1BVY - JenaLib

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Title :   COMPLEX OF THE HEME AND FMN-BINDING DOMAINS OF THE CYTOCHROME P450(BM-3)

Authors :   I. F. Sevrioukova, H. Li, H. Zhang, J. A. Peterson, T. L. Poulos

Date :   21 Sep 98 (Deposition) - 23 Feb 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.03

Chains :   Asym./Biol. Unit : A,B,F

Keywords :   Fatty Acid Monooxygenase, Hemoprotein, Flavoprotein, Electron Transfer, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. F. Sevrioukova, H. Li, H. Zhang, J. A. Peterson, T. L. Poulos
Structure Of A Cytochrome P450-Redox Partner Electron-Transfer Complex.
Proc. Natl. Acad. Sci. Usa V. 96 1863 1999
PubMed-ID: 10051560 | Reference-DOI: 10.1073/PNAS.96.5.1863
(for further references see the PDB file header)

Molecule 1 - PROTEIN (CYTOCHROME P450 BM-3)
	Chains	:	A, B
	EC Number	:	1.14.14.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cell Line	:	DH5AF'IQ
	Expression System Plasmid	:	PPROEX
	Expression System Taxid	:	562
	Fragment	:	HEME-BINDING DOMAIN
	Organism Scientific	:	BACILLUS MEGATERIUM
	Organism Taxid	:	1404
	Other Details	:	SYNTHETIC GENE

Molecule 2 - PROTEIN (CYTOCHROME P450 BM-3)
	Chains	:	F
	EC Number	:	1.14.14.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cell Line	:	DH5AF'IQ
	Expression System Plasmid	:	PPROEX
	Expression System Taxid	:	562
	Fragment	:	FMN-BINDING DOMAIN
	Organism Scientific	:	BACILLUS MEGATERIUM
	Organism Taxid	:	1404
	Other Details	:	SYNTHETIC GENE

		1	2	3
Asymmetric/Biological Unit	:	A	B	F

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 8)

No.	Name	Count	Type	Full Name
1	EDO	5	Ligand/Ion	1,2-ETHANEDIOL
2	FMN	1	Ligand/Ion	FLAVIN MONONUCLEOTIDE
3	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:69 , LEU A:86 , PHE A:87 , TRP A:96 , ALA A:264 , GLY A:265 , THR A:268 , THR A:269 , THR A:327 , PHE A:331 , PRO A:392 , PHE A:393 , GLY A:394 , ARG A:398 , ALA A:399 , CYS A:400 , GLY A:402 , EDO A:1003 , HOH A:1029 , HOH A:1042 , HOH A:1043 , HOH A:1067 , HOH A:1111 , HOH A:1147	BINDING SITE FOR RESIDUE HEM A 1000
2	AC2	SOFTWARE	SER F:488 , ASN F:489 , MET F:490 , GLY F:491 , THR F:492 , ALA F:493 , ALA F:534 , SER F:535 , TYR F:536 , ASN F:537 , GLY F:538 , CYS F:569 , GLY F:570 , ASP F:571 , TRP F:574 , THR F:577 , TYR F:578 , GLN F:579 , HOH F:1007 , HOH F:1026 , HOH F:1034	BINDING SITE FOR RESIDUE FMN F 1002
3	AC3	SOFTWARE	LYS B:69 , LEU B:86 , PHE B:87 , TRP B:96 , ALA B:264 , GLY B:265 , THR B:268 , THR B:269 , LEU B:272 , THR B:327 , PHE B:331 , PRO B:392 , PHE B:393 , GLY B:394 , ARG B:398 , ALA B:399 , CYS B:400 , EDO B:1004 , HOH B:1021 , HOH B:1087 , HOH B:1089 , HOH B:1090 , HOH B:1091 , HOH B:1118	BINDING SITE FOR RESIDUE HEM B 1001
4	AC4	SOFTWARE	PHE A:87 , ALA A:264 , THR A:268 , ALA A:328 , HEM A:1000 , HOH A:1188	BINDING SITE FOR RESIDUE EDO A 1003
5	AC5	SOFTWARE	PHE B:87 , ALA B:264 , THR B:268 , ALA B:328 , HEM B:1001 , HOH B:1045	BINDING SITE FOR RESIDUE EDO B 1004
6	AC6	SOFTWARE	ILE B:39 , ARG B:50 , TYR B:345	BINDING SITE FOR RESIDUE EDO B 1005
7	AC7	SOFTWARE	PRO A:105 , SER A:108 , GLN A:110 , GLY F:495 , ASP F:499	BINDING SITE FOR RESIDUE EDO A 1006
8	AC8	SOFTWARE	TRP B:130 , LEU B:133 , ALA B:448 , HOH B:1048 , HOH B:1049 , HOH B:1179	BINDING SITE FOR RESIDUE EDO B 1007

(no "SS Bond" information available for 1BVY)

(no "Cis Peptide Bond" information available for 1BVY)

(no "SAP(SNP)/Variant" information available for 1BVY)

Asymmetric/Biological Unit (2, 3)

	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
2	FLAVODOXIN_LIKE	PS50902	Flavodoxin-like domain profile.	CPXB_BACMB	483-622	1	F:482-621

(no "Exon" information available for 1BVY)

Asymmetric/Biological 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:439
 aligned with CPXB_BACMB | P14779 from UniProtKB/Swiss-Prot  Length:1049

    Alignment length:439
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450         
           CPXB_BACMB    21 LNTDKPVQALMKIADELGEIFKFEAPGRVTRYLSSQRLIKEACDESRFDKNLSQALKFVRDFAGDGLFTSWTHEKNWKKAHNILLPSFSQQAMKGYHAMMVDIAVQLVQKWERLNADEHIEVPEDMTRLTLDTIGLCGFNYRFNSFYRDQPHPFITSMVRALDEAMNKLQRANPDDPAYDENKRQFQEDIKVMNDLVDKIIADRKASGEQSDDLLTHMLNGKDPETGEPLDDENIRYQIITFLIAGHETTSGLLSFALYFLVKNPHVLQKAAEEAARVLVDPVPSYKQVKQLKYVGMVLNEALRLWPTAPAFSLYAKEDTVLGGEYPLEKGDELMVLIPQLHRDKTIWGDDVEEFRPERFENPSAIPQHAFKPFGNGQRACIGQQFALHEATLVLGMMLKHFDFEDHTNYELDIKETLTLKPEGFVVKAKSKKIPLGGI 459
               SCOP domains d1bvya_ A: Cytochrome P450 bm-3                                                                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1bvyA00 A:20-458 Cytochrome p450                                                                                                                                                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh..eeeeee..eeeeee..hhhhhhh.....eee...hhhhhhhhhh...hhh.....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.....hhh.....hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhh.hhhhhhhhhhhhhh....eeeeee...eee...eee....eeeeehhhhhh.hhhh........hhhh..hhh...........hhh....hhhhhhhhhhhhhhhhhheeee........eee...eee.....eeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME-------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bvy A  20 LNTDKPVQALMKIADELGEIFKFEAPGRVTRYLSSQRLIKEACDESRFDKNLSQALKFVRDFAGDGLFTSWTHEKNWKKAHNILLPSFSQQAMKGYHAMMVDIAVQLVQKWERLNADEHIEVPEDMTRLTLDTIGLCGFNYRFNSFYRDQPHPFITSMVRALDEAMNKLQRANPDDPAYDENKRQFQEDIKVMNDLVDKIIADRKASGEQSDDLLTHMLNGKDPETGEPLDDENIRYQIITFLIAGHETTSGLLSFALYFLVKNPHVLQKAAEEAARVLVDPVPSYKQVKQLKYVGMVLNEALRLWPTAPAFSLYAKEDTVLGGEYPLEKGDELMVLIPQLHRDKTIWGDDVEEFRPERFENPSAIPQHAFKPFGNGQRACIGQQFALHEATLVLGMMLKHFDFEDHTNYELDIKETLTLKPEGFVVKAKSKKIPLGGI 458
                                    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       409       419       429       439       449

Chain B from PDB  Type:PROTEIN  Length:438
 aligned with CPXB_BACMB | P14779 from UniProtKB/Swiss-Prot  Length:1049

    Alignment length:438
                                    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    22 NTDKPVQALMKIADELGEIFKFEAPGRVTRYLSSQRLIKEACDESRFDKNLSQALKFVRDFAGDGLFTSWTHEKNWKKAHNILLPSFSQQAMKGYHAMMVDIAVQLVQKWERLNADEHIEVPEDMTRLTLDTIGLCGFNYRFNSFYRDQPHPFITSMVRALDEAMNKLQRANPDDPAYDENKRQFQEDIKVMNDLVDKIIADRKASGEQSDDLLTHMLNGKDPETGEPLDDENIRYQIITFLIAGHETTSGLLSFALYFLVKNPHVLQKAAEEAARVLVDPVPSYKQVKQLKYVGMVLNEALRLWPTAPAFSLYAKEDTVLGGEYPLEKGDELMVLIPQLHRDKTIWGDDVEEFRPERFENPSAIPQHAFKPFGNGQRACIGQQFALHEATLVLGMMLKHFDFEDHTNYELDIKETLTLKPEGFVVKAKSKKIPLGGI 459
               SCOP domains d1bvyb_ B: Cytochrome P450 bm-3                                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1bvyB00 B:21-458 Cytochrome p450                                                                                                                                                                                                                                                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh..eeeee....eeeee..hhhhhhh.....eee...hhhhhhhhhh...........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.....hhh.....hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhh.hhhhhhhhhhhhh.....eeeeee...eee...eee....eeeeehhhhhh.hhhh........hhhh..hhh...........hhh....hhhhhhhhhhhhhhhhhheeee........eee...eee.....eeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME-------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1bvy B  21 NTDKPVQALMKIADELGEIFKFEAPGRVTRYLSSQRLIKEACDESRFDKNLSQALKFVRDFAGDGLFTSWTHEKNWKKAHNILLPSFSQQAMKGYHAMMVDIAVQLVQKWERLNADEHIEVPEDMTRLTLDTIGLCGFNYRFNSFYRDQPHPFITSMVRALDEAMNKLQRANPDDPAYDENKRQFQEDIKVMNDLVDKIIADRKASGEQSDDLLTHMLNGKDPETGEPLDDENIRYQIITFLIAGHETTSGLLSFALYFLVKNPHVLQKAAEEAARVLVDPVPSYKQVKQLKYVGMVLNEALRLWPTAPAFSLYAKEDTVLGGEYPLEKGDELMVLIPQLHRDKTIWGDDVEEFRPERFENPSAIPQHAFKPFGNGQRACIGQQFALHEATLVLGMMLKHFDFEDHTNYELDIKETLTLKPEGFVVKAKSKKIPLGGI 458
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450

Chain F from PDB  Type:PROTEIN  Length:152
 aligned with CPXB_BACMB | P14779 from UniProtKB/Swiss-Prot  Length:1049

    Alignment length:152
                                   489       499       509       519       529       539       549       559       569       579       589       599       609       619       629  
           CPXB_BACMB   480 NTPLLVLYGSNMGTAEGTARDLADIAMSKGFAPQVATLDSHAGNLPREGAVLIVTASYNGHPPDNAKQFVDWLDQASADEVKGVRYSVFGCGDKNWATTYQKVPAFIDETLAAKGAENIADRGEADASDDFEGTYEEWREHMWSDVAAYFNL 631
               SCOP domains d1bvyf_ F: FMN-binding domain of the cytochrome P450bm-3                                                                                                 SCOP domains
               CATH domains 1bvyF00 F:479-630  [code=3.40.50.360, no name defined]                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....hhhhhhhhhhhhhhhh....eeeehhh.........eeeeeee..........hhhhhhhh...........eeeeeee....hhh..hhhhhhhhhhh..........eeee....hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---FLAVODOXIN_LIKE  PDB: F:482-621 UniProt: 483-622                                                                                            --------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bvy F 479 NTPLLVLYGSNMGTAEGTARDLADIAMSKGFAPQVATLDSHAGNLPREGAVLIVTASYNGHPPDNAKQFVDWLDQASADEVKGVRYSVFGCGDKNWATTYQKVPAFIDETLAAKGAENIADRGEADASDDFEGTYEEWREHMWSDVAAYFNL 630
                                   488       498       508       518       528       538       548       558       568       578       588       598       608       618       628

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/Biological 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	d1bvya_	A:
1b	d1bvyb_	B:

Class: Alpha and beta proteins (a/b) (23833)

Fold: Flavodoxin-like (1057)

Superfamily: Flavoproteins (208)

Family: Flavodoxin-related (81)

Protein domain: FMN-binding domain of the cytochrome P450bm-3 (1)

Bacillus megaterium [TaxId: 1404] (1)

d1bvyf_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.360, no name defined] (150)

Bacillus megaterium. Organism_taxid: 1404. (1)

1bvyF00

F:479-630

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Cytochrome p450 (271)

Homologous Superfamily: Cytochrome p450 (271)

Bacillus megaterium. Organism_taxid: 1404. (9)

2a	1bvyB00	B:21-458
2b	1bvyA00	A:20-458

(no "Pfam Domain" information available for 1BVY)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,F (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.

Asymmetric/Biological Unit
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	1bvy
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(no "Related Entries Specified in the PDB File" available for 1BVY)

Description

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Ligands, Modified Residues, Ions (3, 8)

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