2WI9 - JenaLib

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Asym. Unit - sites (Jmol Viewer)

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Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   SELECTIVE OXIDATION OF CARBOLIDE C-H BONDS BY ENGINEERED MACROLIDE P450 MONOOXYGENASE

Authors :   S. Li, M. R. Chaulagain, A. R. Knauff, L. M. Podust, J. Montgomery, D. H. Sherman

Date :   08 May 09 (Deposition) - 27 Oct 09 (Release) - 24 Nov 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

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

Reference :   S. Li, M. R. Chaulagain, A. R. Knauff, L. M. Podust, J. Montgomery, D. H. Sherman
Selective Oxidation Of Carbolide C-H Bonds By An Engineered Macrolide P450 Mono-Oxygenase.
Proc. Natl. Acad. Sci. Usa V. 106 18463 2009
PubMed-ID: 19833867 | Reference-DOI: 10.1073/PNAS.0907203106

Molecule 1 - CYTOCHROME P450 HYDROXYLASE PIKC
	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
	Mutation	:	YES
	Organism Scientific	:	STREPTOMYCES VENEZUELAE
	Organism Taxid	:	54571
	Synonym	:	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, 7)

No.	Name	Count	Type	Full Name
1	1D2	2	Ligand/Ion	DESOSAMINYL CYCLODODECANE
2	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	1D2	1	Ligand/Ion	DESOSAMINYL CYCLODODECANE
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 5)

No.	Name	Count	Type	Full Name
1	1D2	1	Ligand/Ion	DESOSAMINYL CYCLODODECANE
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (7, 7)

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 , 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 , ALA A:360 , 1D2 A:1409 , HOH A:2294 , HOH A:2295	BINDING SITE FOR RESIDUE HEM A1408
2	AC2	SOFTWARE	LEU A:93 , GLU A:94 , PHE A:178 , VAL A:242 , ALA A:243 , GLU A:246 , ILE A:395 , HEM A:1408 , HOH A:2086 , HOH A:2294 , HOH A:2296	BINDING SITE FOR RESIDUE 1D2 A1409
3	AC3	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 , 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 , ILE B:351 , HIS B:352 , CYS B:354 , ILE B:355 , ALA B:360 , 1D2 B:1409 , HOH B:2276	BINDING SITE FOR RESIDUE HEM B1408
4	AC4	SOFTWARE	GLU B:85 , LEU B:88 , ASN B:91 , LEU B:93 , GLU B:94 , PHE B:178 , HIS B:238 , ILE B:239 , ALA B:243 , GLU B:246 , THR B:247 , THR B:294 , MET B:394 , ILE B:395 , HEM B:1408 , HOH B:2072 , HOH B:2277 , HOH B:2278	BINDING SITE FOR RESIDUE 1D2 B1409
5	AC5	SOFTWARE	ARG B:62 , LEU B:106 , ARG B:109 , THR B:220 , ARG B:227 , HOH B:2279 , HOH B:2280	BINDING SITE FOR RESIDUE SO4 B1410
6	AC6	SOFTWARE	ARG B:60 , ASP B:303 , LEU B:304 , ASP B:305	BINDING SITE FOR RESIDUE SO4 B1411
7	AC7	SOFTWARE	ASP B:167 , TYR B:197 , SER B:204	BINDING SITE FOR RESIDUE SO4 B1412

(no "SS Bond" information available for 2WI9)

Asymmetric Unit

No.	Residues
1	Leu A:20	-	Gly A:21
2	Gly A:21	-	Gln A:22
3	Gln A:22	-	Asp A:23
4	Pro A:97	-	Pro A:98
5	Pro B:97	-	Pro B:98

(no "SAP(SNP)/Variant" information available for 2WI9)

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 2WI9)

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:396
 aligned with PIKC_STRVZ | O87605 from UniProtKB/Swiss-Prot  Length:416

    Alignment length:396
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401      
           PIKC_STRVZ    12 PPVLDLGALGQDFAADPYPTYARLRAEGPAHRVRTPEGDEVWLVVGYDRARAVLADPRFSKDWRNSTTPLTEAEAALNHNMLESDPPRHTRLRKLVAREFTMRRVELLRPRVQEIVDGLVDAMLAAPDGRADLMESLAWPLPITVISELLGVPEPDRAAFRVWTDAFVFPDDPAQAQTAMAEMSGYLSRLIDSKRGQDGEDLLSALVRTSDEDGSRLTSEELLGMAHILLVAGHETTVNLIANGMYALLSHPDQLAALRADMTLLDGAVEEMLRYEGPVESATYRFPVEPVDLDGTVIPAGDTVLVVLADAHRTPERFPDPHRFDIRRDTAGHLAFGHGIHFCIGAPLARLEARIAVRALLERCPDLALDVSPGELVWYPNPMIRGLKALPIRWRR 407
               SCOP domains d2wi9a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 2wi9A00 A:12-407 Cytochrome p450                                                                                                                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee...........hhhhhhhhhhhh.eeeee.....eeeee.hhhhhhhhhh...ee.hhhhh....hhhhhhhh.hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeehhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........ee...eee..eee.....eeehhhhhh................................hhhhhhhhhhhhhhhhhhhh...ee..hhhhh..............eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME--------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2wi9 A  12 PPVLDLGALGQDFAADPYPTYARLRAEGPAHRVRTPEGNEVWLVVGYDRARAVLADPRFSKDWRNSTTPLTEAEAALNHNMLESDPPRHTRLRKLVAREFTMRRVELLRPRVQEIVDGLVDAMLAAPDGRADLMESLAWPLPITVISELLGVPEPDRAAFRVWTDAFVFPDDPAQAQTAMAEMSGYLSRLIDSKRGQDGEDLLSALVRTSDEDGSRLTSEELLGMAHILLVAGHETTVNLIANGMYALLSHPDQLAALRADMTLLDGAVEEMLRYEGPVESATYRFPVEPVDLDGTVIPAGDTVLVVLADAHRTPERFPDPHRFDIRRDTAGHLAFGHGIHFCIGAPLARLEARIAVRALLERCPDLALDVSPGELVWYPNPMIRGLKALPIRWRR 407
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401

Chain B from PDB  Type:PROTEIN  Length:394
 aligned with PIKC_STRVZ | O87605 from UniProtKB/Swiss-Prot  Length:416

    Alignment length:394
                                    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 VLDLGALGQDFAADPYPTYARLRAEGPAHRVRTPEGDEVWLVVGYDRARAVLADPRFSKDWRNSTTPLTEAEAALNHNMLESDPPRHTRLRKLVAREFTMRRVELLRPRVQEIVDGLVDAMLAAPDGRADLMESLAWPLPITVISELLGVPEPDRAAFRVWTDAFVFPDDPAQAQTAMAEMSGYLSRLIDSKRGQDGEDLLSALVRTSDEDGSRLTSEELLGMAHILLVAGHETTVNLIANGMYALLSHPDQLAALRADMTLLDGAVEEMLRYEGPVESATYRFPVEPVDLDGTVIPAGDTVLVVLADAHRTPERFPDPHRFDIRRDTAGHLAFGHGIHFCIGAPLARLEARIAVRALLERCPDLALDVSPGELVWYPNPMIRGLKALPIRWRR 407
               SCOP domains d2wi9b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2wi9B00 B:14-407 Cytochrome p450                                                                                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee....hhhhhhhhhhhhhhhhhhh.eeeee.....eeeee.hhhhhhhhhhh..ee.hhhhh....hhhhhh...hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeehhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........ee...eee..eee.....eeehhhhhh................................hhhhhhhhhhhhhhhhhhhh...ee..hhhhh..............eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME--------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wi9 B  14 VLDLGALGQDFAADPYPTYARLRAEGPAHRVRTPEGNEVWLVVGYDRARAVLADPRFSKDWRNSTTPLTEAEAALNHNMLESDPPRHTRLRKLVAREFTMRRVELLRPRVQEIVDGLVDAMLAAPDGRADLMESLAWPLPITVISELLGVPEPDRAAFRVWTDAFVFPDDPAQAQTAMAEMSGYLSRLIDSKRGQDGEDLLSALVRTSDEDGSRLTSEELLGMAHILLVAGHETTVNLIANGMYALLSHPDQLAALRADMTLLDGAVEEMLRYEGPVESATYRFPVEPVDLDGTVIPAGDTVLVVLADAHRTPERFPDPHRFDIRRDTAGHLAFGHGIHFCIGAPLARLEARIAVRALLERCPDLALDVSPGELVWYPNPMIRGLKALPIRWRR 407
                                    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

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(

)

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)

Streptomyces venezuelae [TaxId: 54571] (11)

1a	d2wi9a_	A:
1b	d2wi9b_	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	2wi9A00	A:12-407
1b	2wi9B00	B:14-407

(no "Pfam Domain" information available for 2WI9)

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.

Asymmetric Unit
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	Cis Peptide Bonds
		Gln A:22 - Asp A:23	[ RasMol ]
		Gly A:21 - Gln A:22	[ RasMol ]
		Leu A:20 - Gly A:21	[ RasMol ]
		Pro A:97 - Pro A:98	[ RasMol ]
		Pro B:97 - Pro B:98	[ RasMol ]

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Access by PDB/NDB ID
	2wi9
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Access by UniProt ID/Accession number
	PIKC_STRVZ \| O87605
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	PIKC_STRVZ \| O87605
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UniProtKB/Swiss-Prot
	PIKC_STRVZ \| O87605	:	2bvj 2c6h 2c7x 2ca0 2cd8 2vz7 2vzm 2whw 3zk5 3zpi 4b7d 4b7s 4bf4 4umz

2bvj	LIGAND-FREE STRUCTURE OF CYTOCHROME P450 PIKC (CYP107L1)
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)
2vz7	CRYSTAL STRUCTURE OF THE YC-17-BOUND PIKC D50N MUTANT
2vzm	CRYSTAL STRUCTURE OF THE NARBOMYCIN-BOUND PIKC D50N MUTANT
2whw	SELECTIVE OXIDATION OF CARBOLIDE C-H BONDS BY ENGINEERED MACROLIDE P450 MONOOXYGENASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

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