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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF THE PROTEIN-PROTEIN COMPLEX BETWEEN F82I CYTOCHROME C AND CYTOCHROME C PEROXIDASE

Authors :   S. A. Kang, B. R. Crane

Date :   15 Sep 05 (Deposition) - 25 Oct 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym./Biol. Unit : A,B

Keywords :   Cytochrome, Electron Transfer, Oxidoreductase-Electron Transport Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. A. Kang, B. R. Crane
Effects Of Interface Mutations On Association Modes And Electron-Transfer Rates Between Proteins
Proc. Natl. Acad. Sci. Usa V. 102 15465 2005
PubMed-ID: 16227441 | Reference-DOI: 10.1073/PNAS.0505176102

Molecule 1 - CYTOCHROME C PEROXIDASE, MITOCHONDRIAL
	Chains	:	A
	EC Number	:	1.11.1.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	CCP1, CCP, CPO
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	CCP

Molecule 2 - CYTOCHROME C ISO-1
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	CYC1
	Mutation	:	YES
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

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

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:44 , VAL A:45 , VAL A:47 , ARG A:48 , TRP A:51 , LEU A:171 , MET A:172 , ALA A:174 , HIS A:175 , GLY A:178 , LYS A:179 , THR A:180 , HIS A:181 , ASN A:184 , SER A:185 , TRP A:191 , THR A:234 , PHE A:266	BINDING SITE FOR RESIDUE ZNH A 295
2	AC2	SOFTWARE	ARG B:13 , CYS B:14 , CYS B:17 , HIS B:18 , VAL B:28 , ILE B:35 , SER B:40 , GLY B:41 , TYR B:46 , TYR B:48 , THR B:49 , ASN B:52 , TRP B:59 , MET B:64 , TYR B:67 , THR B:78 , LYS B:79 , MET B:80 , ILE B:82	BINDING SITE FOR RESIDUE HEM B 109

(no "SS Bond" information available for 2B0Z)

(no "Cis Peptide Bond" information available for 2B0Z)

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

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

Asymmetric/Biological Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	CYC1_YEAST	7-108	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

Asymmetric/Biological Unit (2, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YJR048W	1	YJR048W.1	X:526327-526656	330	CYC1_YEAST	1-109	109	1	B:-4-103	108

2.1	YKR066C	1	YKR066C.1	XI:566840-565755	1086	CCPR_YEAST	1-361	361	1	A:1-294	294

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: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 d2b0za_ A: Cytochrome c peroxidase, CCP                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ---2b0zA01 A:4-144,A:266-294  [code=1.10.520.10, no name defined]                                                                               2b0zA02 A:145-265 Peroxidase, domain 2                                                                                   2b0zA01 A:4-144,A:266-294     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....ee.......hhhhhhhhhhhhhhhhhhh.hhhhhh................................hhhhhhhhhhh.hhhhhhhhh.........hhhhhhhhhhhhhhhhh..............hhhhh...........hhhhhhhhhhh...hhhhhhhhhhhhhh.eehhhhhh..ee.........hhhhhhhhhh..eeee.....eeee.....eehhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------I--------------------------------------------------------------------------------------------------G---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PEROXIDASE_2----------------------------------------------------------------------------------------------------------------PEROXIDASE_--------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 2 Exon 2.1  PDB: A:1-294 UniProt: 1-361 [INCOMPLETE]                                                                                                                                                                                                                                                     Transcript 2
                 2b0z A   1 TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKHDNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQGPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKTHLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQDPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 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:108
 aligned with CYC1_YEAST | P00044 from UniProtKB/Swiss-Prot  Length:109

    Alignment length:108
                                    11        21        31        41        51        61        71        81        91       101        
           CYC1_YEAST     2 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109
               SCOP domains d2b0zb1 B:-4-103 Mitochondrial cytochrome c                                                                  SCOP domains
               CATH domains 2b0zB00 B:-4-103 Cytochrome c                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhhhh..................................hhhhhhh......hhhhhhhhhhhhhh............................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----CYTC  PDB: B:1-102 UniProt: 7-108                                                                     - PROSITE
               Transcript 1 Exon 1.1  PDB: B:-4-103 UniProt: 1-109 [INCOMPLETE]                                                          Transcript 1
                 2b0z B  -4 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWDENNMSEYLTNPKKYIPGTKMAIGGLKKEKDRNDLITYLKKACE 103
                                     5        15        25        35        45        55        65        75        85        95

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: monodomain cytochrome c (197)

Protein domain: Mitochondrial cytochrome c (81)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (49)

d2b0zb1

B:-4-103

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)

d2b0za_

(no "Pfam Domain" information available for 2B0Z)

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.

Chain B (CYC1_YEAST | P00044)

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: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: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: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.
cellular component
	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.

Asymmetric/Biological Unit
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(no "Related Entries Specified in the PDB File" available for 2B0Z)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 2)

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Exons (2, 2)

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