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Asym./Biol. Unit (Jmol Viewer)

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Title :   STRUCTURE OF CYTOCHROME P450 ERYK IN COMPLEX WITH INHIBITOR KETOCONAZOLE (KC)

Authors :   C. Savino, G. Sciara, A. E. Miele, S. G. Kendrew, B. Vallone

Date :   15 Apr 08 (Deposition) - 14 Jul 09 (Release) - 22 Aug 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym./Biol. Unit : A

Keywords :   Iron, Heme, Monooxygenase, Metal-Binding, Antibiotic Biosynthesis, Tie-Rod Mechanism Of Action, Oxidoreductase, Substrate Specificity (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 - CYTOCHROME P450 113A1
	Chains	:	A
	EC Number	:	1.14.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21STAR
	Expression System Taxid	:	511693
	Expression System Vector	:	PET28B
	Mutation	:	YES
	Organism Scientific	:	SACCHAROPOLYSPORA ERYTHRAEA
	Organism Taxid	:	1836
	Other Details	:	CDNA
	Strain	:	NRRL 23338
	Synonym	:	ERYTHROMYCIN B/D C-12 HYDROXYLASE, CYTOCROME P450 CYP113A1

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 4)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	KLN	1	Ligand/Ion	1-ACETYL-4-(4-{[(2S,4R)-2-(2,4-DICHLOROPHENYL)-2-(1H-IMIDAZOL-1-YLMETHYL)-1,3-DIOXOLAYL]METHOXY}PHENYL)PIPERAZINE
3	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:87 , HIS A:88 , HIS A:95 , ARG A:99 , ALA A:241 , THR A:245 , MET A:291 , ARG A:293 , SER A:345 , PHE A:346 , GLY A:347 , VAL A:350 , HIS A:351 , CYS A:353 , GLY A:355 , ALA A:359 , KLN A:413 , HOH A:2064 , HOH A:2065 , HOH A:2228	BINDING SITE FOR RESIDUE HEM A 412
2	AC2	SOFTWARE	HIS A:88 , MET A:174 , ALA A:237 , LEU A:240 , ALA A:241 , PHE A:288 , GLN A:290 , MET A:291 , GLN A:292 , ILE A:392 , HEM A:412 , HOH A:2114 , HOH A:2174 , HOH A:2219	BINDING SITE FOR RESIDUE KLN A 413
3	AC3	SOFTWARE	ARG A:381 , ARG A:385 , LEU A:386 , HIS A:388	BINDING SITE FOR RESIDUE SO4 A 414
4	AC4	SOFTWARE	HIS A:326 , ASP A:327 , ARG A:336 , LYS A:337 , SER A:338	BINDING SITE FOR RESIDUE SO4 A 415

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

Asymmetric/Biological Unit

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

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

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 2JJP)

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

    Alignment length:397
                                    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       330       340       350       360       370       380       390       
           ERYK_SACEN     1 MTTIDEVPGMADETALLDWLGTMREKQPVWQDRYGVWHVFRHADVQTVLRDTATFSSDPTRVIEGASPTPGMIHEIDPPEHRALRKVVSSAFTPRTISDLEPRIRDVTRSLLADAGESFDLVDVLAFPLPVTIVAELLGLPPMDHEQFGDWSGALVDIQMDDPTDPALAERIADVLNPLTAYLKARCAERRADPGDDLISRLVLAEVDGRALDDEEAANFSTALLLAGHITTTVLLGNIVRTLDEHPAHWDAAAEDPGRIPAIVEEVLRYRPPFPQMQRTTTKATEVAGVPIPADVMVNTWVLSANRDSDAHDDPDRFDPSRKSGGAAQLSFGHGVHFCLGAPLARLENRVALEEIIARFGRLTVDRDDERLRHFEQIVLGTRHLPVLAGSSPRQSA 397
               SCOP domains d2jjpa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhh.eee.....eee.hhhhhhhhhhh...ee.hhhhh.........hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeehhhhh.hhhhhhhhhhhhh.........hhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh....eeeeee...eee..eee....eeeeehhhhhh.....................hhhhh.......hhhhhhhhhhhhhhhhhhhhh..ee....................eee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME-------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jjp A  15 LTTIDEVPGMADETALLDWLGTMREKQPVWQDRYGVWHVFRHADVQTVLRDTATFSSDPTRVIEGASPTPGMIHEIDPPEHRALRKVVSSAFTPRTISDLEPRIRDVTRSLLADAGESFDLVDVLAFPLPVTIVAELLGLPPMDHEQFGDWSGALVDIQMDDPTDPALAERIADVLNPLTAYLKARCAERRADPGDDLISRLVLAEVDGRALDDEEAANFSTALLLAGHITTTVLLGNIVRTLDEHPAHWDAAAEDPGRIPAIVEEVLRYRPPFPQMQRTTTKATEVAGVPIPADVMVNTWVLSANRDSDAHDDPDRFDPSRKSGGAAQLSFGHGVHFCLGAPLARLENRVALEEIIARFGRLTVDRDDERLRHFEQIVLGTRHLPVLAGSSPRQSA 411
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404

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(

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Folds(

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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)

d2jjpa_

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

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

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
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	Ligands, Modified Residues, Ions
		HEM	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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	Cis Peptide Bonds
		Pro A:92 - Pro A:93	[ RasMol ]

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	2jjp
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		Orientation in Membranes	:	OPM
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	ERYK_SACEN \| P48635
		Comparative Protein Structure Models	:	ModBase
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	1.14.-.-
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		Disease Information	:	OMIM

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

2jjn	STRUCTURE OF CLOSED CYTOCHROME P450 ERYK
2jjo	STRUCTURE OF CYTOCHROME P450 ERYK IN COMPLEX WITH ITS NATURAL SUBSTRATE ERD
2vru	STRUCTURE OF OPEN HISTIDINE TAGGED CYTOCHROME P450 ERYK
2vrv	STRUCTURE OF HISTIDINE TAGGED CYTOCHROME P450 ERYK IN COMPLEX WITH INHIBITOR CLOTRIMAZOLE (CLT)
2wio	STRUCTURE OF THE OPEN HISTIDINE TAGGED C. SAVINO, CYTOCHROME P450 ERYK

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

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SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (11, 11)

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