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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ELECTRON TRANSFER COMPLEX OF CYTOCHROME P450CAM WITH PUTIDAREDOXIN
 
Authors :  Y. Kikui, Y. Hiruma, M. A. Hass, H. Koteishi, M. Ubbink, M. Nojiri
Date :  03 Apr 13  (Deposition) - 21 Aug 13  (Release) - 21 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Inter-Protein Electron Transfer, Oxidoreductase-Electron Transport 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

(-) Compounds

Molecule 1 - CAMPHOR 5-MONOOXYGENASE
    Chains: A
    EC Number: 1.14.15.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CAMC, CYP101
    Mutation: YES
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 303
    Synonym: CYTOCHROME P450-CAM, CYTOCHROME P450CAM
 
Molecule 2 - PUTIDAREDOXIN
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CAMB
    Mutation: YES
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 303
    Synonym: PDX

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1FES1Ligand/IonFE2/S2 (INORGANIC) CLUSTER
2GOL1Ligand/IonGLYCEROL
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4SO44Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:108 , ARG A:112 , LEU A:244 , LEU A:245 , GLY A:248 , GLY A:249 , THR A:252 , PHE A:256 , ASP A:297 , ARG A:299 , GLN A:322 , THR A:349 , PHE A:350 , GLY A:351 , HIS A:355 , CYS A:357 , GLY A:359 , GOL A:505BINDING SITE FOR RESIDUE HEM A 501
2AC2SOFTWARESER A:267 , PRO A:268 , GLU A:269 , HIS A:270BINDING SITE FOR RESIDUE SO4 A 502
3AC3SOFTWAREALA A:334 , PRO A:335 , MET A:336 , HIS A:337BINDING SITE FOR RESIDUE SO4 A 503
4AC4SOFTWAREPRO A:19 , GLU A:20 , HIS A:21 , ARG A:271BINDING SITE FOR RESIDUE SO4 A 504
5AC5SOFTWAREGLY A:248 , THR A:252 , HEM A:501BINDING SITE FOR RESIDUE GOL A 505
6AC6SOFTWAREGLY B:37 , CYS B:39 , GLY B:41 , ALA B:43 , SER B:44 , CYS B:45 , ALA B:46 , CYS B:48 , CYS B:86BINDING SITE FOR RESIDUE FES B 201
7AC7SOFTWAREHIS B:8 , ALA B:76 , GLU B:77 , ASP B:103 , ARG B:104BINDING SITE FOR RESIDUE SO4 B 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3W9C)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ile A:88 -Pro A:89
2Phe A:98 -Ile A:99
3Ile A:99 -Pro A:100
4Pro A:105 -Pro A:106

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3W9C)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
12FE2S_FER_2PS51085 2Fe-2S ferredoxin-type iron-sulfur binding domain profile.PUTX_PSEPU2-106  1B:1-105
2ADXPS00814 Adrenodoxin family, iron-sulfur binding region signature.PUTX_PSEPU40-50  1B:39-49
3CYTOCHROME_P450PS00086 Cytochrome P450 cysteine heme-iron ligand signature.CPXA_PSEPU351-360  1A:350-359

(-) Exons   (0, 0)

(no "Exon" information available for 3W9C)

(-) Sequences/Alignments

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:401
 aligned with CPXA_PSEPU | P00183 from UniProtKB/Swiss-Prot  Length:415

    Alignment length:405
                                    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     
           CPXA_PSEPU    11 NLAPLPPHVPEHLVFDFDMYNPSNLSAGVQEAWAVLQESNVPDLVWTRCNGGHWIATRGQLIREAYEDYRHFSSECPFIPREAGEAYDFIPTSMDPPEQRQFRALANQVVGMPVVDKLENRIQELACSLIESLRPQGQCNFTEDYAEPFPIRIFMLLAGLPEEDIPHLKYLTDQMTRPDGSMTFAEAKEALYDYLIPIIEQRRQKPGTDAISIVANGQVNGRPITSDEAKRMCGLLLVGGLDTVVNFLSFSMEFLAKSPEHRQELIERPERIPAACEELLRRFSLVADGRILTSDYEFHGVQLKKGDQILLPQMLSGLDERENACPMHVDFSRQKVSHTTFGHGSHLCLGQHLARREIIVTLKEWLTRIPDFSIAPGAQIQHKSGIVSGVQALPLVWDPATTKAV 415
               SCOP domains d3w9ca_ A: Cytochrome P450-CAM                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh.........hhhhhhhhhhhhhhh.....eeeehhhhheeee.hhhhhhhhhh....ee.........----..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeehhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh.ee..ee.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.....eeee...eee..eee....eee...hhhhhh.......................hhhhh..hhhhhhhhhhhhhhhhhh.....ee.......ee.....ee...eee.hhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w9c A  10 NLAPLPPHVPEHLVFDFDMYNPSNLSAGVQEAWAVLQESNVPDLVWTRCNGGHWIATRGQLIREAYEDYRHFSSECPFIPRE----YDFIPTSMDPPEQRQFRALANQVVGMPVVDCLENCIQELACSLIESLRPQGQCNFTEDYAEPFPIRIFMLLAGLPEEDIPHLKYLTDQMTRPDGSMTFAEAKEALYDYLIPIIEQRRQKPGTDAISIVANGQVNGRPITSDEAKRMCGLLLVGGLDTVVNFLSFSMEFLAKSPEHRQELIERPERIPAACEELLRRFSLVADGRILTSDYEFHGVQLKKGDQILLPQMLSGLDERENAAPMHVDFSRQKVSHTTFGHGSHLCLGQHLARREIIVTLKEWLTRIPDFSIAPGAQIQHKSGIVSGVQALPLVWDPATTKAV 414
                                    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     
                                                                                                            91   96                                                                                                                                                                                                                                                                                                                              


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 d3w9cb_ B: 2Fe-2S ferredoxin                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhh...................eeee...hhhhh...hhhhhhhhh.........eee......hhhhh.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
                 3w9c 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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3W9C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3W9C)

(-) Gene Ontology  (13, 15)

Asymmetric/Biological Unit(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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CPXA_PSEPU | P00183: 1akd 1c8j 1cp4 1dz4 1dz6 1dz8 1dz9 1geb 1gek 1gem 1gjm 1iwi 1iwj 1iwk 1j51 1k2o 1lwl 1mpw 1noo 1o76 1p2y 1p7r 1pha 1phb 1phc 1phd 1phe 1phf 1phg 1qmq 1re9 1rf9 1t85 1t86 1t87 1t88 1uyu 1yrc 1yrd 2a1m 2a1n 2a1o 2cp4 2cpp 2fe6 2fer 2feu 2frz 2gqx 2gr6 2h7q 2h7r 2h7s 2l8m 2lqd 2m56 2qbl 2qbm 2qbn 2qbo 2z97 2zaw 2zax 2zuh 2zui 2zuj 2zwt 2zwu 3cp4 3cpp 3fwf 3fwg 3fwi 3fwj 3l61 3l62 3l63 3oia 3ol5 3p6m 3p6n 3p6o 3p6p 3p6q 3p6r 3p6s 3p6t 3p6u 3p6v 3p6w 3p6x 3wrh 3wri 3wrj 3wrk 3wrl 3wrm 4cp4 4cpp 4ek1 4g3r 4jws 4jwu 4jx1 4kky 4l49 4l4a 4l4b 4l4c 4l4d 4l4e 4l4f 4l4g 5cp4 5cpp 5gxg 5ik1 6cp4 6cpp 7cpp 8cpp
        PUTX_PSEPU | P00259: 1gpx 1oqq 1oqr 1pdx 1put 1r7s 1xln 1xlo 1xlp 1xlq 1yji 1yjj 2m56 3lb8 4jws 4jwu 4jx1 5gxg

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3W9C)