2VHD - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE DI-HAEM CYTOCHROME C PEROXIDASE FROM PSEUDOMONAS AERUGINOSA - MIXED VALENCE FORM

Authors :   A. Echalier, T. Brittain, J. Wright, S. Boycheva, G. B. Mortuza, V. Fulo N. J. Watmough

Date :   20 Nov 07 (Deposition) - 12 Feb 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Iron, Heme, Transport, Peroxidase, Metal-Binding, Oxidoreductase, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Echalier, T. Brittain, J. Wright, S. Boycheva, G. B. Mortuza, V. Fulop, N. J. Watmough
Redox-Linked Structural Changes Associated With The Formation Of A Catalytically Competent Form Of The Diheme Cytochrome C Peroxidase From Pseudomonas Aeruginosa
Biochemistry V. 47 1947 2008
PubMed-ID: 18217775 | Reference-DOI: 10.1021/BI702064F

Molecule 1 - CYTOCHROME C551 PEROXIDASE
	Chains	:	A, B
	EC Number	:	1.11.1.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PEC86
	Expression System Strain	:	JM109(DE3)
	Expression System Taxid	:	562
	Expression System Vector	:	PET21D
	Fragment	:	RESIDUES 24-346
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	287
	Synonym	:	CYTOCHROME C PEROXIDASE, CCP

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 6)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	HEC	4	Ligand/Ion	HEME C

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:50 , CYS A:51 , CYS A:54 , HIS A:55 , SER A:68 , VAL A:69 , GLY A:70 , ARG A:78 , SER A:80 , PRO A:81 , GLN A:92 , PHE A:93 , TRP A:94 , ARG A:97 , LEU A:101 , GLN A:104 , PRO A:108 , ILE A:109 , GLU A:114 , MET A:115 , ILE A:156 , GLU A:160 , ARG A:246 , HOH A:2040 , HOH A:2053 , HOH A:2142	BINDING SITE FOR RESIDUE HEC A 401
2	AC2	SOFTWARE	TRP A:94 , CYS A:197 , CYS A:200 , HIS A:201 , PHE A:212 , PHE A:214 , LEU A:216 , PHE A:245 , ARG A:246 , ALA A:247 , ALA A:248 , LEU A:250 , TYR A:259 , PHE A:260 , HIS A:261 , MET A:275 , GLN A:279 , LEU A:280 , HOH A:2099 , HOH A:2143 , HOH A:2144	BINDING SITE FOR RESIDUE HEC A 402
3	AC3	SOFTWARE	ASN A:79 , THR A:256 , PRO A:258 , HOH A:2031 , HOH A:2033 , HOH A:2143 , HOH A:2144	BINDING SITE FOR RESIDUE CA A 403
4	AC4	SOFTWARE	SER B:50 , CYS B:51 , CYS B:54 , HIS B:55 , SER B:68 , VAL B:69 , GLY B:70 , ARG B:78 , SER B:80 , PRO B:81 , PHE B:93 , TRP B:94 , ARG B:97 , LEU B:101 , GLN B:104 , PRO B:108 , ILE B:109 , ILE B:156 , GLU B:160 , ARG B:246 , HOH B:2045 , HOH B:2048 , HOH B:2141 , HOH B:2142	BINDING SITE FOR RESIDUE HEC B 401
5	AC5	SOFTWARE	TRP B:94 , GLY B:196 , CYS B:197 , CYS B:200 , HIS B:201 , PHE B:212 , PHE B:214 , LEU B:216 , PHE B:245 , ARG B:246 , ALA B:247 , ALA B:248 , LEU B:250 , TYR B:259 , PHE B:260 , HIS B:261 , MET B:275 , GLY B:276 , GLN B:279 , LEU B:280 , HOH B:2143 , HOH B:2144	BINDING SITE FOR RESIDUE HEC B 402
6	AC6	SOFTWARE	ASN B:79 , THR B:256 , PRO B:258 , HOH B:2037 , HOH B:2044 , HOH B:2143 , HOH B:2144	BINDING SITE FOR RESIDUE CA B 403

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

Asymmetric/Biological Unit

No.	Residues
1	Ala A:257	-	Pro A:258
2	Ala B:257	-	Pro B:258

Asymmetric/Biological Unit (6, 12)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_CCPR_PSEAE_001 *	G	81	D	CCPR_PSEAE	---	---	A/B	G	58	D
2	UniProt	VAR_CCPR_PSEAE_002 *	G	83	D	CCPR_PSEAE	---	---	A/B	G	60	D
3	UniProt	VAR_CCPR_PSEAE_003 *	I	152	V	CCPR_PSEAE	---	---	A/B	I	129	V
4	UniProt	VAR_CCPR_PSEAE_004 *	P	164	A	CCPR_PSEAE	---	---	A/B	P	141	A
5	UniProt	VAR_CCPR_PSEAE_005 *	K	198	I	CCPR_PSEAE	---	---	A/B	K	175	I
6	UniProt	VAR_CCPR_PSEAE_006 *	L	334	W	CCPR_PSEAE	---	---	A/B	L	311	W
	* ID not provided by source

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

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	CCPR_PSEAE	52-160 206-323	4	A:29-137 B:29-137 A:183-300 B:183-300

(no "Exon" information available for 2VHD)

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:323
 aligned with CCPR_PSEAE | P14532 from UniProtKB/Swiss-Prot  Length:346

    Alignment length:323
                                    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       303       313       323       333       343   
           CCPR_PSEAE    24 DALHDQASALFKPIPEQVTELRGQPISEQQRELGKKLFFDPRLSRSHVLSCNTCHNVGTGGADNVPTSVGHGWQKGPRNSPTVFNAVFNAAQFWDGRAKDLGEQAKGPIQNSVEMHSTPQLVEQTLGSIPEYVDAFRKAFPKAGKPVSFDNMALAIEAYEATLVTPDSPFDLYLKGDDKALDAQQKKGLKAFMDSGCSACHNGINLGGQAYFPFGLVKKPDASVLPSGDKGRFAVTKTQSDEYVFRAAPLRNVALTAPYFHSGQVWELKDAVAIMGNAQLGKQLAPDDVENIVAFLHSLSGKQPRVEYPLLPASTETTPRPAE 346
               SCOP domains d2vhda1 A:1-164 Di-heme cytochrome c peroxidase                                                                                                                     d2vhda2 A:165-323 Di-heme cytochrome c peroxidase                                                                                                               SCOP domains
               CATH domains 2vhdA01         2vhdA02 A:17-164,A:303-323 Cytochrome c                                                                                                             2vhdA01 A:1-16,A:165-302 Cytochrome c                                                                                                     2vhdA02 Cytochrome c  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh........ee..ee.hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.........hhhhh..........hhhhh..........hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh......hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..........eee..................hhhhhhhhhhh.eee.....hhhhh..........hhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------D-D--------------------------------------------------------------------V-----------A---------------------------------I---------------------------------------------------------------------------------------------------------------------------------------W------------ SAPs(SNPs)
                    PROSITE ----------------------------CYTC  PDB: A:29-137 UniProt: 52-160                                                                          ---------------------------------------------CYTC  PDB: A:183-300 UniProt: 206-323                                                                                 ----------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vhd A   1 DALHDQASALFKPIPEQVTELRGQPISEQQRELGKKLFFDPRLSRSHVLSCNTCHNVGTGGADNVPTSVGHGWQKGPRNSPTVFNAVFNAAQFWDGRAKDLGEQAKGPIQNSVEMHSTPQLVEQTLGSIPEYVDAFRKAFPKAGKPVSFDNMALAIEAYEATLVTPDSPFDLYLKGDDKALDAQQKKGLKAFMDSGCSACHNGINLGGQAYFPFGLVKKPDASVLPSGDKGRFAVTKTQSDEYVFRAAPLRNVALTAPYFHSGQVWELKDAVAIMGNAQLGKQLAPDDVENIVAFLHSLSGKQPRVEYPLLPASTETTPRPAE 323
                                    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       300       310       320

Chain B from PDB  Type:PROTEIN  Length:323
 aligned with CCPR_PSEAE | P14532 from UniProtKB/Swiss-Prot  Length:346

    Alignment length:323
                                    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       303       313       323       333       343   
           CCPR_PSEAE    24 DALHDQASALFKPIPEQVTELRGQPISEQQRELGKKLFFDPRLSRSHVLSCNTCHNVGTGGADNVPTSVGHGWQKGPRNSPTVFNAVFNAAQFWDGRAKDLGEQAKGPIQNSVEMHSTPQLVEQTLGSIPEYVDAFRKAFPKAGKPVSFDNMALAIEAYEATLVTPDSPFDLYLKGDDKALDAQQKKGLKAFMDSGCSACHNGINLGGQAYFPFGLVKKPDASVLPSGDKGRFAVTKTQSDEYVFRAAPLRNVALTAPYFHSGQVWELKDAVAIMGNAQLGKQLAPDDVENIVAFLHSLSGKQPRVEYPLLPASTETTPRPAE 346
               SCOP domains d2vhdb1 B:1-164 Di-heme cytochrome c peroxidase                                                                                                                     d2vhdb2 B:165-323 Di-heme cytochrome c peroxidase                                                                                                               SCOP domains
               CATH domains 2vhdB01         2vhdB02 B:17-164,B:303-323 Cytochrome c                                                                                                             2vhdB01 B:1-16,B:165-302 Cytochrome c                                                                                                     2vhdB02 Cytochrome c  CATH domains
           Pfam domains (1) --------------------------CCP_MauG-2vhdB01 B:27-181                                                                                                                                  ---Cytochrom_C-2vhdB03 B:185-300                                                                                       ----------------------- Pfam domains (1)
           Pfam domains (2) --------------------------CCP_MauG-2vhdB02 B:27-181                                                                                                                                  ---Cytochrom_C-2vhdB04 B:185-300                                                                                       ----------------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhh..........ee..ee.hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.........hhhhh..........hhhhh..........hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh......hhhhhhhh......hhhhhhhhhhhhhhhhhhh..........eee.................hhhhhhhhhhhh.eee.....hhhhh..........hhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------D-D--------------------------------------------------------------------V-----------A---------------------------------I---------------------------------------------------------------------------------------------------------------------------------------W------------ SAPs(SNPs)
                    PROSITE ----------------------------CYTC  PDB: B:29-137 UniProt: 52-160                                                                          ---------------------------------------------CYTC  PDB: B:183-300 UniProt: 206-323                                                                                 ----------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vhd B   1 DALHDQASALFKPIPEQVTELRGQPISEQQRELGKKLFFDPRLSRSHVLSCNTCHNVGTGGADNVPTSVGHGWQKGPRNSPTVFNAVFNAAQFWDGRAKDLGEQAKGPIQNSVEMHSTPQLVEQTLGSIPEYVDAFRKAFPKAGKPVSFDNMALAIEAYEATLVTPDSPFDLYLKGDDKALDAQQKKGLKAFMDSGCSACHNGINLGGQAYFPFGLVKKPDASVLPSGDKGRFAVTKTQSDEYVFRAAPLRNVALTAPYFHSGQVWELKDAVAIMGNAQLGKQLAPDDVENIVAFLHSLSGKQPRVEYPLLPASTETTPRPAE 323
                                    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       300       310       320

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: Di-heme cytochrome c peroxidase (6)

Protein domain: Di-heme cytochrome c peroxidase (6)

Pseudomonas aeruginosa [TaxId: 287] (2)

1a	d2vhda1	A:1-164
1b	d2vhda2	A:165-323
1c	d2vhdb1	B:1-164
1d	d2vhdb2	B:165-323

Asymmetric/Biological 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)

Pseudomonas aeruginosa. Organism_taxid: 287. (2)

1a	2vhdA01	A:1-16,A:165-302
1b	2vhdB01	B:1-16,B:165-302
1c	2vhdA02	A:17-164,A:303-323
1d	2vhdB02	B:17-164,B:303-323

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Cytochrome-c (108)

Family: CCP_MauG (10)

Pseudomonas aeruginosa (1)

1a	CCP_MauG-2vhdB01	B:27-181
1b	CCP_MauG-2vhdB02	B:27-181

Family: Cytochrom_C (54)

Pseudomonas aeruginosa (2)

2a	Cytochrom_C-2vhdB03	B:185-300
2b	Cytochrom_C-2vhdB04	B:185-300

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (CCPR_PSEAE | P14532)

molecular function
	GO:0004130	cytochrome-c peroxidase activity	Catalysis of the reaction: 2 ferrocytochrome c + hydrogen peroxide = 2 ferricytochrome c + 2 H2O.
	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: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.
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: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:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		HEC	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ala A:257 - Pro A:258	[ RasMol ]
		Ala B:257 - Pro B:258	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2vhd
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	CCPR_PSEAE \| P14532
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	1.11.1.5
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	CCPR_PSEAE \| P14532
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	CCPR_PSEAE \| P14532	:	1eb7

1eb7	CRYSTAL STRUCTURE OF THE DI-HAEM CYTOCHROME C PEROXIDASE FROM PSEUDOMONAS AERUGINOSA

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (6, 12)

PROSITE Motifs (1, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (1, 4)

Pfam Domains (2, 4)

Gene Ontology (9, 9)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File