3HQ8 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CCPA FROM G. SULFURREDUCENS S134P/V135K VARIANT

Authors :   M. Hoffmann, J. Seidel, O. Einsle

Date :   05 Jun 09 (Deposition) - 22 Sep 09 (Release) - 03 Nov 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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
(for further references see the PDB file header)

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

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 8)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	HEM	4	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	IMD	2	Ligand/Ion	IMIDAZOLE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:71 , SER A:72 , CYS A:73 , CYS A:76 , HIS A:77 , ARG A:100 , PRO A:103 , ASN A:111 , TRP A:116 , VAL A:131 , GLU A:136 , MET A:137 , ILE A:178 , ARG A:268 , IMD A:346	BINDING SITE FOR RESIDUE HEM A 400
2	AC2	SOFTWARE	TRP A:116 , CYS A:219 , CYS A:222 , HIS A:223 , PHE A:236 , GLY A:237 , VAL A:238 , PHE A:267 , ARG A:268 , ALA A:269 , PRO A:270 , LEU A:272 , TYR A:281 , PHE A:282 , HIS A:283 , MET A:297 , GLY A:298 , PHE A:302 , HOH A:381	BINDING SITE FOR RESIDUE HEM A 401
3	AC3	SOFTWARE	ASN A:101 , THR A:278 , PRO A:280 , HOH A:355 , HOH A:381	BINDING SITE FOR RESIDUE CA A 402
4	AC4	SOFTWARE	VAL A:131 , GLN A:132 , GLU A:136 , HEM A:400	BINDING SITE FOR RESIDUE IMD A 346
5	AC5	SOFTWARE	ILE B:71 , SER B:72 , CYS B:73 , CYS B:76 , HIS B:77 , ARG B:100 , PRO B:103 , SER B:108 , ASN B:111 , PHE B:115 , TRP B:116 , MET B:137 , ILE B:178 , GLU B:182 , IMD B:346	BINDING SITE FOR RESIDUE HEM B 400
6	AC6	SOFTWARE	GLY B:218 , CYS B:219 , CYS B:222 , HIS B:223 , PHE B:236 , GLY B:237 , VAL B:238 , ARG B:268 , PRO B:270 , LEU B:272 , TYR B:281 , PHE B:282 , HIS B:283 , MET B:297 , PHE B:302 , ILE B:314	BINDING SITE FOR RESIDUE HEM B 401
7	AC7	SOFTWARE	ASN B:101 , THR B:278 , PRO B:280 , HOH B:394	BINDING SITE FOR RESIDUE CA B 402
8	AC8	SOFTWARE	GLN B:132 , PRO B:134 , GLU B:136 , HOH B:389 , HEM B:400	BINDING SITE FOR RESIDUE IMD B 346

(no "SS Bond" information available for 3HQ8)

Asymmetric/Biological Unit

No.	Residues
1	Ala A:127	-	Lys A:128
2	Tyr A:279	-	Pro A:280
3	Thr B:91	-	Gly B:92
4	Val B:131	-	Gln B:132
5	Tyr B:279	-	Pro B:280

(no "SAP(SNP)/Variant" information available for 3HQ8)

(no "PROSITE Motif" information available for 3HQ8)

(no "Exon" information available for 3HQ8)

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:315
 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 d3hq8a1 A:22-188 automated matches                                                                                                                                     d3hq8a2 A:189-345 automated matches                                                                                                                           SCOP domains
               CATH domains 3hq8A01          3hq8A02 A:39-186,A:325-345 Cytochrome c                                                                                                             3hq8A01 A:22-38,A:187-324 Cytochrome c                                                                                                    3hq8A02 Cytochrome c  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhh...............hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.........hhhhh..........hhhhh.....eeehhhhh...............hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........ee.eeeee...---------..eeeee.....eeee.....hhhhhh.........hhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3hq8 A  22 ADELQQRAQGLFKPVPAKAPTLKGNPASPVKVELGKMLYFDPRLSASHLISCNTCHNVGLGGGDLQATSTGHGWQKGPRNAPTVLNSVFNTAQFWDGRAKDLAEQAKGPVQAPKEMNNTPDQVVKTLNSIPDYVALFKKAFPGEKDPVTFDNMAKAIEVFEATLITPDSPFDQYLKGKKKALDGKQTAGLKLFLDKGCVACHGGLNLGGTGYFPFGVVEKPA---------GRFAVTNTAKDEYVFRAPSLRNVAITYPYFHSGVVWSLKEAVAVMGSAQFGIKLSDDESEAIAAFLGSLTGKQPKVVYPIMPASTDATPRPRL 345
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241 |       - |     261       271       281       291       301       311       321       331       341    
                                                                                                                                                                                                                                                       243       253

Chain B from PDB  Type:PROTEIN  Length:313
 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 d3hq8b1 B:22-188 automated matches                                                                                                                                     d3hq8b2 B:189-345 automated matches                                                                                                                           SCOP domains
               CATH domains 3hq8B01          3hq8B02 B:39-186,B:325-345 Cytochrome c                                                                                                             3hq8B01 B:22-38,B:187-324 Cytochrome c                                                                                                    3hq8B02 Cytochrome c  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhh.................hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.........hhhhh..........hhhhh.....eeehhhhhh..............hhhhhhhhhh.hhhhhhhhhhhh.......hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eee.eeeee.-----------..eeeee.....eeeee....hhhhh............hhhhhhh.hhhhh...hhhhhhhhhhhhhhhh....................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3hq8 B  22 ADELQQRAQGLFKPVPAKAPTLKGNPASPVKVELGKMLYFDPRLSASHLISCNTCHNVGLGGGDLQATSTGHGWQKGPRNAPTVLNSVFNTAQFWDGRAKDLAEQAKGPVQAPKEMNNTPDQVVKTLNSIPDYVALFKKAFPGEKDPVTFDNMAKAIEVFEATLITPDSPFDQYLKGKKKALDGKQTAGLKLFLDKGCVACHGGLNLGGTGYFPFGVVEK-----------GRFAVTNTAKDEYVFRAPSLRNVAITYPYFHSGVVWSLKEAVAVMGSAQFGIKLSDDESEAIAAFLGSLTGKQPKVVYPIMPASTDATPRPRL 345
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241         - |     261       271       281       291       301       311       321       331       341    
                                                                                                                                                                                                                                                     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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Cytochrome c (308)

Superfamily: Cytochrome c (308)

Family: automated matches (31)

Protein domain: automated matches (31)

Geobacter sulfurreducens [TaxId: 35554] (6)

1a	d3hq8a1	A:22-188
1b	d3hq8a2	A:189-345
1c	d3hq8b1	B:22-188
1d	d3hq8b2	B:189-345

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Cytochrome Bc1 Complex; Chain D, domain 2 (279)

Homologous Superfamily: Cytochrome c (279)

Geobacter sulfurreducens. Organism_taxid: 35554. (4)

1a	3hq8B01	B:22-38,B:187-324
1b	3hq8A02	A:39-186,A:325-345
1c	3hq8B02	B:39-186,B:325-345
1d	3hq8A01	A:22-38,A:187-324

(no "Pfam Domain" information available for 3HQ8)

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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala A:127 - Lys A:128	[ RasMol ]
		Thr B:91 - Gly B:92	[ RasMol ]
		Tyr A:279 - Pro A:280	[ RasMol ]
		Tyr B:279 - Pro B:280	[ RasMol ]
		Val B:131 - Gln B:132	[ RasMol ]

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	Q749D0_GEOSL \| Q749D0	:	3hq6 3hq7 3hq9

Description

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Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (5, 5)

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