2VE3 - JenaLib

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Title :   RETINOIC ACID BOUND CYANOBACTERIAL CYP120A1

Authors :   K. Kuhnel, N. Ke, S. G. Sligar, M. A. Schuler, I. Schlichting

Date :   15 Oct 07 (Deposition) - 29 Apr 08 (Release) - 16 Mar 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

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

Reference :   K. Kuhnel, N. Ke, M. J. Cryle, S. G. Sligar, M. A. Schuler, I. Schlichting
Crystal Structures Of Substrate-Free And Retinoic Acid-Bound Cyanobacterial Cytochrome P450 Cyp120A1.
Biochemistry V. 47 6552 2008
PubMed-ID: 18512957 | Reference-DOI: 10.1021/BI800328S

Molecule 1 - PUTATIVE CYTOCHROME P450 120
	Chains	:	A, B
	EC Number	:	1.14.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Organism Scientific	:	SYNECHOCYSTIS SP.
	Organism Taxid	:	1148
	Strain	:	PCC 6803
	Synonym	:	CYTOCHROME P450 ENZYME

		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	REA	2	Ligand/Ion	RETINOIC ACID

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	REA	1	Ligand/Ion	RETINOIC ACID

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	REA	1	Ligand/Ion	RETINOIC ACID

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:101 , ARG A:105 , PHE A:159 , LEU A:250 , LEU A:251 , ALA A:254 , GLY A:255 , THR A:258 , LEU A:259 , PRO A:317 , VAL A:318 , ARG A:323 , TYR A:344 , ILE A:346 , PRO A:383 , PHE A:384 , GLY A:385 , ARG A:389 , CYS A:391 , GLY A:393 , PHE A:396 , ALA A:397 , REA A:1445 , HOH A:2146 , HOH A:2173	BINDING SITE FOR RESIDUE HEM A1444
2	AC2	SOFTWARE	PHE A:29 , PHE A:182 , THR A:258 , GLY A:319 , GLY A:320 , GLN A:345 , HEM A:1444	BINDING SITE FOR RESIDUE REA A1445
3	AC3	SOFTWARE	ALA B:94 , HIS B:101 , ARG B:105 , PHE B:159 , ALA B:254 , GLY B:255 , THR B:258 , LEU B:259 , PRO B:317 , VAL B:318 , ARG B:323 , TYR B:344 , ILE B:346 , PRO B:383 , PHE B:384 , GLY B:385 , ARG B:389 , CYS B:391 , ALA B:397 , REA B:1445 , HOH B:2130	BINDING SITE FOR RESIDUE HEM B1444
4	AC4	SOFTWARE	PHE B:29 , TRP B:80 , PHE B:182 , PHE B:253 , VAL B:318 , GLY B:319 , GLN B:345 , HEM B:1444	BINDING SITE FOR RESIDUE REA B1445

(no "SS Bond" information available for 2VE3)

Asymmetric Unit

No.	Residues
1	Thr A:427	-	Pro A:428
2	Thr B:427	-	Pro B:428

(no "SAP(SNP)/Variant" information available for 2VE3)

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.	CP120_SYNY3	384-393	2	A:384-393 B:384-393

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.	CP120_SYNY3	384-393	1	A:384-393 -

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.	CP120_SYNY3	384-393	1	- B:384-393

(no "Exon" information available for 2VE3)

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:435
 aligned with CP120_SYNY3 | Q59990 from UniProtKB/Swiss-Prot  Length:444

    Alignment length:435
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438     
          CP120_SYNY3     9 NSLPIPPGDFGLPWLGETLNFLNDGDFGKKRQQQFGPIFKTRLFGKNVIFISGALANRFLFTKEQETFQATWPLSTRILLGPNALATQMGEIHRSRRKILYQAFLPRTLDSYLPKMDGIVQGYLEQWGKANEVIWYPQLRRMTFDVAATLFMGEKVSQNPQLFPWFETYIQGLFSLPIPLPNTLFGKSQRARALLLAELEKIIKARQQQPPSEEDALGILLAARDDNNQPLSLPELKDQILLLLFAGHETLTSALSSFCLLLGQHSDIRERVRQEQNKLQLSQELTAETLKKMPYLDQVLQEVLRLIPPVGGGFRELIQDCQFQGFHFPKGWLVSYQISQTHADPDLYPDPEKFDPERFTPDGSATHNPPFAHVPFGGGLRECLGKEFARLEMKLFATRLIQQFDWTLLPGQNLELVVTPSPRPKDNLRVKLHSL 443
               SCOP domains d2ve3a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhh.hhhhhhhhhhh..eeeee..eeeeee.hhhhhhhhh......eeee.hhhhhhhhh..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.eeehhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh.hhhhhhhhhhhhhhh....eeeeee...eee..eee....eeeeehhhhh............hhhhh..................hhhhh..hhhhhhhhhhhhhhhhhhheeeee.......eee...eee....eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME-------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ve3 A   9 NSLPIPPGDFGLPWLGETLNFLNDGDFGKKRQQQFGPIFKTRLFGKNVIFISGALANRFLFTKEQETFQATWPLSTRILLGPNALATQMGEIHRSRRKILYQAFLPRTLDSYLPKMDGIVQGYLEQWGKANEVIWYPQLRRMTFDVAATLFMGEKVSQNPQLFPWFETYIQGLFSLPIPLPNTLFGKSQRARALLLAELEKIIKARQQQPPSEEDALGILLAARDDNNQPLSLPELKDQILLLLFAGHETLTSALSSFCLLLGQHSDIRERVRQEQNKLQLSQELTAETLKKMPYLDQVLQEVLRLIPPVGGGFRELIQDCQFQGFHFPKGWLVSYQISQTHADPDLYPDPEKFDPERFTPDGSATHNPPFAHVPFGGGLRECLGKEFARLEMKLFATRLIQQFDWTLLPGQNLELVVTPSPRPKDNLRVKLHSL 443
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438

Chain B from PDB  Type:PROTEIN  Length:427
 aligned with CP120_SYNY3 | Q59990 from UniProtKB/Swiss-Prot  Length:444

    Alignment length:434
                                    19        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    
          CP120_SYNY3    10 SLPIPPGDFGLPWLGETLNFLNDGDFGKKRQQQFGPIFKTRLFGKNVIFISGALANRFLFTKEQETFQATWPLSTRILLGPNALATQMGEIHRSRRKILYQAFLPRTLDSYLPKMDGIVQGYLEQWGKANEVIWYPQLRRMTFDVAATLFMGEKVSQNPQLFPWFETYIQGLFSLPIPLPNTLFGKSQRARALLLAELEKIIKARQQQPPSEEDALGILLAARDDNNQPLSLPELKDQILLLLFAGHETLTSALSSFCLLLGQHSDIRERVRQEQNKLQLSQELTAETLKKMPYLDQVLQEVLRLIPPVGGGFRELIQDCQFQGFHFPKGWLVSYQISQTHADPDLYPDPEKFDPERFTPDGSATHNPPFAHVPFGGGLRECLGKEFARLEMKLFATRLIQQFDWTLLPGQNLELVVTPSPRPKDNLRVKLHSL 443
               SCOP domains d2ve3b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----p450-2ve3B01 B:14-440                                                                                                                                                                                                                                                                                                                                                                                                                      --- Pfam domains (1)
           Pfam domains (2) ----p450-2ve3B02 B:14-440                                                                                                                                                                                                                                                                                                                                                                                                                      --- Pfam domains (2)
         Sec.struct. author ...............hhhhhhhh.hhhhhhhhhhh..eeeee..eeeeee.hhhhhhhhh......eeee.hhhhhhhhh..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhhhhhhhh..---..hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.----..hhhhhh.hhhhhhhhhhhhhhh....eeeeee...eee..eee....eeeeehhhhhh...........hhhhhh..hhhhhh.........hhhhh..hhhhhhhhhhhhhhhhhhheeeee.......eee...eee....eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME-------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ve3 B  10 SLPIPPGDFGLPWLGETLNFLNDGDFGKKRQQQFGPIFKTRLFGKNVIFISGALANRFLFTKEQETFQATWPLSTRILLGPNALATQMGEIHRSRRKILYQAFLPRTLDSYLPKMDGIVQGYLEQWGKANEVIWYPQLRRMTFDVAATLFMGEK---NPQLFPWFETYIQGLFSLPIPLPNTLFGKSQRARALLLAELEKIIKARQQQPPSEEDALGILLAARDDNNQPLSLPELKDQILLLLFAGHETLTSALSSFCLLLGQHSDIRERVRQEQNKL----ELTAETLKKMPYLDQVLQEVLRLIPPVGGGFRELIQDCQFQGFHFPKGWLVSYQISQTHADPDLYPDPEKFDPERFTPDGSATHNPPFAHVPFGGGLRECLGKEFARLEMKLFATRLIQQFDWTLLPGQNLELVVTPSPRPKDNLRVKLHSL 443
                                    19        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       | -  |    299       309       319       329       339       349       359       369       379       389       399       409       419       429       439    
                                                                                                                                                                                   163 167                                                                                                                     287  292

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)

Synechocystis sp. [TaxId: 1148] (2)

1a	d2ve3a_	A:
1b	d2ve3b_	B:

(no "CATH Domain" information available for 2VE3)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: p450 (161)

Synechocystis sp. (strain ATCC 27184 / PCC 6803 / N-1) (2)

1a	p450-2ve3B01	B:14-440
1b	p450-2ve3B02	B:14-440

Asymmetric Unit(hide GO term definitions)

Chain A,B (CP120_SYNY3 | Q59990)

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: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
		Thr A:427 - Pro A:428	[ RasMol ]
		Thr B:427 - Pro B:428	[ RasMol ]

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	2ve3
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	1.14.-.-
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UniProtKB/Swiss-Prot
	CP120_SYNY3 \| Q59990	:	2ve4

2ve4	SUBSTRATE FREE CYANOBACTERIAL CYP120A1

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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