2M56 - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - model 1, sites (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   THE STRUCTURE OF THE COMPLEX OF CYTOCHROME P450CAM AND ITS ELECTRON DONOR PUTIDAREDOXIN DETERMINED BY PARAMAGNETIC NMR SPECTROSCOPY

Authors :   Y. Hiruma, M. A. S. Hass, M. Ubbink

Date :   14 Feb 13 (Deposition) - 21 Aug 13 (Release) - 21 Aug 13 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B  (10x)
NMR Structure *: A,B  (1x)

Keywords :   Camphor, Heme, Iron-Sulphor, Lanthanide, Paramagnetic, Electron Transfer, Ferredoxin, Oxidoreductase-Metal Binding Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Hiruma, M. A. Hass, Y. Kikui, W. M. Liu, B. Olmez, S. P. Skinner, A. Blok, A. Kloosterman, H. Koteishi, F. Lohr, H. Schwalbe, M. Nojiri, M. Ubbink
The Structure Of The Cytochrome P450Cam-Putidaredoxin Complex Determined By Paramagnetic Nmr Spectroscopy And Crystallography.
J. Mol. Biol. 2013
PubMed-ID: 23856620 | Reference-DOI: 10.1016/J.JMB.2013.07.006

Molecule 1 - CAMPHOR 5-MONOOXYGENASE
	Chains	:	A
	EC Number	:	1.14.15.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21 DE3 PLYSS
	Expression System Taxid	:	562
	Expression System Vector	:	PET28A
	Expression System Vector Type	:	VECTOR
	Fragment	:	UNP RESIDUES 12-415
	Gene	:	CAMC, CYP101
	Organism Scientific	:	PSEUDOMONAS PUTIDA
	Organism Taxid	:	303
	Other Details	:	XHO1/NCO1 RESTRICTION SITES, KANAMYCIN RESISTANCE
	Synonym	:	CYTOCHROME P450-CAM, CYTOCHROME P450CAM

Molecule 2 - PUTIDAREDOXIN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21 DE3 PLYSS
	Expression System Taxid	:	562
	Expression System Vector	:	PET28A
	Expression System Vector Type	:	VECTOR
	Gene	:	CAMB
	Mutation	:	YES
	Organism Scientific	:	PSEUDOMONAS PUTIDA
	Organism Taxid	:	303
	Other Details	:	XHO1/NCO1 RESTRICTION SITES, KANAMYCIN RESISTANCE
	Synonym	:	PDX

		1	2
NMR Structure (10x)	:	A	B
NMR Structure * (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

NMR Structure (3, 3)

No.	Name	Count	Type	Full Name
1	CAM	1	Ligand/Ion	CAMPHOR
2	FES	1	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER
3	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

NMR Structure * (3, 3)

No.	Name	Count	Type	Full Name
1	CAM	1	Ligand/Ion	CAMPHOR
2	FES	1	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER
3	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

NMR Structure (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:100 , THR A:101 , GLN A:108 , ARG A:112 , LEU A:244 , LEU A:245 , GLY A:248 , THR A:252 , VAL A:295 , ASP A:297 , ARG A:299 , GLN A:322 , THR A:349 , PHE A:350 , GLY A:351 , HIS A:355 , CYS A:357 , CAM A:502	BINDING SITE FOR RESIDUE HEM A 501
2	AC2	SOFTWARE	PHE A:87 , TYR A:96 , HEM A:501	BINDING SITE FOR RESIDUE CAM A 502
3	AC3	SOFTWARE	MET B:24 , GLY B:37 , CYS B:39 , GLY B:41 , ALA B:43 , CYS B:45 , CYS B:48 , CYS B:86	BINDING SITE FOR RESIDUE FES B 201

(no "SS Bond" information available for 2M56)

(no "Cis Peptide Bond" information available for 2M56)

(no "SAP(SNP)/Variant" information available for 2M56)

NMR Structure (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	2FE2S_FER_2	PS51085	2Fe-2S ferredoxin-type iron-sulfur binding domain profile.	PUTX_PSEPU	2-106	1	B:1-105
2	ADX	PS00814	Adrenodoxin family, iron-sulfur binding region signature.	PUTX_PSEPU	40-50	1	B:39-49
3	CYTOCHROME_P450	PS00086	Cytochrome P450 cysteine heme-iron ligand signature.	CPXA_PSEPU	351-360	1	A:350-359

NMR Structure * (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	2FE2S_FER_2	PS51085	2Fe-2S ferredoxin-type iron-sulfur binding domain profile.	PUTX_PSEPU	2-106	1	B:1-105
2	ADX	PS00814	Adrenodoxin family, iron-sulfur binding region signature.	PUTX_PSEPU	40-50	1	B:39-49
3	CYTOCHROME_P450	PS00086	Cytochrome P450 cysteine heme-iron ligand signature.	CPXA_PSEPU	351-360	1	A:350-359

(no "Exon" information available for 2M56)

NMR Structure

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:404
 aligned with CPXA_PSEPU | P00183 from UniProtKB/Swiss-Prot  Length:415

    Alignment length:404
                                    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    
           CPXA_PSEPU    12 LAPLPPHVPEHLVFDFDMYNPSNLSAGVQEAWAVLQESNVPDLVWTRCNGGHWIATRGQLIREAYEDYRHFSSECPFIPREAGEAYDFIPTSMDPPEQRQFRALANQVVGMPVVDKLENRIQELACSLIESLRPQGQCNFTEDYAEPFPIRIFMLLAGLPEEDIPHLKYLTDQMTRPDGSMTFAEAKEALYDYLIPIIEQRRQKPGTDAISIVANGQVNGRPITSDEAKRMCGLLLVGGLDTVVNFLSFSMEFLAKSPEHRQELIERPERIPAACEELLRRFSLVADGRILTSDYEFHGVQLKKGDQILLPQMLSGLDERENACPMHVDFSRQKVSHTTFGHGSHLCLGQHLARREIIVTLKEWLTRIPDFSIAPGAQIQHKSGIVSGVQALPLVWDPATTKAV 415
               SCOP domains d2m56a_ A: Cytochrome P450-CAM                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhh.........hhhhhhhhhhhhhhh.....eeeehhhhheeee.hhhhhhhhhhh...ee......hhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeehhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh.ee..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.....eeee...eee..eee....eee.hhhhhhhh..............................hhhhhhhhhhhhhhhhhhhh...ee.......ee.....ee...eee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2m56 A  11 LAPLPPHVPEHLVFDFDMYNPSNLSAGVQEAWAVLQESNVPDLVWTRCNGGHWIATRGQLIREAYEDYRHFSSECPFIPREAGEAYDFIPTSMDPPEQRQFRALANQVVGMPVVDKLENRIQELACSLIESLRPQGQCNFTEDYAEPFPIRIFMLLAGLPEEDIPHLKYLTDQMTRPDGSMTFAEAKEALYDYLIPIIEQRRQKPGTDAISIVANGQVNGRPITSDEAKRMCGLLLVGGLDTVVNFLSFSMEFLAKSPEHRQELIQRPERIPAACEELLRRFSLVADGRILTSDYEFHGVQLKKGDQILLPQMLSGLDERENACPMHVDFSRQKVSHTTFGHGSHLCLGQHLARREIIVTLKEWLTRIPDFSIAPGAQIQHKSGIVSGVQALPLVWDPATTKAV 414
                                    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       350       360       370       380       390       400       410

Chain B from PDB  Type:PROTEIN  Length:106
 aligned with PUTX_PSEPU | P00259 from UniProtKB/Swiss-Prot  Length:107

    Alignment length:106
                                    11        21        31        41        51        61        71        81        91       101      
           PUTX_PSEPU     2 SKVVYVSHDGTRRELDVADGVSLMQAAVSNGIYDIVGDCGGSASCATCHVYVNEAFTDKVPAANEREIGMLECVTAELKPNSRLCCQIIMTPELDGIVVDVPDRQW 107
               SCOP domains d2m56b_ B: 2Fe-2S ferredoxin                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhh..................eeee...hhhhh...hhhhhhhhh.........eee.hhh........eeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) 2FE2S_FER_2  PDB: B:1-105 UniProt: 2-106                                                                 - PROSITE (1)
                PROSITE (2) --------------------------------------ADX        --------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 2m56 B   1 SKVVYVSHDGTRRELDVADGVSLMQAAVSNGIYDIVGDCGGSASCATCHVYVNEAFTDKVPAANEREIGMLESVTAELKPNSRLCCQIIMTPELDGIVVDVPDRQW 106
                                    10        20        30        40        50        60        70        80        90       100

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 '\|'

(no "CATH Domain" information available for 2M56)

(no "Pfam Domain" information available for 2M56)

NMR Structure(hide GO term definitions)

Chain A (CPXA_PSEPU | P00183)

molecular function
	GO:0018683	camphor 5-monooxygenase activity	Catalysis of the reaction: (+)-camphor + putidaredoxin + O2 = (+)-exo-5-hydroxycamphor + oxidized putidaredoxin + H2O.
	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:0019383	(+)-camphor catabolic process	The chemical reactions and pathways resulting in the breakdown of (+)-camphor, a bicyclic monoterpene ketone.
	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.

Chain B (PUTX_PSEPU | P00259)

molecular function
	GO:0051537	2 iron, 2 sulfur cluster binding	Interacting selectively and non-covalently with a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
	GO:0009055	electron carrier activity	Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	GO:0051536	iron-sulfur cluster binding	Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
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.

NMR Structure
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2m56)

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1dz4
1xlp	RELATED ID: 19038 RELATED DB: BMRB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (0, 0)

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