=1.10.520.10, no name defined]                                                                      3e2nA02 A:138-258 Peroxidase, domain 2                                                                                   3e2nA01 A:6-137,A:259-287     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhh-------hhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..............hhhhh...........hhhhhhhhhhh...hhhhhhhhhhhhhh.eehhhhhh..ee.........hhhhhhhhhh.eeeee.....eeeee....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhh. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------I--------------------------------------------------------------------------------------------------G---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------PEROXIDASE_2----------------------------------------------------------------------------------------------------------------PEROXIDASE_--------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:6-287 (gaps) UniProt: 1-361 [INCOMPLETE]                                                                                                                                                                                                                                         Transcript 1
                 3e2n A   6 HVASVEKGRSYEDFQKVYNAIALKIAEKK-------CGPVLVRLAWHTSGTWDKHDNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQGPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKTHLKRSGYEGPFGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQDPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 287
                                    15        25        |-      | 38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278         
                                                       34      35
   Legend:   → Mismatch (orange background)
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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, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3E2N)

(-) Gene Ontology  (16, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CCPR_YEAST | P00431)
molecular function
    GO:0004130    cytochrome-c peroxidase activity    Catalysis of the reaction: 2 ferrocytochrome c + hydrogen peroxide = 2 ferricytochrome c + 2 H2O.
    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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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:0034599    cellular response to oxidative stress    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
    GO:0042744    hydrogen peroxide catabolic process    The chemical reactions and pathways resulting in the breakdown of hydrogen peroxide (H2O2).
    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.
    GO:0006979    response to oxidative stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
cellular component
    GO:0005758    mitochondrial intermembrane space    The region between the inner and outer lipid bilayers of the mitochondrial envelope.
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        APX1_PEA | P48534: 1apx
        CCPR_YEAST | P00431: 1a2f 1a2g 1aa4 1ac4 1ac8 1aeb 1aed 1aee 1aef 1aeg 1aeh 1aej 1aek 1aem 1aen 1aeo 1aeq 1aes 1aet 1aeu 1aev 1bej 1bek 1bem 1bep 1beq 1bes 1bj9 1bva 1cca 1ccb 1ccc 1cce 1ccg 1cci 1ccj 1cck 1ccl 1ccp 1cmp 1cmq 1cmt 1cmu 1cpd 1cpe 1cpf 1cpg 1cyf 1dcc 1dj1 1dj5 1ds4 1dse 1dsg 1dso 1dsp 1ebe 1jci 1jdr 1kok 1krj 1kxm 1kxn 1mk8 1mkq 1mkr 1ml2 1ryc 1s6v 1s73 1sbm 1sdq 1sog 1stq 1u74 1u75 1z53 1zby 1zbz 2anz 2aqd 2as1 2as2 2as3 2as4 2as6 2b0z 2b10 2b11 2b12 2bcn 2ccp 2cep 2cyp 2eun 2euo 2eup 2euq 2eur 2eus 2eut 2euu 2gb8 2ia8 2icv 2jti 2n18 2pcb 2pcc 2rbt 2rbu 2rbv 2rbw 2rbx 2rby 2rbz 2rc0 2rc1 2rc2 2v23 2v2e 2x07 2x08 2xil 2xj5 2xj8 2y5a 2ycg 3ccp 3ccx 3e2o 3exb 3m23 3m25 3m26 3m27 3m28 3m29 3m2a 3m2b 3m2c 3m2d 3m2e 3m2f 3m2g 3m2h 3m2i 3r98 3r99 4a6z 4a71 4a78 4a7m 4ccp 4ccx 4cvi 4cvj 4jb4 4nfg 4p4q 4xv4 4xv5 4xv6 4xv7 4xv8 4xva 5ccp 5cib 5cic 5cid 5cie 5cif 5cig 5cih 5d6m 5ejt 5ejx 6ccp 7ccp

(-) Related Entries Specified in the PDB File

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