2BVJ - JenaLib

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Title :   LIGAND-FREE STRUCTURE OF CYTOCHROME P450 PIKC (CYP107L1)

Authors :   D. H. Sherman, S. Li, L. V. Yermalitskaya, Y. Kim, J. A. Smith, M. R. Waterman, L. M. Podust

Date :   28 Jun 05 (Deposition) - 03 Jul 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Cytochrome P450, Pikc, Cyp107L1, Macrolide Monooxygenase, Antibiotic Biosynthesis, Heme, Iron, Metal-Binding, Monooxygenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. H. Sherman, S. Li, L. V. Yermalitskaya, Y. Kim, J. A. Smith, M. R. Waterman, L. M. Podust
The Structural Basis For Substrate Anchoring, Active Site Selectivity, And Product Formation By P450 Pikc From Streptomyces Venezuelae.
J. Biol. Chem. V. 281 26289 2006
PubMed-ID: 16825192 | Reference-DOI: 10.1074/JBC.M605478200

Molecule 1 - CYTOCHROME P450 MONOOXYGENASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	HMS174(DE3)
	Expression System Taxid	:	562
	Expression System Vector	:	PET
	Organism Scientific	:	STREPTOMYCES VENEZUELAE
	Organism Taxid	:	54571
	Synonym	:	CYTOCHROME P450 PIKC CYP107L1, CYTOCHROME P450 HYDROXYLASE PIKC

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 5)

No.	Name	Count	Type	Full Name
1	BME	2	Ligand/Ion	BETA-MERCAPTOETHANOL
2	DTT	1	Ligand/Ion	2,3-DIHYDROXY-1,4-DITHIOBUTANE
3	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL
2	DTT	1	Ligand/Ion	2,3-DIHYDROXY-1,4-DITHIOBUTANE
3	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL
2	DTT	-1	Ligand/Ion	2,3-DIHYDROXY-1,4-DITHIOBUTANE
3	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:72 , MET A:92 , LEU A:93 , HIS A:100 , ARG A:104 , PHE A:111 , ALA A:243 , GLY A:244 , THR A:247 , THR A:248 , LEU A:251 , PRO A:289 , ALA A:293 , THR A:294 , ARG A:296 , ALA A:346 , PHE A:347 , GLY A:348 , ILE A:351 , HIS A:352 , CYS A:354 , ILE A:355 , GLY A:356 , ALA A:360 , HOH A:2087 , HOH A:2144	BINDING SITE FOR RESIDUE HEM A1408
2	AC2	SOFTWARE	LEU A:135 , ARG A:374 , CYS A:375 , TRP A:405 , HOH A:2143	BINDING SITE FOR RESIDUE BME A1409
3	AC3	SOFTWARE	ARG A:120 , ASP A:277 , ARG A:365 , ARG A:369 , HOH A:2098 , GLY B:21 , GLN B:22	BINDING SITE FOR RESIDUE DTT A1410
4	AC4	SOFTWARE	LYS B:72 , MET B:92 , LEU B:93 , HIS B:100 , ARG B:104 , PHE B:111 , LEU B:240 , ALA B:243 , GLY B:244 , THR B:247 , THR B:248 , LEU B:251 , ALA B:293 , THR B:294 , ARG B:296 , ALA B:346 , PHE B:347 , GLY B:348 , HIS B:352 , CYS B:354 , ILE B:355 , ALA B:360 , HOH B:2101 , HOH B:2140	BINDING SITE FOR RESIDUE HEM B1408
5	AC5	SOFTWARE	LEU B:135 , ARG B:374 , CYS B:375 , TRP B:405 , HOH B:2168 , HOH B:2169	BINDING SITE FOR RESIDUE BME B1409

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

Asymmetric Unit

No.	Residues
1	Pro A:97	-	Pro A:98
2	Pro B:97	-	Pro B:98

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTOCHROME_P450	PS00086	Cytochrome P450 cysteine heme-iron ligand signature.	PIKC_STRVZ	347-356	2	A:347-356 B:347-356

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTOCHROME_P450	PS00086	Cytochrome P450 cysteine heme-iron ligand signature.	PIKC_STRVZ	347-356	1	A:347-356 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTOCHROME_P450	PS00086	Cytochrome P450 cysteine heme-iron ligand signature.	PIKC_STRVZ	347-356	1	- B:347-356

(no "Exon" information available for 2BVJ)

Asymmetric 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:395
 aligned with PIKC_STRVZ | O87605 from UniProtKB/Swiss-Prot  Length:416

    Alignment length:395
                                    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       403     
           PIKC_STRVZ    14 VLDLGALGQDFAADPYPTYARLRAEGPAHRVRTPEGDEVWLVVGYDRARAVLADPRFSKDWRNSTTPLTEAEAALNHNMLESDPPRHTRLRKLVAREFTMRRVELLRPRVQEIVDGLVDAMLAAPDGRADLMESLAWPLPITVISELLGVPEPDRAAFRVWTDAFVFPDDPAQAQTAMAEMSGYLSRLIDSKRGQDGEDLLSALVRTSDEDGSRLTSEELLGMAHILLVAGHETTVNLIANGMYALLSHPDQLAALRADMTLLDGAVEEMLRYEGPVESATYRFPVEPVDLDGTVIPAGDTVLVVLADAHRTPERFPDPHRFDIRRDTAGHLAFGHGIHFCIGAPLARLEARIAVRALLERCPDLALDVSPGELVWYPNPMIRGLKALPIRWRRG 408
               SCOP domains d2bvja_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2bvjA00 A:14-408 Cytochrome p450                                                                                                                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...hhhhhhhhhhhhhhhhhhhh.eeeee.....eeeee.hhhhhhhhhhh..ee.hhhhh....hhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeehhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........ee...eee..eee.....eeehhhhhh................................hhhhhhhhhhhhhhhhhhhh...ee..hhhhh..............eee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME---------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bvj A  14 VLDLGALGQDFAADPYPTYARLRAEGPAHRVRTPEGDEVWLVVGYDRARAVLADPRFSKDWRNSTTPLTEAEAALNHNMLESDPPRHTRLRKLVAREFTMRRVELLRPRVQEIVDGLVDAMLAAPDGRADLMESLAWPLPITVISELLGVPEPDRAAFRVWTDAFVFPDDPAQAQTAMAEMSGYLSRLIDSKRGQDGEDLLSALVRTSDEDGSRLTSEELLGMAHILLVAGHETTVNLIANGMYALLSHPDQLAALRADMTLLDGAVEEMLRYEGPVESATYRFPVEPVDLDGTVIPAGDTVLVVLADAHRTPERFPDPHRFDIRRDTAGHLAFGHGIHFCIGAPLARLEARIAVRALLERCPDLALDVSPGELVWYPNPMIRGLKALPIRWRRG 408
                                    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       403

Chain B from PDB  Type:PROTEIN  Length:392
 aligned with PIKC_STRVZ | O87605 from UniProtKB/Swiss-Prot  Length:416

    Alignment length:398
                                    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       400        
           PIKC_STRVZ    11 SPPVLDLGALGQDFAADPYPTYARLRAEGPAHRVRTPEGDEVWLVVGYDRARAVLADPRFSKDWRNSTTPLTEAEAALNHNMLESDPPRHTRLRKLVAREFTMRRVELLRPRVQEIVDGLVDAMLAAPDGRADLMESLAWPLPITVISELLGVPEPDRAAFRVWTDAFVFPDDPAQAQTAMAEMSGYLSRLIDSKRGQDGEDLLSALVRTSDEDGSRLTSEELLGMAHILLVAGHETTVNLIANGMYALLSHPDQLAALRADMTLLDGAVEEMLRYEGPVESATYRFPVEPVDLDGTVIPAGDTVLVVLADAHRTPERFPDPHRFDIRRDTAGHLAFGHGIHFCIGAPLARLEARIAVRALLERCPDLALDVSPGELVWYPNPMIRGLKALPIRWRRG 408
               SCOP domains d2bvjb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2bvjB00 B:11-408 Cytochrome p450                                                                                                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.hhhhhhhhhhhhhhhhhhhhhh.eeeee.....eeeee.hhhhhhhhhhh..ee.hhhhh....------...hhhhh..hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.....eeehhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........ee...eee..eee.....eeehhhhhh................................hhhhhhhhhhhhhhhhhhhh...ee..hhhhh..............eee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME---------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bvj B  11 SPPVLDLGALGQDFAADPYPTYARLRAEGPAHRVRTPEGDEVWLVVGYDRARAVLADPRFSKDWRNSTTPL------LNHNMLESDPPRHTRLRKLVAREFTMRRVELLRPRVQEIVDGLVDAMLAAPDGRADLMESLAWPLPITVISELLGVPEPDRAAFRVWTDAFVFPDDPAQAQTAMAEMSGYLSRLIDSKRGQDGEDLLSALVRTSDEDGSRLTSEELLGMAHILLVAGHETTVNLIANGMYALLSHPDQLAALRADMTLLDGAVEEMLRYEGPVESATYRFPVEPVDLDGTVIPAGDTVLVVLADAHRTPERFPDPHRFDIRRDTAGHLAFGHGIHFCIGAPLARLEARIAVRALLERCPDLALDVSPGELVWYPNPMIRGLKALPIRWRRG 408
                                    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       400        
                                                                                                 81     88

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 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)

Streptomyces venezuelae [TaxId: 54571] (11)

1a	d2bvja_	A:
1b	d2bvjb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Cytochrome p450 (271)

Homologous Superfamily: Cytochrome p450 (271)

Streptomyces venezuelae. Organism_taxid: 54571. (9)

1a	2bvjA00	A:14-408
1b	2bvjB00	B:11-408

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (PIKC_STRVZ | O87605)

molecular function
	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.
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.

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	2bvj
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	PIKC_STRVZ \| O87605
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	PIKC_STRVZ \| O87605	:	2c6h 2c7x 2ca0 2cd8 2vz7 2vzm 2whw 2wi9 3zk5 3zpi 4b7d 4b7s 4bf4 4umz

2c6h	CRYSTAL STRUCTURE OF YC-17-BOUND CYTOCHROME P450 PIKC (CYP107L1)
2c7x	CRYSTAL STRUCTURE OF NARBOMYCIN-BOUND CYTOCHROME P450 PIKC (CYP107L1)
2ca0	CRYSTAL STRUCTURE OF YC-17-BOUND CYTOCHROME P450 PIKC (CYP107L1)
2cd8	CRYSTAL STRUCTURE OF YC-17-BOUND CYTOCHROME P450 PIKC (CYP107L1)

Description

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Ligands, Modified Residues, Ions (3, 5)

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Cis Peptide Bonds (2, 2)

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