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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A COMPLEX BETWEEN ELECTRON TRANSFER PARTNERS, CYTOCHROME C PEROXIDASE AND CYTOCHROME C

Authors :   H. Pelletier, J. Kraut

Date :   14 Apr 93 (Deposition) - 15 Jul 93 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C  (1x)

Keywords :   Oxidoreductase/Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Pelletier, J. Kraut
Crystal Structure Of A Complex Between Electron Transfer Partners, Cytochrome C Peroxidase And Cytochrome C.
Science V. 258 1748 1992
PubMed-ID: 1334573
(for further references see the PDB file header)

Molecule 1 - CYTOCHROME C PEROXIDASE (CCP)
	Chains	:	A, C
	Engineered	:	YES
	Organ	:	HEART
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

Molecule 2 - CYTOCHROME C
	Chains	:	B
	Engineered	:	YES
	Organ	:	HEART
	Organism Common	:	HORSE
	Organism Scientific	:	EQUUS CABALLUS
	Organism Taxid	:	9796

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	HEM	3	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:44 , ARG A:48 , TRP A:51 , PRO A:145 , ASP A:146 , MET A:172 , 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 , TRP A:191 , LEU A:232 , THR A:234 , PHE A:266 , HOH A:364 , HOH A:397	BINDING SITE FOR RESIDUE HEM A 295
2	AC2	SOFTWARE	LYS B:13 , CYS B:14 , CYS B:17 , HIS B:18 , THR B:28 , LYS B:39 , THR B:40 , GLY B:41 , PHE B:46 , TYR B:48 , THR B:49 , ASN B:52 , TRP B:59 , TYR B:67 , THR B:78 , LYS B:79 , MET B:80 , PHE B:82	BINDING SITE FOR RESIDUE HEM B 105
3	AC3	SOFTWARE	PRO C:44 , VAL C:47 , ARG C:48 , TRP C:51 , ASP C:146 , PHE C:158 , MET C:172 , ALA C:174 , HIS C:175 , LEU C:177 , GLY C:178 , LYS C:179 , THR C:180 , HIS C:181 , ASN C:184 , SER C:185 , TRP C:191 , THR C:234 , HOH C:603 , HOH C:606 , HOH C:610 , HOH C:616	BINDING SITE FOR RESIDUE HEM C 295

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

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

Asymmetric Unit (2, 4)

								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/C	I	53	I
2	UniProt	VAR_CCPR_YEAST_002 *	D	219	G	CCPR_YEAST	---	---	A/C	G	152	G
	* ID not provided by source

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

Biological Unit 1 (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)

Biological Unit 2 (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	---	---	C	I	53	I
2	UniProt	VAR_CCPR_YEAST_002 *	D	219	G	CCPR_YEAST	---	---	C	G	152	G
	* ID not provided by source

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

Asymmetric Unit (3, 5)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	CYC_HORSE	2-103	1	B:1-102
2	PEROXIDASE_2	PS00436	Peroxidases active site signature.	CCPR_YEAST	110-121	2	A:43-54 C:43-54
3	PEROXIDASE_1	PS00435	Peroxidases proximal heme-ligand signature.	CCPR_YEAST	234-244	2	A:167-177 C:167-177

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	CYC_HORSE	2-103	1	B:1-102
2	PEROXIDASE_2	PS00436	Peroxidases active site signature.	CCPR_YEAST	110-121	1	A:43-54 -
3	PEROXIDASE_1	PS00435	Peroxidases proximal heme-ligand signature.	CCPR_YEAST	234-244	1	A:167-177 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	CYC_HORSE	2-103	0	-
2	PEROXIDASE_2	PS00436	Peroxidases active site signature.	CCPR_YEAST	110-121	1	- C:43-54
3	PEROXIDASE_1	PS00435	Peroxidases proximal heme-ligand signature.	CCPR_YEAST	234-244	1	- C:167-177

Asymmetric Unit (1, 2)

	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	2	A:1-294 C:1-294	294 294

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:294
 aligned with CCPR_YEAST | P00431 from UniProtKB/Swiss-Prot  Length:361

    Alignment length:294
                                    77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357    
           CCPR_YEAST    68 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKHDNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQGPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKTHLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQDPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361
               SCOP domains d2pcba_ A: Cytochrome c peroxidase, CCP                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ---2pcbA01 A:4-144,A:266-294  [code=1.10.520.10, no name defined]                                                                               2pcbA02 A:145-265 Peroxidase, domain 2                                                                                   2pcbA01 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..eeee.....eeee.....eehhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee............hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------I--------------------------------------------------------------------------------------------------G---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PEROXIDASE_2----------------------------------------------------------------------------------------------------------------PEROXIDASE_--------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-294 UniProt: 1-361 [INCOMPLETE]                                                                                                                                                                                                                                                     Transcript 1
                 2pcb A   1 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKHDNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQGPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKTHLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQDPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294
                                    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

Chain B from PDB  Type:PROTEIN  Length:104
 aligned with CYC_HORSE | P00004 from UniProtKB/Swiss-Prot  Length:105

    Alignment length:104
                                    11        21        31        41        51        61        71        81        91       101    
            CYC_HORSE     2 GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFTYTDANKNKGITWKEETLMEYLENPKKYIPGTKMIFAGIKKKTEREDLIAYLKKATNE 105
               SCOP domains d2pcbb_ B: Mitochondrial cytochrome c                                                                    SCOP domains
               CATH domains 2pcbB00 B:1-104 Cytochrome c                                                                             CATH domains
               Pfam domains --Cytochrom_C-2pcbB01 B:3-102                                                                         -- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh..................................hhhhhh.....hhhhhhhhh.hhhhhh............hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE CYTC  PDB: B:1-102 UniProt: 2-103                                                                     -- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 2pcb B   1 GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFTYTDANKNKGITWKEETLMEYLENPKKYIPGTKMIFAGIKKKTEREDLIAYLKKATNE 104
                                    10        20        30        40        50        60        70        80        90       100

Chain C from PDB  Type:PROTEIN  Length:294
 aligned with CCPR_YEAST | P00431 from UniProtKB/Swiss-Prot  Length:361

    Alignment length:294
                                    77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357    
           CCPR_YEAST    68 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKHDNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQGPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKTHLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQDPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 361
               SCOP domains d2pcbc_ C: Cytochrome c peroxidase, CCP                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ---2pcbC01 C:4-144,C:266-294  [code=1.10.520.10, no name defined]                                                                               2pcbC02 C:145-265 Peroxidase, domain 2                                                                                   2pcbC01 C:4-144,C:266-294     CATH domains
           Pfam domains (1) -----------------------peroxidase-2pcbC01 C:24-254                                                                                                                                                                                                            ---------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------peroxidase-2pcbC02 C:24-254                                                                                                                                                                                                            ---------------------------------------- Pfam domains (2)
         Sec.struct. author ..............hhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhh.............hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..............................hhhhhhhhhhh...hhhhhhhhhhhhhh...hhhhhh.............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: C:1-294 UniProt: 1-361 [INCOMPLETE]                                                                                                                                                                                                                                                     Transcript 1
                 2pcb C   1 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKHDNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQGPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKTHLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQDPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294
                                    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

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 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)

Baker's yeast (Saccharomyces cerevisiae) (49)

2pcbB00

B:1-104

Topology: Peroxidase; domain 1 (244)

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

Baker's yeast (Saccharomyces cerevisiae) (120)

2a	2pcbA01	A:4-144,A:266-294
2b	2pcbC01	C:4-144,C:266-294

Topology: Peroxidase; domain 2 (241)

Homologous Superfamily: Peroxidase, domain 2 (241)

Baker's yeast (Saccharomyces cerevisiae) (120)

3a	2pcbA02	A:145-265
3b	2pcbC02	C:145-265

Asymmetric Unit(hide GO term definitions)

Chain A,C (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.

Chain B (CYC_HORSE | P00004)

molecular function
	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:0045155	electron transporter, transferring electrons from CoQH2-cytochrome c reductase complex and cytochrome c oxidase complex activity	Enables the directed movement of electrons from the CoQH2-cytochrome c reductase complex and the cytochrome c oxidase complex.
	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.
biological process
	GO:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	GO:0006123	mitochondrial electron transport, cytochrome c to oxygen	The transfer of electrons from cytochrome c to oxygen that occurs during oxidative phosphorylation, mediated by the multisubunit enzyme known as complex IV.
	GO:0006122	mitochondrial electron transport, ubiquinol to cytochrome c	The transfer of electrons from ubiquinol to cytochrome c that occurs during oxidative phosphorylation, mediated by the multisubunit enzyme known as complex III.
	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:0043280	positive regulation of cysteine-type endopeptidase activity involved in apoptotic process	Any process that activates or increases the activity of a cysteine-type endopeptidase involved in the apoptotic process.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005758	mitochondrial intermembrane space	The region between the inner and outer lipid bilayers of the mitochondrial envelope.
	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.
	GO:0070469	respiratory chain	The protein complexes that form the electron transport system (the respiratory chain), associated with a cell membrane, usually the plasma membrane (in prokaryotes) or the inner mitochondrial membrane (on eukaryotes). The respiratory chain complexes transfer electrons from an electron donor to an electron acceptor and are associated with a proton pump to create a transmembrane electrochemical gradient.

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