2VZM - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE NARBOMYCIN-BOUND PIKC D50N MUTANT

Authors :   S. Li, D. H. Sherman, L. M. Podust

Date :   01 Aug 08 (Deposition) - 12 Aug 08 (Release) - 03 Mar 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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

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

Reference :   S. Li, H. Ouellet, D. H. Sherman, L. M. Podust
Analysis Of Transient And Catalytic Desosamine Binding Pockets In Cytochrome P450 Pikc From Streptomyces Venezuelae.
J. Biol. Chem. V. 284 5723 2009
PubMed-ID: 19124459 | Reference-DOI: 10.1074/JBC.M807592200

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
	Mutation	:	YES
	Organism Scientific	:	STREPTOMYCES VENEZUELAE
	Organism Taxid	:	54571
	Synonym	:	PIKC, 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 (2, 4)

No.	Name	Count	Type	Full Name
1	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	NRB	2	Ligand/Ion	NARBOMYCIN

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	NRB	1	Ligand/Ion	NARBOMYCIN

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	NRB	1	Ligand/Ion	NARBOMYCIN

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	MET A:92 , LEU A:93 , HIS A:100 , ARG A:104 , PHE A:111 , ILE A:157 , 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:2323	BINDING SITE FOR RESIDUE HEM A 1407
2	AC2	SOFTWARE	LYS B:72 , MET B:92 , LEU B:93 , HIS B:100 , ARG B:104 , LEU B:240 , 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 , GLY B:356 , ALA B:360 , HOH B:2316	BINDING SITE FOR RESIDUE HEM B 1407
3	AC3	SOFTWARE	GLU A:85 , GLU A:94 , PHE A:178 , MET A:191 , HIS A:238 , ILE A:239 , ALA A:243 , GLU A:246 , THR A:294 , TYR A:295 , MET A:394 , ILE A:395 , HOH A:2233	BINDING SITE FOR RESIDUE NRB A 1408
4	AC4	SOFTWARE	GLU B:85 , GLU B:94 , PHE B:178 , MET B:191 , HIS B:238 , ILE B:239 , ALA B:243 , THR B:294 , ASN B:392 , MET B:394 , ILE B:395 , HOH B:2318	BINDING SITE FOR RESIDUE NRB B 1408

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

Asymmetric Unit

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

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

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 2VZM)

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
                                    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 PPVLDLGALGQDFAADPYPTYARLRAEGPAHRVRTPEGDEVWLVVGYDRARAVLADPRFSKDWRNSTTPLTEAEAALNHNMLESDPPRHTRLRKLVAREFTMRRVELLRPRVQEIVDGLVDAMLAAPDGRADLMESLAWPLPITVISELLGVPEPDRAAFRVWTDAFVFPDDPAQAQTAMAEMSGYLSRLIDSKRGQDGEDLLSALVRTSDEDGSRLTSEELLGMAHILLVAGHETTVNLIANGMYALLSHPDQLAALRADMTLLDGAVEEMLRYEGPVESATYRFPVEPVDLDGTVIPAGDTVLVVLADAHRTPERFPDPHRFDIRRDTAGHLAFGHGIHFCIGAPLARLEARIAVRALLERCPDLALDVSPGELVWYPNPMIRGLKALPIRWR 406
               SCOP domains d2vzma_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2vzmA00 A:12-406 Cytochrome p450                                                                                                                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee...........hhhhhhhhhhhh.eeeee.....eeeee.hhhhhhhhhhh..ee.hhhhh....hhhhhh...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
                 2vzm A  12 PPVLDLGALGQDFAADPYPTYARLRAEGPAHRVRTPEGNEVWLVVGYDRARAVLADPRFSKDWRNSTTPLTEAEAALNHNMLESDPPRHTRLRKLVAREFTMRRVELLRPRVQEIVDGLVDAMLAAPDGRADLMESLAWPLPITVISELLGVPEPDRAAFRVWTDAFVFPDDPAQAQTAMAEMSGYLSRLIDSKRGQDGEDLLSALVRTSDEDGSRLTSEELLGMAHILLVAGHETTVNLIANGMYALLSHPDQLAALRADMTLLDGAVEEMLRYEGPVESATYRFPVEPVDLDGTVIPAGDTVLVVLADAHRTPERFPDPHRFDIRRDTAGHLAFGHGIHFCIGAPLARLEARIAVRALLERCPDLALDVSPGELVWYPNPMIRGLKALPIRWR 406
                                    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
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402    
           PIKC_STRVZ    13 PVLDLGALGQDFAADPYPTYARLRAEGPAHRVRTPEGDEVWLVVGYDRARAVLADPRFSKDWRNSTTPLTEAEAALNHNMLESDPPRHTRLRKLVAREFTMRRVELLRPRVQEIVDGLVDAMLAAPDGRADLMESLAWPLPITVISELLGVPEPDRAAFRVWTDAFVFPDDPAQAQTAMAEMSGYLSRLIDSKRGQDGEDLLSALVRTSDEDGSRLTSEELLGMAHILLVAGHETTVNLIANGMYALLSHPDQLAALRADMTLLDGAVEEMLRYEGPVESATYRFPVEPVDLDGTVIPAGDTVLVVLADAHRTPERFPDPHRFDIRRDTAGHLAFGHGIHFCIGAPLARLEARIAVRALLERCPDLALDVSPGELVWYPNPMIRGLKALPIRWR 406
               SCOP domains d2vzmb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2vzmB00 B:13-406 Cytochrome p450                                                                                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.hhhhhhhhhhhhhhhhhhhhhh.eeeee.....eeeee.hhhhhhhhhhh..ee.hhhhh....hhhhhh...hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeehhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........ee...eee..eee.....eeehhhhhhh...............................hhhhhhhhhhhhhhhhhhhh...ee.....................eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME-------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vzm B  13 PVLDLGALGQDFAADPYPTYARLRAEGPAHRVRTPEGNEVWLVVGYDRARAVLADPRFSKDWRNSTTPLTEAEAALNHNMLESDPPRHTRLRKLVAREFTMRRVELLRPRVQEIVDGLVDAMLAAPDGRADLMESLAWPLPITVISELLGVPEPDRAAFRVWTDAFVFPDDPAQAQTAMAEMSGYLSRLIDSKRGQDGEDLLSALVRTSDEDGSRLTSEELLGMAHILLVAGHETTVNLIANGMYALLSHPDQLAALRADMTLLDGAVEEMLRYEGPVESATYRFPVEPVDLDGTVIPAGDTVLVVLADAHRTPERFPDPHRFDIRRDTAGHLAFGHGIHFCIGAPLARLEARIAVRALLERCPDLALDVSPGELVWYPNPMIRGLKALPIRWR 406
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402

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( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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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	d2vzma_	A:
1b	d2vzmb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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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	2vzmA00	A:12-406
1b	2vzmB00	B:13-406

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

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

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Access by PDB/NDB ID
	2vzm
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	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 2whw 2wi9 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)
2vsj	CRYSTAL STRUCTURE OF THE YC-17-BOUND PIKC D50N MUTANT
2vz7	CRYSTAL STRUCTURE OF THE YC-17-BOUND PIKC D50N MUTANT

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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)

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Gene Ontology (9, 9)

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