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(-) Description

Title :  CCPA FROM G. SULFURREDUCENS, S134P VARIANT
 
Authors :  M. Hoffmann, J. Seidel, O. Einsle
Date :  05 Jun 09  (Deposition) - 22 Sep 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.52
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cytochrome C Peroxidase, Oxidoreductase, Peroxidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Hoffmann, J. Seidel, O. Einsle
Ccpa From Geobacter Sulfurreducens Is A Basic Di-Heme Cytochrome C Peroxidase.
J. Mol. Biol. V. 393 951 2009
PubMed-ID: 19735665  |  Reference-DOI: 10.1016/J.JMB.2009.09.001

(-) Compounds

Molecule 1 - CYTOCHROME C551 PEROXIDASE
    Chains: A, B
    EC Number: 1.11.1.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CCPA, CCPA-2, GSU2813
    Mutation: YES
    Organism Scientific: GEOBACTER SULFURREDUCENS
    Organism Taxid: 35554

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 16)

Asymmetric/Biological Unit (5, 16)
No.NameCountTypeFull Name
1BU32Ligand/Ion(R,R)-2,3-BUTANEDIOL
2CA2Ligand/IonCALCIUM ION
3HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4IMD4Ligand/IonIMIDAZOLE
5OXL4Ligand/IonOXALATE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE A:71 , SER A:72 , CYS A:73 , CYS A:76 , HIS A:77 , SER A:90 , THR A:91 , GLY A:92 , ARG A:100 , PRO A:103 , SER A:108 , ASN A:111 , PHE A:115 , TRP A:116 , GLU A:136 , GLU A:182 , IMD A:346 , BU3 A:350 , HOH A:382 , HOH A:404 , HOH A:421 , HOH A:455 , HOH A:475 , HOH A:536BINDING SITE FOR RESIDUE HEM A 400
02AC2SOFTWARETRP A:116 , CYS A:219 , CYS A:222 , HIS A:223 , PHE A:236 , GLY A:237 , VAL A:238 , ARG A:268 , ALA A:269 , PRO A:270 , LEU A:272 , TYR A:281 , PHE A:282 , HIS A:283 , MET A:297 , PHE A:302 , ILE A:314 , HOH A:353 , HOH A:354 , HOH A:548 , HOH A:579BINDING SITE FOR RESIDUE HEM A 401
03AC3SOFTWAREASN A:101 , THR A:278 , PRO A:280 , HOH A:353 , HOH A:354 , HOH A:363 , HOH A:379BINDING SITE FOR RESIDUE CA A 402
04AC4SOFTWAREILE B:71 , SER B:72 , CYS B:73 , CYS B:76 , HIS B:77 , SER B:90 , ARG B:100 , PRO B:103 , ASN B:111 , PHE B:115 , TRP B:116 , GLU B:136 , ILE B:178 , GLU B:182 , IMD B:346 , HOH B:351 , HOH B:440 , HOH B:508 , HOH B:552 , HOH B:575BINDING SITE FOR RESIDUE HEM B 400
05AC5SOFTWARETRP B:116 , CYS B:219 , CYS B:222 , HIS B:223 , PHE B:236 , GLY B:237 , VAL B:238 , ARG B:268 , ALA B:269 , PRO B:270 , LEU B:272 , TYR B:281 , PHE B:282 , HIS B:283 , MET B:297 , PHE B:302 , ILE B:314 , HOH B:383 , HOH B:405 , HOH B:549 , HOH B:649BINDING SITE FOR RESIDUE HEM B 401
06AC6SOFTWAREASN B:101 , THR B:278 , PRO B:280 , HOH B:383 , HOH B:394 , HOH B:405 , HOH B:460BINDING SITE FOR RESIDUE CA B 402
07AC7SOFTWAREVAL A:131 , GLN A:132 , ALA A:133 , GLU A:136 , BU3 A:350 , HEM A:400BINDING SITE FOR RESIDUE IMD A 346
08AC8SOFTWAREPRO B:134 , HEM B:400BINDING SITE FOR RESIDUE IMD B 346
09AC9SOFTWARELEU A:81 , LEU A:86 , ILE A:277 , TYR A:279 , ARG B:64 , MET B:333 , PRO B:334 , ALA B:335BINDING SITE FOR RESIDUE IMD A 347
10BC1SOFTWAREARG A:64 , MET A:333 , PRO A:334 , ALA A:335 , LEU B:81 , GLY B:82 , LEU B:86 , ILE B:277 , TYR B:279BINDING SITE FOR RESIDUE IMD B 347
11BC2SOFTWARETRP A:288 , SER B:336 , THR B:337 , HOH B:353 , HOH B:423 , HOH B:477BINDING SITE FOR RESIDUE OXL B 348
12BC3SOFTWAREVAL A:131 , GLN A:132 , ALA A:133 , PHE A:171 , MET A:174 , HOH A:468 , HOH A:494BINDING SITE FOR RESIDUE OXL A 348
13BC4SOFTWARESER A:336 , THR A:337 , ASP A:338 , HOH A:411 , HOH A:527 , HOH A:554 , TRP B:288BINDING SITE FOR RESIDUE OXL A 349
14BC5SOFTWARETHR A:75 , HOH B:385BINDING SITE FOR RESIDUE OXL B 349
15BC6SOFTWAREGLN A:114 , PHE A:115 , VAL A:131 , GLN A:132 , IMD A:346 , HEM A:400 , HOH A:563 , HOH A:576 , GLY B:164BINDING SITE FOR RESIDUE BU3 A 350
16BC7SOFTWAREALA B:175 , GLU B:179 , HOH B:572BINDING SITE FOR RESIDUE BU3 B 350

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3HQ9)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:279 -Pro A:280
2Tyr B:279 -Pro B:280

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3HQ9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3HQ9)

(-) Exons   (0, 0)

(no "Exon" information available for 3HQ9)

(-) 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:312
 aligned with Q749D0_GEOSL | Q749D0 from UniProtKB/TrEMBL  Length:345

    Alignment length:324
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341    
         Q749D0_GEOSL    22 ADELQQRAQGLFKPVPAKAPTLKGNPASPVKVELGKMLYFDPRLSASHLISCNTCHNVGLGGGDLQATSTGHGWQKGPRNAPTVLNSVFNTAQFWDGRAKDLAEQAKGPVQASVEMNNTPDQVVKTLNSIPDYVALFKKAFPGEKDPVTFDNMAKAIEVFEATLITPDSPFDQYLKGKKKALDGKQTAGLKLFLDKGCVACHGGLNLGGTGYFPFGVVEKPAENILPLGDKGRFAVTNTAKDEYVFRAPSLRNVAITYPYFHSGVVWSLKEAVAVMGSAQFGIKLSDDESEAIAAFLGSLTGKQPKVVYPIMPASTDATPRPRL 345
               SCOP domains d3hq9a1 A:22-188 automated matches                                                                                                                                     d3hq9a2 A:189-345 automated matches                                                                                                                           SCOP domains
               CATH domains 3hq9A01          3hq9A02 A:39-186,A:325-345 Cytochrome c                                                                                                             3hq9A01 A:22-38,A:187-324 Cytochrome c                                                                                                    3hq9A02 Cytochrome c  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhh.....hhhhhh.............eehhhee.........hhhhh.....eeehhhhh........hhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh......hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..........ee.eeee.------------...eeee.hhh.eeee.....hhhhh..........hhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3hq9 A  22 ADELQQRAQGLFKPVPAKAPTLKGNPASPVKVELGKMLYFDPRLSASHLISCNTCHNVGLGGGDLQATSTGHGWQKGPRNAPTVLNSVFNTAQFWDGRAKDLAEQAKGPVQAPVEMNNTPDQVVKTLNSIPDYVALFKKAFPGEKDPVTFDNMAKAIEVFEATLITPDSPFDQYLKGKKKALDGKQTAGLKLFLDKGCVACHGGLNLGGTGYFPFGVVE------------GRFAVTNTAKDEYVFRAPSLRNVAITYPYFHSGVVWSLKEAVAVMGSAQFGIKLSDDESEAIAAFLGSLTGKQPKVVYPIMPASTDATPRPRL 345
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231        |-         - |     261       271       281       291       301       311       321       331       341    
                                                                                                                                                                                                                                                    240          253                                                                                            


Chain B from PDB  Type:PROTEIN  Length:306
 aligned with Q749D0_GEOSL | Q749D0 from UniProtKB/TrEMBL  Length:345

    Alignment length:325
                                    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       330       340     
         Q749D0_GEOSL    21 AADELQQRAQGLFKPVPAKAPTLKGNPASPVKVELGKMLYFDPRLSASHLISCNTCHNVGLGGGDLQATSTGHGWQKGPRNAPTVLNSVFNTAQFWDGRAKDLAEQAKGPVQASVEMNNTPDQVVKTLNSIPDYVALFKKAFPGEKDPVTFDNMAKAIEVFEATLITPDSPFDQYLKGKKKALDGKQTAGLKLFLDKGCVACHGGLNLGGTGYFPFGVVEKPAENILPLGDKGRFAVTNTAKDEYVFRAPSLRNVAITYPYFHSGVVWSLKEAVAVMGSAQFGIKLSDDESEAIAAFLGSLTGKQPKVVYPIMPASTDATPRPRL 345
               SCOP domains d3hq9b1 B:21-188 automated matches                                                                                                                                      d3hq9b2 B:189-345 automated matches                                                                                                                           SCOP domains
               CATH domains 3hq9B01           3hq9B02 B:39-186,B:325-345 Cytochrome c                                                                                                             3hq9B01 B:21-38,B:187-324 Cytochrome c                                                                                                    3hq9B02 Cytochrome c  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh.................hhhhhhhhhhhhhhhhhh.....hhhhhh..............hhhhh..........hhhhh.....eee....--------..hhhhh.hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh......hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..........ee.eeeee.-----------..eeeee.hhh.eeee.....hhhhh..........hhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hq9 B  21 AADELQQRAQGLFKPVPAKAPTLKGNPASPVKVELGKMLYFDPRLSASHLISCNTCHNVGLGGGDLQATSTGHGWQKGPRNAPTVLNSVFNTAQFWDGRAKDL--------QAPVEMNNTPDQVVKTLNSIPDYVALFKKAFPGEKDPVTFDNMAKAIEVFEATLITPDSPFDQYLKGKKKALDGKQTAGLKLFLDKGCVACHGGLNLGGTGYFPFGVVEK-----------GRFAVTNTAKDEYVFRAPSLRNVAITYPYFHSGVVWSLKEAVAVMGSAQFGIKLSDDESEAIAAFLGSLTGKQPKVVYPIMPASTDATPRPRL 345
                                    30        40        50        60        70        80        90       100       110       120  |      - |     140       150       160       170       180       190       200       210       220       230       240|        -  |    260       270       280       290       300       310       320       330       340     
                                                                                                                                123      132                                                                                                          241         253
   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/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HQ9)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q749D0_GEOSL | Q749D0)
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.

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 Related Entries

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UniProtKB/TrEMBL
        Q749D0_GEOSL | Q749D0: 3hq6 3hq7 3hq8

(-) Related Entries Specified in the PDB File

3hq6 3hq7 3hq8