2XFH - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   STRUCTURE OF CYTOCHROME P450 ERYK COCRYSTALLIZED WITH INHIBITOR CLOTRIMAZOLE.

Authors :   C. Savino, L. C. Montemiglio, S. Gianni, B. Vallone

Date :   24 May 10 (Deposition) - 29 Sep 10 (Release) - 05 Feb 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A

Keywords :   Monoxygenase, Erythromycin A Biosynthesis, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. C. Montemiglio, S. Gianni, B. Vallone, C. Savino
Azole Drugs Trap Cytochrome P450 Eryk In Alternative Conformational States.
Biochemistry V. 49 9199 2010
PubMed-ID: 20845962 | Reference-DOI: 10.1021/BI101062V

Molecule 1 - ERYTHROMYCIN B/D C-12 HYDROXYLASE
	Chains	:	A
	EC Number	:	1.14.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET28B
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	SACCHAROPOLYSPORA ERYTHRAEA
	Organism Taxid	:	1836
	Synonym	:	CYTOCROME P450 CYP113A1, CYTOCHROME P450 113A1

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 4)

No.	Name	Count	Type	Full Name
1	CL6	2	Ligand/Ion	1-[(2-CHLOROPHENYL)(DIPHENYL)METHYL]-1H-IMIDAZOLE
2	DMS	1	Ligand/Ion	DIMETHYL SULFOXIDE
3	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:87 , HIS A:88 , HIS A:95 , ARG A:99 , LEU A:238 , ALA A:241 , THR A:245 , PHE A:288 , MET A:291 , ARG A:293 , SER A:345 , PHE A:346 , GLY A:347 , HIS A:351 , CYS A:353 , GLY A:355 , ALA A:359 , CL6 A:1413 , HOH A:2384 , HOH A:2385 , HOH A:2386	BINDING SITE FOR RESIDUE HEM A1412
2	AC2	SOFTWARE	HIS A:88 , GLN A:173 , ALA A:241 , THR A:245 , PHE A:288 , HEM A:1412 , CL6 A:1414	BINDING SITE FOR RESIDUE CL6 A1413
3	AC3	SOFTWARE	MET A:86 , HIS A:88 , LEU A:169 , GLN A:173 , ILE A:186 , LEU A:190 , LEU A:240 , CL6 A:1413 , HOH A:2119 , HOH A:2387	BINDING SITE FOR RESIDUE CL6 A1414
4	AC4	SOFTWARE	PRO A:92 , HIS A:95 , ARG A:96 , GLU A:184 , VAL A:350 , HOH A:2043 , HOH A:2388	BINDING SITE FOR RESIDUE DMS A1415

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

Asymmetric/Biological Unit

No.	Residues
1	Pro A:92	-	Pro A:93

(no "SAP(SNP)/Variant" information available for 2XFH)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTOCHROME_P450	PS00086	Cytochrome P450 cysteine heme-iron ligand signature.	ERYK_SACEN	332-341	1	A:346-355

(no "Exon" information available for 2XFH)

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:394
 aligned with ERYK_SACEN | P48635 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:394
                                    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       303       313       323       333       343       353       363       373       383       393    
           ERYK_SACEN     4 IDEVPGMADETALLDWLGTMREKQPVWQDRYGVWHVFRHADVQTVLRDTATFSSDPTRVIEGASPTPGMIHEIDPPEHRALRKVVSSAFTPRTISDLEPRIRDVTRSLLADAGESFDLVDVLAFPLPVTIVAELLGLPPMDHEQFGDWSGALVDIQMDDPTDPALAERIADVLNPLTAYLKARCAERRADPGDDLISRLVLAEVDGRALDDEEAANFSTALLLAGHITTTVLLGNIVRTLDEHPAHWDAAAEDPGRIPAIVEEVLRYRPPFPQMQRTTTKATEVAGVPIPADVMVNTWVLSANRDSDAHDDPDRFDPSRKSGGAAQLSFGHGVHFCLGAPLARLENRVALEEIIARFGRLTVDRDDERLRHFEQIVLGTRHLPVLAGSSPRQSA 397
               SCOP domains d2xfha_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhh.eee.....eee.hhhhhhhhhhh...ee..hhhhh........hhhhh..hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...eeehhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhee..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh....eeeeee...eee..eee....eeeeehhhhhh.................hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh..ee....................eee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME-------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xfh A  18 IDEVPGMADETALLDWLGTMREKQPVWQDRYGVWHVFRHADVQTVLRDTATFSSDPTRVIEGASPTPGMIHEIDPPEHRALRKVVSSAFTPRTISDLEPRIRDVTRSLLADAGESFDLVDVLAFPLPVTIVAELLGLPPMDHEQFGDWSGALVDIQMDDPTDPALAERIADVLNPLTAYLKARCAERRADPGDDLISRLVLAEVDGRALDDEEAANFSTALLLAGHITTTVLLGNIVRTLDEHPAHWDAAAEDPGRIPAIVEEVLRYRPPFPQMQRTTTKATEVAGVPIPADVMVNTWVLSANRDSDAHDDPDRFDPSRKSGGAAQLSFGHGVHFCLGAPLARLENRVALEEIIARFGRLTVDRDDERLRHFEQIVLGTRHLPVLAGSSPRQSA 411
                                    27        37        47        57        67        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       367       377       387       397       407

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 P450 (480)

Superfamily: Cytochrome P450 (480)

Family: automated matches (157)

Protein domain: automated matches (157)

Saccharopolyspora erythraea [TaxId: 1836] (5)

d2xfha_

(no "CATH Domain" information available for 2XFH)

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (ERYK_SACEN | P48635)

molecular function
	GO:0050661	NADP binding	Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004497	monooxygenase activity	Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
	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:0016705	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen	Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor.
	GO:0016709	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen	Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from NADH or NADPH and one other donor, and one atom of oxygen is incorporated into one donor.
biological process
	GO:0017000	antibiotic biosynthetic process	The chemical reactions and pathways resulting in the formation of an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
	GO:0033068	macrolide biosynthetic process	The chemical reactions and pathways leading to the formation of macrolides, any of a large group of polyketide compounds that contain a large lactone ring with few or no double bonds and no nitrogen atoms, linked glycosidically to one or more sugar groups. The macrolides include the carbomycins, the erythromycins, oleandomycin, oligomycins, and the spiramycins, and act as antibiotics, mainly against Gram-positive bacteria.
	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.

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
		CL6	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		DMS	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		HEM	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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

	Cis Peptide Bonds
		Pro A:92 - Pro A:93	[ 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
	2xfh
		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
	ERYK_SACEN \| P48635
		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)
	1.14.-.-
		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
	ERYK_SACEN \| P48635
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	ERYK_SACEN \| P48635	:	2jjn 2jjo 2jjp 2wio 3zkp

2jjn	STRUCTURE OF CLOSED CYTOCHROME P450 ERYK
2jjo	STRUCTURE OF CYTOCHROME P450 ERYK IN COMPLEX WITH ITS NATURAL SUBSTRATE ERD
2jjp	STRUCTURE OF CYTOCHROME P450 ERYK IN COMPLEX WITH INHIBITOR KETOCONAZOLE (KC)
2vrv	STRUCTURE OF HISTIDINE TAGGED CYTOCHROME P450 ERYK IN COMPLEX WITH INHIBITOR CLOTRIMAZOLE (CLT)
2wio	STRUCTURE OF THE HISTIDINE TAGGED, OPEN CYTOCHROME P450 ERYK FROM S. ERYTHRAEA

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (11, 11)

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