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Description

Title :   CYTOCHROME C PEROXIDASE IN COMPLEX WITH 3-FLUOROCATECHOL

Authors :   R. Brenk, S. W. Vetter, S. E. Boyce, D. B. Goodin, B. K. Shoichet

Date :   22 Aug 05 (Deposition) - 11 Apr 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.30

Chains :   Asym./Biol. Unit : A

Keywords :   Oxidoreductase, Peroxidase, Model Binding Site (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Brenk, S. W. Vetter, S. E. Boyce, D. B. Goodin, B. K. Shoichet
Probing Molecular Docking In A Charged Model Binding Site.
J. Mol. Biol. V. 357 1449 2006
PubMed-ID: 16490206 | Reference-DOI: 10.1016/J.JMB.2006.01.034
(for further references see the PDB file header)

Compounds

Molecule 1 - CYTOCHROME C PEROXIDASE, MITOCHONDRIAL
	Chains	:	A
	EC Number	:	1.11.1.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PT7CCP
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	CYTOCHROME C PEROXIDASE
	Gene	:	CCP1, CCP, CPO
	Mutation	:	YES
	Organism Common	:	BAKER'S YEAST
	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 (3, 4)

Asymmetric/Biological Unit (3, 4)

No.	Name	Count	Type	Full Name
1	3FA	2	Ligand/Ion	3-FLUOROBENZENE-1,2-DIOL
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	K	1	Ligand/Ion	POTASSIUM ION

Sites (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:175 , LEU A:177 , HOH A:1000 , HOH A:1003 , HOH A:1004	BINDING SITE FOR RESIDUE K A 600
2	AC2	SOFTWARE	PRO A:44 , ARG A:48 , TRP A:51 , PRO A:145 , ASP A:146 , ALA A:147 , LEU A:171 , ALA A:174 , HIS A:175 , LEU A:177 , GLY A:178 , LYS A:179 , THR A:180 , HIS A:181 , ASN A:184 , SER A:185 , LEU A:232 , THR A:234 , 3FA A:500 , HOH A:1121 , HOH A:1136 , HOH A:1161 , HOH A:1415	BINDING SITE FOR RESIDUE HEM A 400
3	AC3	SOFTWARE	HIS A:175 , GLY A:178 , LYS A:179 , GLY A:189 , PRO A:190 , GLY A:191 , MET A:230 , MET A:231 , LEU A:232 , ASP A:235 , HEM A:400 , HOH A:1000 , HOH A:1001 , HOH A:1002 , HOH A:1003 , HOH A:1004	BINDING SITE FOR RESIDUE 3FA A 500
4	AC4	SOFTWARE	PHE A:89 , GLU A:93 , HIS A:96 , SER A:104 , LEU A:107 , PHE A:108 , HOH A:1411	BINDING SITE FOR RESIDUE 3FA A 700

SS Bonds (0, 0)

(no "SS Bond" information available for 2AS4)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 2AS4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 2)

Asymmetric/Biological Unit (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_CCPR_YEAST_001 *	T	120	I	CCPR_YEAST	---	---	A	I	53	I
2	UniProt	VAR_CCPR_YEAST_002 *	D	219	G	CCPR_YEAST	---	---	A	G	152	G
	* ID not provided by source

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

PROSITE Motifs (2, 2)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEROXIDASE_2	PS00436	Peroxidases active site signature.	CCPR_YEAST	110-121	1	A:43-54
2	PEROXIDASE_1	PS00435	Peroxidases proximal heme-ligand signature.	CCPR_YEAST	234-244	1	A:167-177

Exons (1, 1)

Asymmetric/Biological Unit (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YKR066C	1	YKR066C.1	XI:566840-565755	1086	CCPR_YEAST	1-361	361	1	A:4-294	291

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:291
 aligned with CCPR_YEAST | P00431 from UniProtKB/Swiss-Prot  Length:361

    Alignment length:291
                                    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       350       360 
           CCPR_YEAST    71 LVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKHDNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQGPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKTHLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQDPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361
               SCOP domains d2as4a_ A: Cytochrome c peroxidase, CCP                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 2as4A01 A:4-144,A:266-294  [code=1.10.520.10, no name defined]                                                                               2as4A02 A:145-265 Peroxidase, domain 2                                                                                   2as4A01 A:4-144,A:266-294     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.......hhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..............hhhhh...........hhhhhhhhhhh...hhhhhhhhhhhhhh.eehhhhhh..ee.........hhhhhhhhhh.eeeee.....eeeee....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee............hhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------I--------------------------------------------------------------------------------------------------G---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------PEROXIDASE_2----------------------------------------------------------------------------------------------------------------PEROXIDASE_--------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:4-294 UniProt: 1-361 [INCOMPLETE]                                                                                                                                                                                                                                                  Transcript 1
                 2as4 A   4 LVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKHDNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQGPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKTHLKNSGYEGPGGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQDPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294
                                    13        23        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

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, 1)

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Heme-dependent peroxidases (402)

Superfamily: Heme-dependent peroxidases (402)

Family: CCP-like (292)

Protein domain: Cytochrome c peroxidase, CCP (170)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (170)

d2as4a_

CATH Domains (2, 2)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Peroxidase; domain 1 (244)

Homologous Superfamily: [code=1.10.520.10, no name defined] (241)

Baker's yeast (Saccharomyces cerevisiae) (120)

2as4A01

A:4-144,A:266-294

Topology: Peroxidase; domain 2 (241)

Homologous Superfamily: Peroxidase, domain 2 (241)

Baker's yeast (Saccharomyces cerevisiae) (120)

2as4A02

A:145-265

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 2AS4)

Gene Ontology (14, 14)

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
	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 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 3e2n 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

1aa4	APO-STRUCTURE
2anz	SAME PROTEIN, DIFFERENT LIGAND
2aqd	SAME PROTEIN, DIFFERENT LIGAND
2as1	SAME PROTEIN, DIFFERENT LIGAND
2as2	SAME PROTEIN, DIFFERENT LIGAND
2as3	SAME PROTEIN, DIFFERENT LIGAND