4B7S - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   PIKC D50N MUTANT BOUND TO THE 10-DML ANALOG WITH THE 3-(N,N-DIMETHYLAMINO)PROPANOATE ANCHORING GROUP

Authors :   L. M. Podust

Date :   21 Aug 12 (Deposition) - 28 Aug 13 (Release) - 16 Apr 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.84

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

Keywords :   Oxidoreductase, Monooxygenase, Pikromycin Biosynthesis, Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Negretti, A. R. H. Narayan, K. C. Chiou, P. M. Kells, J. L. Stachowski D. A. Hansen, L. M. Podust, J. Montgomery, D. H. Sherman
Directing Group-Controlled Regioselectivity In An Enzymatic C-H Bond Oxygenation.
J. Am. Chem. Soc. V. 136 4901 2014
PubMed-ID: 24627965 | Reference-DOI: 10.1021/JA5016052

Molecule 1 - CYTOCHROME P450 HYDROXYLASE PIKC
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	HMS174(DE3)
	Expression System Taxid	:	562
	Expression System Vector	:	PET28B
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	STREPTOMYCES VENEZUELAE
	Organism Taxid	:	54571
	Other Details	:	THIOLATE LINK BETWEEN C 354 AND HEM 1407
	Synonym	:	PIKC, CYTOCHROME P450 MONOOXYGENASE

		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 (4, 19)

No.	Name	Count	Type	Full Name
1	GOL	7	Ligand/Ion	GLYCEROL
2	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	QLE	2	Ligand/Ion	[(3R,4S,5S,7R,9E,11R,12R)-12-ETHYL-3,5,7,11-TETRAMETHYL-2,8-BIS(OXIDANYLIDENE)-1-XACYCLODODEC-9-EN-4-YL] 3-(DIMETHYLAMINO)PROPANOATE
4	SO4	8	Ligand/Ion	SULFATE ION

Biological Unit 1 (4, 14)

No.	Name	Count	Type	Full Name
1	GOL	6	Ligand/Ion	GLYCEROL
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	QLE	1	Ligand/Ion	[(3R,4S,5S,7R,9E,11R,12R)-12-ETHYL-3,5,7,11-TETRAMETHYL-2,8-BIS(OXIDANYLIDENE)-1-XACYCLODODEC-9-EN-4-YL] 3-(DIMETHYLAMINO)PROPANOATE
4	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 2 (4, 5)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	QLE	1	Ligand/Ion	[(3R,4S,5S,7R,9E,11R,12R)-12-ETHYL-3,5,7,11-TETRAMETHYL-2,8-BIS(OXIDANYLIDENE)-1-XACYCLODODEC-9-EN-4-YL] 3-(DIMETHYLAMINO)PROPANOATE
4	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (19, 19)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LYS A:72 , MET A:92 , LEU A:93 , HIS A:100 , ARG A:104 , PHE A:111 , ILE A:157 , 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:2373	BINDING SITE FOR RESIDUE HEM A1407
02	AC2	SOFTWARE	GLU A:85 , GLU A:94 , PHE A:178 , VAL A:179 , HIS A:238 , ILE A:239 , VAL A:242 , ALA A:243 , THR A:294 , MET A:394 , ILE A:395 , GOL A:1415	BINDING SITE FOR RESIDUE QLE A1408
03	AC3	SOFTWARE	MET B:92 , LEU B:93 , HIS B:100 , ARG B:104 , PHE B:111 , ALA B:243 , GLY B:244 , THR B:247 , THR B:248 , LEU B:251 , PRO B:289 , 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 , HOH B:2307	BINDING SITE FOR RESIDUE HEM B1407
04	AC4	SOFTWARE	GLU B:85 , ASN B:89 , LEU B:93 , GLU B:94 , PHE B:178 , VAL B:179 , HIS B:238 , ILE B:239 , VAL B:242 , ALA B:243 , GLU B:246 , THR B:247 , THR B:294 , MET B:394 , ILE B:395 , GOL B:1411 , HOH B:2194	BINDING SITE FOR RESIDUE QLE B1408
05	AC5	SOFTWARE	LEU A:106 , THR A:220 , ARG A:227	BINDING SITE FOR RESIDUE SO4 A1409
06	AC6	SOFTWARE	ARG A:114 , ARG A:115 , HOH A:2186	BINDING SITE FOR RESIDUE SO4 A1410
07	AC7	SOFTWARE	VAL A:173 , GLU A:193 , HOH A:2396 , HOH A:2397 , HOH A:2398 , ARG B:75	BINDING SITE FOR RESIDUE SO4 A1411
08	AC8	SOFTWARE	THR B:112 , ARG B:114 , HOH B:2143	BINDING SITE FOR RESIDUE SO4 B1409
09	AC9	SOFTWARE	HIS B:262 , PRO B:263 , ASP B:264 , GLN B:265 , ARG B:334	BINDING SITE FOR RESIDUE SO4 B1410
10	BC1	SOFTWARE	ARG A:36 , PRO A:326 , HOH A:2044	BINDING SITE FOR RESIDUE SO4 A1412
11	BC2	SOFTWARE	ARG A:75 , HIS A:90 , ARG A:99 , HOH A:2117 , HOH A:2157	BINDING SITE FOR RESIDUE SO4 A1413
12	BC3	SOFTWARE	GLU A:223 , ASP A:224 , HOH A:2304	BINDING SITE FOR RESIDUE SO4 A1414
13	BC4	SOFTWARE	THR A:294 , TYR A:295 , QLE A:1408 , HOH A:2122	BINDING SITE FOR RESIDUE GOL A1415
14	BC5	SOFTWARE	THR B:294 , TYR B:295 , MET B:394 , QLE B:1408 , HOH B:2115	BINDING SITE FOR RESIDUE GOL B1411
15	BC6	SOFTWARE	PRO A:98 , ARG A:99 , ARG A:102 , HOH A:2167 , HOH A:2399	BINDING SITE FOR RESIDUE GOL A1416
16	BC7	SOFTWARE	TYR A:29 , ASN A:254 , TYR A:257 , TYR A:286 , GLU A:287 , ARG A:324 , TRP A:389 , ARG A:396 , HOH A:2339	BINDING SITE FOR RESIDUE GOL A1417
17	BC8	SOFTWARE	ARG A:361 , ARG A:365 , HOH A:2382	BINDING SITE FOR RESIDUE GOL A1418
18	BC9	SOFTWARE	ARG A:62 , HIS A:349 , HOH A:2401 , HOH A:2402	BINDING SITE FOR RESIDUE GOL A1419
19	CC1	SOFTWARE	VAL A:14 , LEU A:15 , ARG A:34 , GLU A:38 , HOH A:2048	BINDING SITE FOR RESIDUE GOL A1420

(no "SS Bond" information available for 4B7S)

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 4B7S)

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 4B7S)

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:397
 aligned with PIKC_STRVZ | O87605 from UniProtKB/Swiss-Prot  Length:416

    Alignment length:397
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       
           PIKC_STRVZ    10 ASPPVLDLGALGQDFAADPYPTYARLRAEGPAHRVRTPEGDEVWLVVGYDRARAVLADPRFSKDWRNSTTPLTEAEAALNHNMLESDPPRHTRLRKLVAREFTMRRVELLRPRVQEIVDGLVDAMLAAPDGRADLMESLAWPLPITVISELLGVPEPDRAAFRVWTDAFVFPDDPAQAQTAMAEMSGYLSRLIDSKRGQDGEDLLSALVRTSDEDGSRLTSEELLGMAHILLVAGHETTVNLIANGMYALLSHPDQLAALRADMTLLDGAVEEMLRYEGPVESATYRFPVEPVDLDGTVIPAGDTVLVVLADAHRTPERFPDPHRFDIRRDTAGHLAFGHGIHFCIGAPLARLEARIAVRALLERCPDLALDVSPGELVWYPNPMIRGLKALPIRWR 406
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee...hhhhhhhhhhhhhhhhhhhh.eeeee.....eeeee.hhhhhhhhhhh..ee.hhhhh......hhhhh..hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeehhhhh.hhhhhhhhhhhhh.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
                 4b7s A  10 ASPPVLDLGALGQDFAADPYPTYARLRAEGPAHRVRTPEGNEVWLVVGYDRARAVLADPRFSKDWRNSTTPLTEAEAALNHNMLESDPPRHTRLRKLVAREFTMRRVELLRPRVQEIVDGLVDAMLAAPDGRADLMESLAWPLPITVISELLGVPEPDRAAFRVWTDAFVFPDDPAQAQTAMAEMSGYLSRLIDSKRGQDGEDLLSALVRTSDEDGSRLTSEELLGMAHILLVAGHETTVNLIANGMYALLSHPDQLAALRADMTLLDGAVEEMLRYEGPVESATYRFPVEPVDLDGTVIPAGDTVLVVLADAHRTPERFPDPHRFDIRRDTAGHLAFGHGIHFCIGAPLARLEARIAVRALLERCPDLALDVSPGELVWYPNPMIRGLKALPIRWR 406
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399

Chain B from PDB  Type:PROTEIN  Length:393
 aligned with PIKC_STRVZ | O87605 from UniProtKB/Swiss-Prot  Length:416

    Alignment length:393
                                    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 VLDLGALGQDFAADPYPTYARLRAEGPAHRVRTPEGDEVWLVVGYDRARAVLADPRFSKDWRNSTTPLTEAEAALNHNMLESDPPRHTRLRKLVAREFTMRRVELLRPRVQEIVDGLVDAMLAAPDGRADLMESLAWPLPITVISELLGVPEPDRAAFRVWTDAFVFPDDPAQAQTAMAEMSGYLSRLIDSKRGQDGEDLLSALVRTSDEDGSRLTSEELLGMAHILLVAGHETTVNLIANGMYALLSHPDQLAALRADMTLLDGAVEEMLRYEGPVESATYRFPVEPVDLDGTVIPAGDTVLVVLADAHRTPERFPDPHRFDIRRDTAGHLAFGHGIHFCIGAPLARLEARIAVRALLERCPDLALDVSPGELVWYPNPMIRGLKALPIRWR 406
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...hhhhhhhhhhhhhhhhhhhh.eeeee.....eeeee.hhhhhhhhhhh..ee.hhhhh....hhhhhh...hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....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
                 4b7s B  14 VLDLGALGQDFAADPYPTYARLRAEGPAHRVRTPEGNEVWLVVGYDRARAVLADPRFSKDWRNSTTPLTEAEAALNHNMLESDPPRHTRLRKLVAREFTMRRVELLRPRVQEIVDGLVDAMLAAPDGRADLMESLAWPLPITVISELLGVPEPDRAAFRVWTDAFVFPDDPAQAQTAMAEMSGYLSRLIDSKRGQDGEDLLSALVRTSDEDGSRLTSEELLGMAHILLVAGHETTVNLIANGMYALLSHPDQLAALRADMTLLDGAVEEMLRYEGPVESATYRFPVEPVDLDGTVIPAGDTVLVVLADAHRTPERFPDPHRFDIRRDTAGHLAFGHGIHFCIGAPLARLEARIAVRALLERCPDLALDVSPGELVWYPNPMIRGLKALPIRWR 406
                                    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 '\|'

(no "SCOP Domain" information available for 4B7S)

(no "CATH Domain" information available for 4B7S)

(no "Pfam Domain" information available for 4B7S)

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
		Pro A:97 - Pro A:98	[ RasMol ]
		Pro B:97 - Pro B:98	[ RasMol ]

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	4b7s
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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 2wi9 3zk5 3zpi 4b7d 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
2wi9	SELECTIVE OXIDATION OF CARBOLIDE C-H BONDS BY ENGINEERED MACROLIDE P450 MONOOXYGENASE
3zk5	PIKC D50N MUTANT BOUND TO THE 10-DML ANALOG WITH THE 3-(N,N-DIMETHYLAMINO)ETHANOATE ANCHORING GROUP
4b7d	PIKC BOUND TO THE 10-DML ANALOG WITH THE 3-(N,N -DIMETHYLAMINO)PROPANOATE ANCHORING GROUP

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 19)

Sites (19, 19)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

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