2Y5N - JenaLib

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Title :   STRUCTURE OF THE MIXED-FUNCTION P450 MYCG IN COMPLEX WITH MYCINAMICIN V IN P21 SPACE GROUP

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

Date :   15 Jan 11 (Deposition) - 01 Feb 12 (Release) - 14 Nov 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.62

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

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

Reference :   S. Li, D. R. Tietz, F. U. Rutaganira, P. M. Kells, Y. Anzai, F. Kato, T. C. Pochapsky, D. H. Sherman, L. M. Podust
Substrate Recognition By The Multifunctional Cytochrome P450 Mycg In Mycinamicin Hydroxylation And Epoxidation Reactions.
J. Biol. Chem. V. 287 37880 2012
PubMed-ID: 22952225 | Reference-DOI: 10.1074/JBC.M112.410340

Molecule 1 - P-450-LIKE PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	MICROMONOSPORA GRISEORUBIDA
	Organism Taxid	:	28040
	Synonym	:	MYCG

		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, 18)

No.	Name	Count	Type	Full Name
1	GOL	13	Ligand/Ion	GLYCEROL
2	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	MG	1	Ligand/Ion	MAGNESIUM ION
4	MYV	2	Ligand/Ion	MYCINAMICIN V

Biological Unit 1 (3, 10)

No.	Name	Count	Type	Full Name
1	GOL	8	Ligand/Ion	GLYCEROL
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	MYV	1	Ligand/Ion	MYCINAMICIN V

Biological Unit 2 (3, 7)

No.	Name	Count	Type	Full Name
1	GOL	5	Ligand/Ion	GLYCEROL
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	MYV	1	Ligand/Ion	MYCINAMICIN V

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LEU A:83 , LEU A:84 , HIS A:91 , ARG A:95 , PHE A:102 , ALA A:234 , GLY A:235 , SER A:238 , THR A:239 , GLN A:242 , PHE A:286 , ARG A:288 , GLY A:338 , PHE A:339 , GLY A:340 , HIS A:344 , CYS A:346 , LEU A:347 , GLY A:348 , ALA A:352 , MYV A:460 , HOH A:2397 , HOH A:2566 , HOH A:2567	BINDING SITE FOR RESIDUE HEM A 450
02	AC2	SOFTWARE	ARG A:75 , VAL A:79 , GLY A:81 , GLY A:82 , LEU A:84 , PHE A:168 , VAL A:174 , MET A:179 , VAL A:233 , ALA A:234 , LEU A:386 , HEM A:450 , HOH A:2313 , HOH A:2399 , HOH A:2569 , HOH A:2570 , HOH A:2571	BINDING SITE FOR RESIDUE MYV A 460
03	AC3	SOFTWARE	ARG A:113 , GLU A:120 , ARG A:145 , SER A:155 , HIS A:158 , HOH A:2572	BINDING SITE FOR RESIDUE GOL A1398
04	AC4	SOFTWARE	THR A:18 , LEU A:19 , ALA A:20 , GLY A:21 , HOH A:2573	BINDING SITE FOR RESIDUE GOL A1399
05	AC5	SOFTWARE	GLU A:292 , HOH A:2575 , HOH A:2576	BINDING SITE FOR RESIDUE GOL A1400
06	AC6	SOFTWARE	GLY A:191 , ASP A:195 , HOH A:2346 , HOH A:2578	BINDING SITE FOR RESIDUE GOL A1401
07	AC7	SOFTWARE	ARG A:140 , THR A:240 , THR A:241 , ALA A:244 , GLY A:389 , PRO A:390 , LEU A:391 , HOH A:2579	BINDING SITE FOR RESIDUE GOL A1402
08	AC8	SOFTWARE	ARG A:140 , THR A:171 , LEU A:391 , HOH A:2311 , HOH A:2561 , HOH A:2581 , HOH A:2582	BINDING SITE FOR RESIDUE GOL A1403
09	AC9	SOFTWARE	ASP A:325 , HOH A:2483 , HOH A:2485	BINDING SITE FOR RESIDUE GOL A1404
10	BC1	SOFTWARE	ARG A:73 , THR A:74 , VAL A:282 , GLY A:283 , ALA A:285 , MET A:385 , LEU A:386 , HOH A:2439 , HOH A:2583 , HOH A:2584	BINDING SITE FOR RESIDUE GOL A1405
11	BC2	SOFTWARE	HOH A:2103 , HOH A:2251 , HOH A:2260 , HOH A:2263	BINDING SITE FOR RESIDUE MG A1406
12	BC3	SOFTWARE	LEU B:83 , LEU B:84 , HIS B:91 , ARG B:95 , PHE B:102 , ALA B:234 , GLY B:235 , SER B:238 , THR B:239 , ALA B:285 , PHE B:286 , ARG B:288 , GLY B:338 , PHE B:339 , GLY B:340 , HIS B:344 , CYS B:346 , GLY B:348 , MYV B:460 , HOH B:2381 , HOH B:2543	BINDING SITE FOR RESIDUE HEM B 450
13	BC4	SOFTWARE	ARG B:75 , GLU B:77 , VAL B:79 , GLY B:81 , GLY B:82 , LEU B:83 , LEU B:84 , PHE B:168 , SER B:170 , VAL B:174 , MET B:179 , VAL B:233 , ALA B:234 , LEU B:386 , HEM B:450 , HOH B:2545 , HOH B:2546 , HOH B:2547	BINDING SITE FOR RESIDUE MYV B 460
14	BC5	SOFTWARE	ARG B:253 , GLU B:255 , ILE B:327 , HOH B:2464 , HOH B:2469	BINDING SITE FOR RESIDUE GOL B1398
15	BC6	SOFTWARE	ARG B:140 , THR B:240 , THR B:241 , ALA B:244 , GLY B:389 , PRO B:390 , LEU B:391 , HOH B:2548	BINDING SITE FOR RESIDUE GOL B1399
16	BC7	SOFTWARE	LEU B:56 , GLY B:57 , GLY B:59 , PHE B:61 , PRO B:88 , GLY B:342 , VAL B:343 , HOH B:2201 , HOH B:2549	BINDING SITE FOR RESIDUE GOL B1400
17	BC8	SOFTWARE	THR B:2 , ARG B:34 , GLU B:41 , GLU B:42 , ALA B:43 , TRP B:44 , GLU B:305 , PRO B:306 , HOH B:2551	BINDING SITE FOR RESIDUE GOL B1401
18	BC9	SOFTWARE	TYR B:248 , THR B:252 , ARG B:253 , GLU B:376 , HOH B:2552 , HOH B:2553	BINDING SITE FOR RESIDUE GOL B1402

(no "SS Bond" information available for 2Y5N)

Asymmetric Unit

No.	Residues
1	Tyr A:9	-	Pro A:10
2	Pro A:88	-	Pro A:89
3	Gln A:130	-	Pro A:131
4	Thr A:332	-	Pro A:333
5	Tyr B:9	-	Pro B:10
6	Pro B:88	-	Pro B:89
7	Gln B:130	-	Pro B:131
8	Thr B:332	-	Pro B:333

(no "SAP(SNP)/Variant" information available for 2Y5N)

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.	MYCG_MICGR	339-348	2	A:339-348 B:339-348

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.	MYCG_MICGR	339-348	1	A:339-348 -

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.	MYCG_MICGR	339-348	1	- B:339-348

(no "Exon" information available for 2Y5N)

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:394
 aligned with MYCG_MICGR | Q59523 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:394
                                    13        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    
           MYCG_MICGR     4 AEPRAYPFNDVHGLTLAGRYGELQETEPVSRVRPPYGEEAWLVTRYEDVRAVLGDGRFVRGPSMTRDEPRTRPEMVKGGLLSMDPPEHSRLRRLVVKAFTARRAESLRPRAREIAHELVDQMAATGQPADLVAMFARQLPVRVICELLGVPSADHDRFTRWSGAFLSTAEVTAEEMQEAAEQAYAYMGDLIDRRRKEPTDDLVSALVQARDQQDSLSEQELLDLAIGLLVAGYESTTTQIADFVYLLMTRPELRRQLLDRPELIPSAVEELTRWVPLGVGTAFPRYAVEDVTLRGVTIRAGEPVLASTGAANRDQAQFPDADRIDVDRTPNQHLGFGHGVHHCLGAPLARVELQVALEVLLQRLPGIRLGIPETQLRWSEGMLLRGPLELPVVW 397
               SCOP domains d2y5na_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee...........hhhhhhhhhhh.eeeee......eeee.hhhhhhhhhh...eehhhhhh.............hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhh..hhhhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.........eee...eee..eee....eeeehhhhhh................................hhhhhhhhhhhhhhhhhhhh...ee..hhhhh..............eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y5n A   4 AEPRAYPFNDVHGLTLAGRYGELQETEPVSRVRPPYGEEAWLVTRYEDVRAVLGDGRFVRGPSMTRDEPRTRPEMVKGGLLSMDPPEHSRLRRLVVKAFTARRAESLRPRAREIAHELVDQMAATGQPADLVAMFARQLPVRVICELLGVPSADHDRFTRWSGAFLSTAEVTAEEMQEAAEQAYAYMGDLIDRRRKEPTDDLVSALVQARDQQDSLSEQELLDLAIGLLVAGYESTTTQIADFVYLLMTRPELRRQLLDRPELIPSAVEELTRWVPLGVGTAFPRYAVEDVTLRGVTIRAGEPVLASTGAANRDQAQFPDADRIDVDRTPNQHLGFGHGVHHCLGAPLARVELQVALEVLLQRLPGIRLGIPETQLRWSEGMLLRGPLELPVVW 397
                                    13        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

Chain B from PDB  Type:PROTEIN  Length:400
 aligned with MYCG_MICGR | Q59523 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:400
                               1                                                                                                                                                                                                                                                                                                                                                                                                            
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397
           MYCG_MICGR     - ---MTSAEPRAYPFNDVHGLTLAGRYGELQETEPVSRVRPPYGEEAWLVTRYEDVRAVLGDGRFVRGPSMTRDEPRTRPEMVKGGLLSMDPPEHSRLRRLVVKAFTARRAESLRPRAREIAHELVDQMAATGQPADLVAMFARQLPVRVICELLGVPSADHDRFTRWSGAFLSTAEVTAEEMQEAAEQAYAYMGDLIDRRRKEPTDDLVSALVQARDQQDSLSEQELLDLAIGLLVAGYESTTTQIADFVYLLMTRPELRRQLLDRPELIPSAVEELTRWVPLGVGTAFPRYAVEDVTLRGVTIRAGEPVLASTGAANRDQAQFPDADRIDVDRTPNQHLGFGHGVHHCLGAPLARVELQVALEVLLQRLPGIRLGIPETQLRWSEGMLLRGPLELPVVW 397
               SCOP domains d2y5nb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........ee...........hhhhhhhhhhh.eeeee......eeee.hhhhhhhhhhh..eehhhhhh.............hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhh..hhhhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.........eee...eee..eee....eeeehhhhhh................................hhhhhhhhhhhhhhhhhhhh...ee..hhhhh..............eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y5n B  -2 GSHMTSAEPRAYPFNDVHGLTLAGRYGELQETEPVSRVRPPYGEEAWLVTRYEDVRAVLGDGRFVRGPSMTRDEPRTRPEMVKGGLLSMDPPEHSRLRRLVVKAFTARRAESLRPRAREIAHELVDQMAATGQPADLVAMFARQLPVRVICELLGVPSADHDRFTRWSGAFLSTAEVTAEEMQEAAEQAYAYMGDLIDRRRKEPTDDLVSALVQARDQQDSLSEQELLDLAIGLLVAGYESTTTQIADFVYLLMTRPELRRQLLDRPELIPSAVEELTRWVPLGVGTAFPRYAVEDVTLRGVTIRAGEPVLASTGAANRDQAQFPDADRIDVDRTPNQHLGFGHGVHHCLGAPLARVELQVALEVLLQRLPGIRLGIPETQLRWSEGMLLRGPLELPVVW 397
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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)

Micromonospora griseorubida [TaxId: 28040] (8)

1a	d2y5na_	A:
1b	d2y5nb_	B:

(no "CATH Domain" information available for 2Y5N)

(no "Pfam Domain" information available for 2Y5N)

Asymmetric Unit(hide GO term definitions)

Chain A,B (MYCG_MICGR | Q59523)

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: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:130 - Pro A:131	[ RasMol ]
		Gln B:130 - Pro B:131	[ RasMol ]
		Pro A:88 - Pro A:89	[ RasMol ]
		Pro B:88 - Pro B:89	[ RasMol ]
		Thr A:332 - Pro A:333	[ RasMol ]
		Thr B:332 - Pro B:333	[ RasMol ]
		Tyr A:9 - Pro A:10	[ RasMol ]
		Tyr B:9 - Pro B:10	[ RasMol ]

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	2y5n
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	MYCG_MICGR \| Q59523
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UniProtKB/Swiss-Prot
	MYCG_MICGR \| Q59523	:	2y46 2y5z 2y98 2yca 2ygx 3zsn 4aw3

2y46	STRUCTURE OF THE MIXED-FUNCTION P450 MYCG IN COMPLEX WITH MYCINAMICIN IV
2y4h	STRUCTURE OF THE MIXED-FUNCTION P450 MYCG IN COMPLEX WITH MYCINAMICIN IV IN P21212 SPACE GROUP

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 18)

Sites (18, 18)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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SCOP Domains (1, 2)

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