2X7Y - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   P450 BM3 F87A IN COMPLEX WITH DMSO

Authors :   J. Kuper, T. S. Wong, D. Roccatano, M. Wilmanns, U. Schwaneberg

Date :   04 Mar 10 (Deposition) - 23 Mar 11 (Release) - 19 Sep 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Electron Transport, Oxidoreductase, Dmso-Inhibition, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Kuper, K. L. Tee, M. Wilmanns, D. Roccatano, U. Schwaneberg, T. S. Wong
The Role Of Active-Site Phe87 In Modulating The Organic Co- Solvent Tolerance Of Cytochrome P450 Bm3 Monooxygenase.
Acta Crystallogr. , Sect. F V. 68 1013 2012
PubMed-ID: 22949185 | Reference-DOI: 10.1107/S1744309112031570

Molecule 1 - BIFUNCTIONAL P-450/NADPH-P450 REDUCTASE
	Chains	:	A, B
	EC Number	:	1.14.14.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PETM11
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	HEME DOMAIN, RESIDUES 1-455
	Mutation	:	YES
	Organism Scientific	:	BACILLUS MEGATERIUM
	Organism Taxid	:	1404
	Synonym	:	P450 BM3, CYTOCHROME P450, BM-3, P450BM-3

		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, 8)

No.	Name	Count	Type	Full Name
1	DMS	2	Ligand/Ion	DIMETHYL SULFOXIDE
2	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	DMS	1	Ligand/Ion	DIMETHYL SULFOXIDE
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	DMS	1	Ligand/Ion	DIMETHYL SULFOXIDE
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:69 , LEU A:75 , LEU A:86 , ALA A:87 , TRP A:96 , PHE A:107 , PHE A:261 , ALA A:264 , GLY A:265 , THR A:268 , THR A:269 , PHE A:331 , PRO A:392 , PHE A:393 , GLY A:394 , ARG A:398 , CYS A:400 , ILE A:401 , GLY A:402 , ALA A:406 , DMS A:1460 , HOH A:2272 , HOH A:2273 , HOH A:2274 , HOH A:2275 , HOH A:2276 , HOH A:2277 , HOH A:2279	BINDING SITE FOR RESIDUE HEM A1456
2	AC2	SOFTWARE	ASP A:231 , HIS A:236 , HIS A:285 , HOH A:2278	BINDING SITE FOR RESIDUE ZN A1457
3	AC3	SOFTWARE	HIS A:92 , LYS A:336 , GLU B:373	BINDING SITE FOR RESIDUE ZN A1458
4	AC4	SOFTWARE	ASP A:338 , GLU A:348 , HIS B:285	BINDING SITE FOR RESIDUE ZN A1459
5	AC5	SOFTWARE	ALA A:264 , HEM A:1456 , HOH A:2279	BINDING SITE FOR RESIDUE DMS A1460
6	AC6	SOFTWARE	LYS B:69 , LEU B:86 , ALA B:87 , TRP B:96 , PHE B:107 , PHE B:261 , ALA B:264 , GLY B:265 , THR B:268 , THR B:269 , ALA B:328 , PHE B:331 , PRO B:392 , PHE B:393 , GLY B:394 , ARG B:398 , ALA B:399 , CYS B:400 , ILE B:401 , GLY B:402 , DMS B:1458 , HOH B:2194 , HOH B:2268 , HOH B:2269 , HOH B:2270 , HOH B:2272	BINDING SITE FOR RESIDUE HEM B1456
7	AC7	SOFTWARE	ASP B:231 , HIS B:236 , GLU B:430	BINDING SITE FOR RESIDUE ZN B1457
8	AC8	SOFTWARE	HEM B:1456 , HOH B:2273	BINDING SITE FOR RESIDUE DMS B1458

(no "SS Bond" information available for 2X7Y)

(no "Cis Peptide Bond" information available for 2X7Y)

(no "SAP(SNP)/Variant" information available for 2X7Y)

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.	CPXB_BACMB	394-403	2	A:393-402 B:393-402

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.	CPXB_BACMB	394-403	1	A:393-402 -

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.	CPXB_BACMB	394-403	1	- B:393-402

(no "Exon" information available for 2X7Y)

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:437
 aligned with CPXB_BACMB | P14779 from UniProtKB/Swiss-Prot  Length:1049

    Alignment length:455
                                    11        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       411       421       431       441       451     
           CPXB_BACMB     2 TIKEMPQPKTFGELKNLPLLNTDKPVQALMKIADELGEIFKFEAPGRVTRYLSSQRLIKEACDESRFDKNLSQALKFVRDFAGDGLFTSWTHEKNWKKAHNILLPSFSQQAMKGYHAMMVDIAVQLVQKWERLNADEHIEVPEDMTRLTLDTIGLCGFNYRFNSFYRDQPHPFITSMVRALDEAMNKLQRANPDDPAYDENKRQFQEDIKVMNDLVDKIIADRKASGEQSDDLLTHMLNGKDPETGEPLDDENIRYQIITFLIAGHETTSGLLSFALYFLVKNPHVLQKAAEEAARVLVDPVPSYKQVKQLKYVGMVLNEALRLWPTAPAFSLYAKEDTVLGGEYPLEKGDELMVLIPQLHRDKTIWGDDVEEFRPERFENPSAIPQHAFKPFGNGQRACIGQQFALHEATLVLGMMLKHFDFEDHTNYELDIKETLTLKPEGFVVKAKSKKIPL 456
               SCOP domains d2x7ya_ A: Cytochrome P450 bm-3                                                                                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhh..hhhhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhh....eee..hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhhh...hhhhh...hhhhhhhhhhhhhhhhhh--------------hhhhhhhhhhhhhhhhhhhhhhh.----.hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh....eeeeee...eee...eee....eeeeehhhhh.hhhhhh......hhhhhhhhhhh.........hhhhh..hhhhhhhhhhhhhhhhhhheeee........eee...eee...eeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x7y A   1 TIKEMPQPKTFGELKNLPLLNTDKPVQALMKIADELGEIFKFEAPGRVTRYLSSQRLIKEACDESRFDKNLSQALKFVRDFAGDGLATSWTHEKNWKKAHNILLPSFSQQAMKGYHAMMVDIAVQLVQKWERLNADEHIEVPEDMTRLTLDTIGLCGFNYRFNSFYRDQPHPFITSMVRALDEAMNKL--------------RQFQEDIKVMNDLVDKIIADRKAS----DDLLTHMLNGKDPETGEPLDDENIRYQIITFLIAGHETTSGLLSFALYFLVKNPHVLQKAAEEAARVLVDPVPSYKQVKQLKYVGMVLNEALRLWPTAPAFSLYAKEDTVLGGEYPLEKGDELMVLIPQLHRDKTIWGDDVEEFRPERFENPSAIPQHAFKPFGNGQRACIGQQFALHEATLVLGMMLKHFDFEDHTNYELDIKETLTLKPEGFVVKAKSKKIPL 455
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       | -         -  |    210       220     |   -|      240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450     
                                                                                                                                                                                                                     188            203                    226  231

Chain B from PDB  Type:PROTEIN  Length:439
 aligned with CPXB_BACMB | P14779 from UniProtKB/Swiss-Prot  Length:1049

    Alignment length:455
                                    11        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       411       421       431       441       451     
           CPXB_BACMB     2 TIKEMPQPKTFGELKNLPLLNTDKPVQALMKIADELGEIFKFEAPGRVTRYLSSQRLIKEACDESRFDKNLSQALKFVRDFAGDGLFTSWTHEKNWKKAHNILLPSFSQQAMKGYHAMMVDIAVQLVQKWERLNADEHIEVPEDMTRLTLDTIGLCGFNYRFNSFYRDQPHPFITSMVRALDEAMNKLQRANPDDPAYDENKRQFQEDIKVMNDLVDKIIADRKASGEQSDDLLTHMLNGKDPETGEPLDDENIRYQIITFLIAGHETTSGLLSFALYFLVKNPHVLQKAAEEAARVLVDPVPSYKQVKQLKYVGMVLNEALRLWPTAPAFSLYAKEDTVLGGEYPLEKGDELMVLIPQLHRDKTIWGDDVEEFRPERFENPSAIPQHAFKPFGNGQRACIGQQFALHEATLVLGMMLKHFDFEDHTNYELDIKETLTLKPEGFVVKAKSKKIPL 456
               SCOP domains d2x7yb_ B: Cytochrome P450 bm-3                                                                                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhh..hhhhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhh....eee..hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhhh...hhhhh...hhhhhhhhhhhhhhhhhh------------hhhhhhhhhhhhhhhhhhhhhhhhh.----.hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh....eeeeee...eee...eee....eeeeehhhhh.hhhhhh......hhhhhhhhhhh.........hhhhh..hhhhhhhhhhhhhhhhhhheeee........eee...eee...eeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x7y B   1 TIKEMPQPKTFGELKNLPLLNTDKPVQALMKIADELGEIFKFEAPGRVTRYLSSQRLIKEACDESRFDKNLSQALKFVRDFAGDGLATSWTHEKNWKKAHNILLPSFSQQAMKGYHAMMVDIAVQLVQKWERLNADEHIEVPEDMTRLTLDTIGLCGFNYRFNSFYRDQPHPFITSMVRALDEAMNKL------------NKRQFQEDIKVMNDLVDKIIADRKAS----DDLLTHMLNGKDPETGEPLDDENIRYQIITFLIAGHETTSGLLSFALYFLVKNPHVLQKAAEEAARVLVDPVPSYKQVKQLKYVGMVLNEALRLWPTAPAFSLYAKEDTVLGGEYPLEKGDELMVLIPQLHRDKTIWGDDVEEFRPERFENPSAIPQHAFKPFGNGQRACIGQQFALHEATLVLGMMLKHFDFEDHTNYELDIKETLTLKPEGFVVKAKSKKIPL 455
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       | -         -|      210       220     |   -|      240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450     
                                                                                                                                                                                                                     188          201                      226  231

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: Cytochrome P450 (323)

Protein domain: Cytochrome P450 bm-3 (60)

Bacillus megaterium [TaxId: 1404] (60)

1a	d2x7ya_	A:
1b	d2x7yb_	B:

(no "CATH Domain" information available for 2X7Y)

(no "Pfam Domain" information available for 2X7Y)

Asymmetric Unit(hide GO term definitions)

Chain A,B (CPXB_BACMB | P14779)

molecular function
	GO:0010181	FMN binding	Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
	GO:0003958	NADPH-hemoprotein reductase activity	Catalysis of the reaction: NADPH + H+ + n oxidized hemoprotein = NADP+ + n reduced hemoprotein.
	GO:0070330	aromatase activity	Catalysis of the reduction of an aliphatic ring to yield an aromatic ring.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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.
	GO:0016712	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen	Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from reduced flavin or flavoprotein and one other donor, and one atom of oxygen is incorporated into one donor.
biological process
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2x7y)

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1bu7	CRYOGENIC STRUCTURE OF CYTOCHROME P450BM-3 HEME DOMAIN
1bvy	COMPLEX OF THE HEME AND FMN-BINDING DOMAINS OF THE CYTOCHROME P450(BM-3)
1fag	STRUCTURE OF CYTOCHROME P450
1fah	STRUCTURE OF CYTOCHROME P450
1jme	CRYSTAL STRUCTURE OF PHE393HIS CYTOCHROME P450 BM3
1jpz	CRYSTAL STRUCTURE OF A COMPLEX OF THE HEME DOMAIN OF P450BM-3 WITH N-PALMITOYLGLYCINE
1p0v	F393A MUTANT HEME DOMAIN OF FLAVOCYTOCHROME P450 BM3
1p0w	F393W MUTANT HEME DOMAIN OF FLAVOCYTOCHROME P450 BM3
1p0x	F393Y MUTANT HEME DOMAIN OF FLAVOCYTOCHROME P450 BM3
1smi	A SINGLE MUTATION OF P450 BM3 INDUCES THE CONFORMATIONALREARRANGEMENT SEEN UPON SUBSTRATE-BINDING IN WILD-TYPEENZYME
1smj	STRUCTURE OF THE A264E MUTANT OF CYTOCHROME P450 BM3COMPLEXED WITH PALMITOLEATE
1yqo	T268A MUTANT HEME DOMAIN OF FLAVOCYTOCHROME P450 BM3
1yqp	T268N MUTANT CYTOCHROME DOMAIN OF FLAVOCYTOCHROME P450 BM3
2bmh
2hpd
2j1m	BM3 P450 IN COMPLEX WITH DMSO
2j4s	P450 BM3 HEME DOMAIN IN COMPLEX WITH DMSO
2uwh	CYTOCHROME P450 BM3 MUTANT IN COMPLEX WITH PALMITIC ACID
2x80	P450 BM3 F87A IN COMPLEX WITH DMSO

Description

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Ligands, Modified Residues, Ions (3, 8)

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