2RFB - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A CYTOCHROME P450 FROM THE THERMOACIDOPHILIC ARCHAEON PICROPHILUS TORRIDUS

Authors :   W. W. Ho, H. Li, T. L. Poulos, C. R. Nishida, P. R. Ortiz De Montellano

Date :   28 Sep 07 (Deposition) - 29 Jan 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)

Keywords :   Cytochrome P450 Thermophile, Heme, Iron, Metal-Binding, Monooxygenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. W. Ho, H. Li, C. R. Nishida, P. R. Ortiz De Montellano, T. L. Poulos
Crystal Structure And Properties Of Cyp231A2 From The Thermoacidophilic Archaeon Picrophilus Torridus.
Biochemistry V. 47 2071 2008
PubMed-ID: 18197710 | Reference-DOI: 10.1021/BI702240K

Molecule 1 - CYTOCHROME P450
	Chains	:	A, B, C
	EC Number	:	1.14.14.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PCWORI
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	PICROPHILUS TORRIDUS
	Organism Taxid	:	82076

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 7)

No.	Name	Count	Type	Full Name
1	HEM	3	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:99 , PHE A:325 , LYS A:326	BINDING SITE FOR RESIDUE SO4 A 900
2	AC2	SOFTWARE	PHE A:280 , ASP A:281 , ARG A:290	BINDING SITE FOR RESIDUE SO4 A 910
3	AC3	SOFTWARE	ILE A:54 , SER A:55 , LYS A:189	BINDING SITE FOR RESIDUE SO4 A 920
4	AC4	SOFTWARE	PHE C:280 , ASP C:281 , ARG C:290 , ARG C:291 , HOH C:931	BINDING SITE FOR RESIDUE SO4 C 910
5	AC5	SOFTWARE	PHE A:56 , ILE A:57 , HIS A:64 , ARG A:68 , LEU A:194 , GLY A:197 , GLY A:198 , THR A:201 , ILE A:241 , ARG A:247 , LEU A:270 , ALA A:296 , PHE A:297 , GLY A:298 , ILE A:301 , HIS A:302 , CYS A:304 , GLY A:306 , HOH A:944 , HOH A:946	BINDING SITE FOR RESIDUE HEM A 410
6	AC6	SOFTWARE	PHE B:56 , ILE B:57 , HIS B:64 , ARG B:68 , PHE B:75 , LEU B:193 , LEU B:194 , GLY B:197 , GLY B:198 , THR B:201 , HIS B:246 , ARG B:247 , LEU B:270 , ALA B:296 , PHE B:297 , GLY B:298 , ILE B:301 , HIS B:302 , CYS B:304 , GLY B:306 , LEU B:309 , ALA B:310 , HOH B:412 , HOH B:419 , HOH B:420	BINDING SITE FOR RESIDUE HEM B 410
7	AC7	SOFTWARE	PHE C:56 , ILE C:57 , HIS C:64 , ARG C:68 , LEU C:194 , GLY C:197 , GLY C:198 , THR C:201 , LEU C:205 , LEU C:235 , LEU C:244 , ARG C:247 , ALA C:296 , PHE C:297 , GLY C:298 , ILE C:301 , HIS C:302 , CYS C:304 , GLY C:306	BINDING SITE FOR RESIDUE HEM C 410

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

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

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

(no "PROSITE Motif" information available for 2RFB)

(no "Exon" information available for 2RFB)

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:338
 aligned with Q6KZ68_PICTO | Q6KZ68 from UniProtKB/TrEMBL  Length:343

    Alignment length:341
                                    12        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 
         Q6KZ68_PICTO     3 LNDPVHYDGAWHVYKYSDVKHVLMNDKIFSSNPGNRYSNAGGISFITMDNPEHKEFRDISAPYFLPSKINDYKDFIEETSNDLIKNIDNKDIISEYAVRLPVNIISKILGIPDSDMPLFKLWSDYIIGNKRDENFNYVNNRMVSRLLEIFKSDSHGIINVLAGSSLKNRKLTMDEKIKYIMLLIIGGNETTTNLIGNMIRVIDENPDIIDDALKNRSGFVEETLRYYSPIQFLPHRFAAEDSYINNKKIKKGDQVIVYLGSANRDETFFDEPDLFKIGRREMHLAFGIGIHMCLGAPLARLEASIALNDILNHFKRIKIDYKKSRLLDNKMVLGYDKLFLS 343
               SCOP domains d2rfba_ A: automated matches                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 2rfbA00 A:12-352 Cytochrome p450                                                                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eeee.hhhhhhhhhhh...ee........---.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.....hhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh...hhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.........ee...eee..eee....eeeehhhhhh...............................hhhhhhhhhhhhhhhhhhhh..........ee........eee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rfb A  12 LNDPVHYDGAWHVYKYSDVKHVLMNDKIFSSNPGNRYS---GISFITMDNPEHKEFRDISAPYFLPSKINDYKDFIEETSNDLIKNIDNKDIISEYAVRLPVNIISKILGIPDSDMPLFKLWSDYIIGNKRDENFNYVNNRMVSRLLEIFKSDSHGIINVLAGSSLKNRKLTMDEKIKYIMLLIIGGNETTTNLIGNMIRVIDENPDIIDDALKNRSGFVEETLRYYSPIQFLPHRFAAEDSYINNKKIKKGDQVIVYLGSANRDETFFDEPDLFKIGRREMHLAFGIGIHMCLGAPLARLEASIALNDILNHFKRIKIDYKKSRLLDNKMVLGYDKLFLS 352
                                    21        31        41       | - |      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 
                                                                49  53

Chain B from PDB  Type:PROTEIN  Length:335
 aligned with Q6KZ68_PICTO | Q6KZ68 from UniProtKB/TrEMBL  Length:343

    Alignment length:343
                                    10        20        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   
         Q6KZ68_PICTO     1 MRLNDPVHYDGAWHVYKYSDVKHVLMNDKIFSSNPGNRYSNAGGISFITMDNPEHKEFRDISAPYFLPSKINDYKDFIEETSNDLIKNIDNKDIISEYAVRLPVNIISKILGIPDSDMPLFKLWSDYIIGNKRDENFNYVNNRMVSRLLEIFKSDSHGIINVLAGSSLKNRKLTMDEKIKYIMLLIIGGNETTTNLIGNMIRVIDENPDIIDDALKNRSGFVEETLRYYSPIQFLPHRFAAEDSYINNKKIKKGDQVIVYLGSANRDETFFDEPDLFKIGRREMHLAFGIGIHMCLGAPLARLEASIALNDILNHFKRIKIDYKKSRLLDNKMVLGYDKLFLS 343
               SCOP domains d2rfbb_ B: automated matches                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 2rfbB00 B:10-352 Cytochrome p450                                                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eeee.hhhhhhhhhhh...ee..--------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh...hhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....eeeeeee...eee..eee....eeeeehhhhh...............................hhhhhhhhhhhhhhhhhhhh..........ee........eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rfb B  10 MRLNDPVHYDGAWHVYKYSDVKHVLMNDKIFSSN--------GGISFITMDNPEHKEFRDISAPYFLPSKINDYKDFIEETSNDLIKNIDNKDIISEYAVRLPVNIISKILGIPDSDMPLFKLWSDYIIGNKRDENFNYVNNRMVSRLLEIFKSDSHGIINVLAGSSLKNRKLTMDEKIKYIMLLIIGGNETTTNLIGNMIRVIDENPDIIDDALKNRSGFVEETLRYYSPIQFLPHRFAAEDSYINNKKIKKGDQVIVYLGSANRDETFFDEPDLFKIGRREMHLAFGIGIHMCLGAPLARLEASIALNDILNHFKRIKIDYKKSRLLDNKMVLGYDKLFLS 352
                                    19        29        39   |     -  |     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   
                                                            43       52

Chain C from PDB  Type:PROTEIN  Length:333
 aligned with Q6KZ68_PICTO | Q6KZ68 from UniProtKB/TrEMBL  Length:343

    Alignment length:341
                                    12        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 
         Q6KZ68_PICTO     3 LNDPVHYDGAWHVYKYSDVKHVLMNDKIFSSNPGNRYSNAGGISFITMDNPEHKEFRDISAPYFLPSKINDYKDFIEETSNDLIKNIDNKDIISEYAVRLPVNIISKILGIPDSDMPLFKLWSDYIIGNKRDENFNYVNNRMVSRLLEIFKSDSHGIINVLAGSSLKNRKLTMDEKIKYIMLLIIGGNETTTNLIGNMIRVIDENPDIIDDALKNRSGFVEETLRYYSPIQFLPHRFAAEDSYINNKKIKKGDQVIVYLGSANRDETFFDEPDLFKIGRREMHLAFGIGIHMCLGAPLARLEASIALNDILNHFKRIKIDYKKSRLLDNKMVLGYDKLFLS 343
               SCOP domains d2rfbc_ C: automated matches                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 2rfbC00 C:12-352 Cytochrome p450                                                                                                                                                                                                                                                                                                                      CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------p450-2rfbC01 C:228-349                                                                                                    --- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------p450-2rfbC02 C:228-349                                                                                                    --- Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------p450-2rfbC03 C:228-349                                                                                                    --- Pfam domains (3)
         Sec.struct. author ....ee....eee.hhhhhhhhhhh...ee..--------..hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh..hhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....eeeeeee...eee..eee....eeeeehhhhh...............................hhhhhhhhhhhhhhhhhhhh..........ee........eee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rfb C  12 LNDPVHYDGAWHVYKYSDVKHVLMNDKIFSSN--------GGISFITMDNPEHKEFRDISAPYFLPSKINDYKDFIEETSNDLIKNIDNKDIISEYAVRLPVNIISKILGIPDSDMPLFKLWSDYIIGNKRDENFNYVNNRMVSRLLEIFKSDSHGIINVLAGSSLKNRKLTMDEKIKYIMLLIIGGNETTTNLIGNMIRVIDENPDIIDDALKNRSGFVEETLRYYSPIQFLPHRFAAEDSYINNKKIKKGDQVIVYLGSANRDETFFDEPDLFKIGRREMHLAFGIGIHMCLGAPLARLEASIALNDILNHFKRIKIDYKKSRLLDNKMVLGYDKLFLS 352
                                    21        31        41 |       -|       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 
                                                          43       52

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: automated matches (157)

Protein domain: automated matches (157)

Picrophilus torridus [TaxId: 82076] (2)

1a	d2rfba_	A:
1b	d2rfbb_	B:
1c	d2rfbc_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Cytochrome p450 (271)

Homologous Superfamily: Cytochrome p450 (271)

Picrophilus torridus. Organism_taxid: 82076. (2)

1a	2rfbA00	A:12-352
1b	2rfbB00	B:10-352
1c	2rfbC00	C:12-352

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: p450] (161)

Family: p450 (161)

Picrophilus torridus (strain ATCC 700027 / DSM 9790 / JCM 10055 / NBRC 100828) (2)

1a	p450-2rfbC01	C:228-349
1b	p450-2rfbC02	C:228-349
1c	p450-2rfbC03	C:228-349

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (Q6KZ68_PICTO | Q6KZ68)

molecular function
	GO:0070330	aromatase activity	Catalysis of the reduction of an aliphatic ring to yield an aromatic ring.
	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: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.

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Description

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