2JTI - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - model 1, sites (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   SOLUTION STRUCTURE OF THE YEAST ISO-1-CYTOCHROME C (T12A) : YEAST CYTOCHROME C PEROXIDASE COMPLEX

Authors :   M. Ubbink, A. N. Volkov

Date :   01 Aug 07 (Deposition) - 22 Jul 08 (Release) - 15 Sep 10 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B  (10x)
NMR Structure *: A,B  (1x)

Keywords :   Protein/Protein, Heme, Hydrogen Peroxide, Iron, Metal-Binding, Mitochondrion, Oxidoreductase, Peroxidase, Transit Peptide, Electron Transport, Methylation, Respiratory Chain, Transport, Oxidoreductase-Electron Transport Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. N. Volkov, Q. Bashir, J. A. Worrall, G. M. Ullmann, M. Ubbink
Shifting The Equilibrium Between The Encounter State And Th Specific Form Of A Protein Complex By Interfacial Point Mutations.
J. Am. Chem. Soc. V. 132 11487 2010
PubMed-ID: 20672804 | Reference-DOI: 10.1021/JA100867C

Molecule 1 - CYTOCHROME C PEROXIDASE, MITOCHONDRIAL
	Chains	:	A
	EC Number	:	1.11.1.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector	:	PT7CCP
	Expression System Vector Type	:	VECTOR
	Gene	:	CCP1, CCP, CPO
	Mutation	:	YES
	Organism Common	:	YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Strain	:	DBY939
	Synonym	:	CCP

Molecule 2 - CYTOCHROME C ISO-1
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector	:	PBTR1
	Expression System Vector Type	:	VECTOR
	Gene	:	CYC1
	Mutation	:	YES
	Organism Common	:	YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Strain	:	OVIFORMIS

		1	2
NMR Structure (10x)	:	A	B
NMR Structure * (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

NMR Structure (2, 2)

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

NMR Structure * (2, 2)

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

NMR Structure (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:44 , VAL A:47 , ARG A:48 , PRO A:145 , ASP A:146 , ALA A:147 , 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 , THR A:234	BINDING SITE FOR RESIDUE HEM A 295
2	AC2	SOFTWARE	ALA A:193 , ALA A:194 , CYS B:14 , CYS B:17 , HIS B:18 , VAL B:28 , PRO B:30 , ILE B:35 , SER B:40 , GLY B:41 , TYR B:46 , TYR B:48 , THR B:49 , ASN B:52 , TRP B:59 , LEU B:68 , LYS B:79 , MET B:80 , PHE B:82	BINDING SITE FOR RESIDUE HEC B 104

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

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

NMR Structure (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)

NMR Structure * (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)

NMR Structure (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

NMR Structure * (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

NMR Structure (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:1-103	103

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

NMR Structure

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 d2jtia_ A: Cytochrome c peroxidase, CCP                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ---2jtiA01 A:4-144,A:266-294  [code=1.10.520.10, no name defined]                                                                               2jtiA02 A:145-265 Peroxidase, domain 2                                                                                   2jtiA01 A:4-144,A:266-294     CATH domains
               Pfam domains -----------------------peroxidase-2jtiA01 A:24-254                                                                                                                                                                                                            ---------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..............hhhhh...........hhhhhhhhhhhh..hhhhhhhhhhhhhh.eehhhhhh..ee.........hhhhhhhhhh.eeeee.....eeeee....eehhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhh. 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
                 2jti 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:103
 aligned with CYC1_YEAST | P00044 from UniProtKB/Swiss-Prot  Length:109

    Alignment length:103
                                    16        26        36        46        56        66        76        86        96       106   
           CYC1_YEAST     7 GSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109
               SCOP domains d2jtib_ B: Mitochondrial cytochrome c                                                                   SCOP domains
               CATH domains 2jtiB00 B:1-103 Cytochrome c                                                                            CATH domains
               Pfam domains --Cytochrom_C-2jtiB01 B:3-101                                                                        -- Pfam domains
         Sec.struct. author ..hhhhhhhhh.....................................hhhhhh........hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE CYTC  PDB: B:1-102 UniProt: 7-108                                                                     - PROSITE
               Transcript 1 Exon 1.1  PDB: B:1-103 UniProt: 1-109 [INCOMPLETE]                                                      Transcript 1
                 2jti B   1 GSAKKGATLFKARCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 103
                                    10        20        30        40        50        60        70        80        90       100

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 '\|'

NMR Structure(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.

NMR Structure
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1ycc	CRYSTAL STRUCTURE OF YEAST ISO-1-CYTOCHROME C
1zby	HIGH-RESOLUTION CRYSTAL STRUCTURE OF YEAST CYTOCHROME C PEROXIDASE
2gb8	SOLUTION STRUCTURE OF WT CC-CCP COMPLEX
2pcc	CRYSTAL STRUCTURE OF WT CC-CCP COMPLEX

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