3M2E - JenaLib

Title :   CRYSTALLOGRAPHIC AND SINGLE CRYSTAL SPECTRAL ANALYSIS OF THE PEROXIDASE FERRYL INTERMEDIATE

Authors :   Y. T. Meharenna, T. L. Poulos

Date :   07 Mar 10 (Deposition) - 12 May 10 (Release) - 12 May 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

Chains :   Asym./Biol. Unit : A

Keywords :   Cytochrome C Peroxidase (Ccp), Oxidoreductase, Heme, Hydrogen Peroxide, Iron, Metal-Binding, Mitochondrion, Organic Radical, Peroxidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. T. Meharenna, T. Doukov, H. Li, S. M. Soltis, T. L. Poulos
Crystallographic And Single-Crystal Spectral Analysis Of The Peroxidase Ferryl Intermediate.
Biochemistry V. 49 2984 2010
PubMed-ID: 20230048 | Reference-DOI: 10.1021/BI100238R

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)

PROSITE Motifs (2, 2)

Exons (1, 1)

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
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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 d3m2ea_ A: automated matches                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.......hhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..............hhhhh...........hhhhhhhhhhh...hhhhhhhhhhhhhh...hhhhhh.............hhhhhhhhhh..eeee.....eeee.....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
                 3m2e A   4 LVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKHDNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQGPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKTHLKRSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQDPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 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)

CATH Domains (0, 0)

Pfam Domains (0, 0)

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)

Related Entries Specified in the PDB File

1dsg
1dso
1zby
2v23
3e2n
3e2o	CRYSTAL STRUCTURE OF CYTOCHROME C PEROXIDASE, N184R MUTANT
3m23	COMPOUND I (1) COMPOSITE STRUCTURE OF CYTOCHROME C PEROXIDASE, N184R MUTANT
3m25	COMPOUND I (2) COMPOSITE STRUCTURE OF CYTOCHROME C PEROXIDASE, N184R MUTANT
3m26	COMPOUND I (3) COMPOSITE STRUCTURE OF CYTOCHROME C PEROXIDASE, N184R MUTANT
3m27	COMPOUND I (4) COMPOSITE STRUCTURE OF CYTOCHROME C PEROXIDASE, N184R MUTANT
3m28	COMPOUND I (5) COMPOSITE STRUCTURE OF CYTOCHROME C PEROXIDASE, N184R MUTANT
3m29	COMPOUND I (6) COMPOSITE STRUCTURE OF CYTOCHROME C PEROXIDASE, N184R MUTANT
3m2a	COMPOUND I (7) COMPOSITE STRUCTURE OF CYTOCHROME C PEROXIDASE, N184R MUTANT
3m2b	COMPOUND I (8) COMPOSITE STRUCTURE OF CYTOCHROME C PEROXIDASE, N184R MUTANT
3m2c	COMPOUND I (9) COMPOSITE STRUCTURE OF CYTOCHROME C PEROXIDASE, N184R MUTANT
3m2d	COMPOUND I (10) COMPOSITE STRUCTURE OF CYTOCHROME C PEROXIDASE, N184R MUTANT
3m2f
3m2g
3m2h
3m2i
5ccp

Description