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(-) Description

Title :  DISULFIDE CROSSLINKED CYTOCHROME P450 REDUCTASE INACTIVE
 
Authors :  C. Xia, D. Hamdane, A. Shen, V. Choi, C. Kasper, H. Zhang, S. -C. Im, L. Was J. P. Kim
Date :  23 Aug 10  (Deposition) - 23 Feb 11  (Release) - 18 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Cytochrome P450 Reductase, Cypor, Disulfide Crosslinked, Inactive, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Xia, D. Hamdane, A. L. Shen, V. Choi, C. B. Kasper, N. M. Pearl, H. Zhang, S. C. Im, L. Waskell, J. J. Kim
Conformational Changes Of Nadph-Cytochrome P450 Oxidoreductase Are Essential For Catalysis And Cofactor Binding.
J. Biol. Chem. V. 286 16246 2011
PubMed-ID: 21345800  |  Reference-DOI: 10.1074/JBC.M111.230532

(-) Compounds

Molecule 1 - NADPH-CYTOCHROME P450 REDUCTASE
    ChainsA
    EC Number1.6.2.4
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET23B-CK377
    Expression System StrainROSETTA GAMI(DE3) PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL DELETION, UNP RESIDUES 57-678
    GeneCYPOR, POR
    MutationYES
    Organism CommonRAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymCPR, P450R

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
3NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:38 , SER A:86 , GLN A:87 , THR A:88 , GLY A:89 , THR A:90 , ALA A:91 , ALA A:138 , THR A:139 , TYR A:140 , GLY A:141 , LEU A:173 , GLY A:174 , ASN A:175 , TYR A:178 , HIS A:180 , PHE A:181 , ASN A:182 , ASP A:208 , LEU A:212 , VAL A:676 , TRP A:677 , SER A:678BINDING SITE FOR RESIDUE FMN A 751
2AC2SOFTWAREHOH A:10 , HOH A:28 , HOH A:29 , HOH A:40 , HIS A:319 , ARG A:424 , ARG A:454 , TYR A:455 , TYR A:456 , SER A:457 , THR A:472 , ALA A:473 , VAL A:474 , TYR A:478 , GLY A:488 , VAL A:489 , ALA A:490 , THR A:491 , TRP A:677BINDING SITE FOR RESIDUE FAD A 752
3AC3SOFTWAREARG A:298 , THR A:535 , ALA A:566 , ARG A:567 , SER A:596 , ARG A:597 , LYS A:602 , TYR A:604 , GLN A:606 , ASP A:632 , ASN A:635 , MET A:636 , ASP A:639BINDING SITE FOR RESIDUE NAP A 753

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Pro A:274 -Pro A:275
2Thr A:363 -Pro A:364
3Gly A:652 -Pro A:653

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FLAVODOXIN_LIKEPS50902 Flavodoxin-like domain profile.NCPR_RAT80-224  1A:80-224
2FAD_FRPS51384 Ferredoxin reductase-type FAD binding domain profile.NCPR_RAT279-521  1A:279-521

(-) Exons   (14, 14)

Asymmetric/Biological Unit (14, 14)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000019611ENSRNOE00000313628chr12:22154339-2215431327NCPR_RAT-00--
1.2ENSRNOT000000019612ENSRNOE00000013698chr12:22097301-22097110192NCPR_RAT1-60600--
1.3ENSRNOT000000019613ENSRNOE00000013699chr12:22086163-2208611549NCPR_RAT60-76171A:67-7610
1.4ENSRNOT000000019614ENSRNOE00000013700chr12:22084470-22084342129NCPR_RAT77-119431A:77-11943
1.5ENSRNOT000000019615ENSRNOE00000013701chr12:22083630-22083481150NCPR_RAT120-169501A:120-16950
1.6ENSRNOT000000019616ENSRNOE00000013702chr12:22083067-22082943125NCPR_RAT170-211421A:170-21142
1.7ENSRNOT000000019617ENSRNOE00000013703chr12:22082851-2208276290NCPR_RAT211-241311A:211-24131
1.8ENSRNOT000000019618ENSRNOE00000013704chr12:22082368-2208227099NCPR_RAT241-274341A:241-27434
1.9ENSRNOT000000019619ENSRNOE00000013705chr12:22081493-22081377117NCPR_RAT274-313401A:274-31340
1.10ENSRNOT0000000196110ENSRNOE00000013706chr12:22081288-22081170119NCPR_RAT313-353411A:313-35341
1.11ENSRNOT0000000196111ENSRNOE00000013707chr12:22080459-22080278182NCPR_RAT353-413611A:353-41361
1.12ENSRNOT0000000196112ENSRNOE00000013708chr12:22080183-22080034150NCPR_RAT414-463501A:414-46350
1.13ENSRNOT0000000196113ENSRNOE00000013709chr12:22079929-22079659271NCPR_RAT464-554911A:464-554 (gaps)91
1.14ENSRNOT0000000196114ENSRNOE00000013710chr12:22079578-22079433146NCPR_RAT554-602491A:554-60249
1.15ENSRNOT0000000196115ENSRNOE00000013711chr12:22079343-2207925886NCPR_RAT603-631291A:603-63129
1.16ENSRNOT0000000196116ENSRNOE00000211856chr12:22079134-22078629506NCPR_RAT631-678481A:631-67848

(-) 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:607
 aligned with NCPR_RAT | P00388 from UniProtKB/Swiss-Prot  Length:678

    Alignment length:612
                                    76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676  
             NCPR_RAT    67 SSFVEKMKKTGRNIIVFYGSQTGTAEEFANRLSKDAHRYGMRGMSADPEEYDLADLSSLPEIDKSLVVFCMATYGEGDPTDNAQDFYDWLQETDVDLTGVKFAVFGLGNKTYEHFNAMGKYVDQRLEQLGAQRIFELGLGDDDGNLEEDFITWREQFWPAVCEFFGVEATGEESSIRQYELVVHEDMDVAKVYTGEMGRLKSYENQKPPFDAKNPFLAAVTANRKLNQGTERHLMHLELDISDSKIRYESGDHVAVYPANDSALVNQIGEILGADLDVIMSLNNLDEESNKKHPFPCPTTYRTALTYYLDITNPPRTNVLYELAQYASEPSEQEHLHKMASSSGEGKELYLSWVVEARRHILAILQDYPSLRPPIDHLCELLPRLQARYYSIASSSKVHPNSVHICAVAVEYEAKSGRVNKGVATSWLRAKEPAGENGGRALVPMFVRKSQFRLPFKSTTPVIMVGPGTGIAPFMGFIQERAWLREQGKEVGETLLYYGCRRSDEDYLYREELARFHKDGALTQLNVAFSREQAHKVYVQHLLKRDREHLWKLIHEGGAHIYVCGDARNMAKDVQNTFYDIVAEFGPMEHTQAVDYVKKLMTKGRYSLDVWS 678
               SCOP domains d3ojxa1 A:67-239 automated matches                                                                                                                                           d3ojxa2 A:240-518 automated matches                                                                                                                                                                                                                                                    d3ojxa3 A:519-678 automated matches                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ---------------Flavodoxin_1-3ojxA02 A:82-219                                                                                                             ------------------------------------------------------FAD_binding_1-3ojxA01 A:274-493                                                                                                                                                                                             ------------------------------------NAD_binding_1-3ojxA03 A:530-642                                                                                  ------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhh....eeeeee...hhhhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhh...eeeeeee.hhhhh.hhhhhhhhhhhhhh.......eeeeeeee.......hhhhhhhhhhhhhh..ee....eeee...hhhhhhhhhhhhhhhhhhhhhh............eeeee....hhhhh.......................eeeeeeeeee........eeeeeee............eeee....hhhhhhhhhhhhh.....eeeeee..............eehhhhhhhh.......hhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhh.....hhhhhhhhh.....hhhhhhhhh.....eeee..........eeeeeee..eee.....eeehhhhhhhhhh...-----..eeeeeee.............eeee.hhhhhhhhhhhhhhhhhhhhh......eeeeeee........hhhhhhhhhhh....eeeeee........hhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..eeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------FLAVODOXIN_LIKE  PDB: A:80-224 UniProt: 80-224                                                                                                   ------------------------------------------------------FAD_FR  PDB: A:279-521 UniProt: 279-521                                                                                                                                                                                                            ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3  Exon 1.4  PDB: A:77-119 UniProt: 77-119    Exon 1.5  PDB: A:120-169 UniProt: 120-169         Exon 1.6  PDB: A:170-211 UniProt: 170-211 -----------------------------Exon 1.8  PDB: A:241-274          --------------------------------------Exon 1.10  PDB: A:313-353                ------------------------------------------------------------Exon 1.12  PDB: A:414-463 UniProt: 414-463        Exon 1.13  PDB: A:464-554 (gaps) UniProt: 464-554                                          ------------------------------------------------Exon 1.15  PDB: A:603-631    ----------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.7  PDB: A:211-241       --------------------------------Exon 1.9  PDB: A:274-313                ---------------------------------------Exon 1.11  PDB: A:353-413 UniProt: 353-413                   --------------------------------------------------------------------------------------------------------------------------------------------Exon 1.14  PDB: A:554-602 UniProt: 554-602       ----------------------------Exon 1.16  PDB: A:631-678 UniProt: 631-678       Transcript 1 (2)
                 3ojx A  67 SSFVEKMKKTGRNIIVFYGSQTGTAEEFANRLSKDAHRYGMRGMSADPEEYDLADLSSLPEIDKSLVVFAMATYGEGDPTCNAQDFYDWLQETDVDLTGVKFAVFGLGNKTYEHFNAMGKYVDQRLEQLGAQRIFELGLGDDDGNLEEDFITWREQFWPAVAEFFGVEATGEESSIRQYELVVHEDMDVAKVYTGEMGRLKSYENQKPPFDAKNPFLAAVTANRKLNQGTERHLMHLELDISDSKIRYESGDHVAVYPANDSALVNQIGEILGADLDVIMSLNNLDEESNKKHPFPTPTTYRTALTYYLDITNPPRTNVLYELAQYASEPSEQEHLHKMASSSGEGKELYLSWVVEARRHILAILQDYPSLRPPIDHLLELLPRLQARYYSIASSSKVHPNSVHITAVAVEYEAKSGRVNKGVATSWLRAKEPA-----RALVPMFVCKSQFRLPFKSTTPVIMVGPGTGIAPFMGFIQERAWLREQGKEVGETLLYYGARRSDEDYLYREELARFHKDGALTQLNVAFSREQAHKVYVQHLLKRDREHLWKLIHEGGAHIYVCGDARNMAKDVQNTFYDIVAEFGPMEHTQAVDYVKKLMTKGRYSLDVWS 678
                                    76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496   |   506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                           500   506                                                                                                                                                                            

   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  (3, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit

(-) Gene Ontology  (42, 42)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NCPR_RAT | P00388)
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:0050661    NADP binding    Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
    GO:0003958    NADPH-hemoprotein reductase activity    Catalysis of the reaction: NADPH + H+ + n oxidized hemoprotein = NADP+ + n reduced hemoprotein.
    GO:0030586    [methionine synthase] reductase activity    Catalysis of the reaction: [methionine synthase]-cob(II)alamin + NADPH + H+ + S-adenosyl methionine = [methionine synthase]-methylcob(I)alamin + S-adenosylhomocysteine + NADP+.
    GO:0004128    cytochrome-b5 reductase activity, acting on NAD(P)H    Catalysis of the reaction: NAD(P)H + H+ + 2 ferricytochrome b(5) = NAD(P)+ + 2 ferrocytochrome b(5).
    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:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0047726    iron-cytochrome-c reductase activity    Catalysis of the reaction: ferrocytochrome c + Fe3+ = ferricytochrome c + Fe2+.
    GO:0008941    nitric oxide dioxygenase activity    Catalysis of the reaction: 2 NO + 2 O2 + NADPH + H+ = 2 nitrate + NADP+.
    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.
biological process
    GO:0009437    carnitine metabolic process    The chemical reactions and pathways involving carnitine (hydroxy-trimethyl aminobutyric acid), a compound that participates in the transfer of acyl groups across the inner mitochondrial membrane.
    GO:0090346    cellular organofluorine metabolic process    The chemical reactions and pathways involving organofluorine compounds, as carried out by individual cells.
    GO:0071372    cellular response to follicle-stimulating hormone stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a follicle-stimulating hormone stimulus.
    GO:0071371    cellular response to gonadotropin stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a gonadotropin stimulus.
    GO:0071375    cellular response to peptide hormone stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptide hormone stimulus. A peptide hormone is any of a class of peptides that are secreted into the blood stream and have endocrine functions in living animals.
    GO:0070988    demethylation    The process of removing one or more methyl groups from a molecule.
    GO:0019395    fatty acid oxidation    The removal of one or more electrons from a fatty acid, with or without the concomitant removal of a proton or protons, by reaction with an electron-accepting substance, by addition of oxygen or by removal of hydrogen.
    GO:0009812    flavonoid metabolic process    The chemical reactions and pathways involving flavonoids, a group of water-soluble phenolic derivatives containing a flavan skeleton including flavones, flavonols and flavanoids, and anthocyanins.
    GO:0018393    internal peptidyl-lysine acetylation    The addition of an acetyl group to a non-terminal lysine residue in a protein.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0043154    negative regulation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of a cysteine-type endopeptidase activity involved in the apoptotic process.
    GO:0060192    negative regulation of lipase activity    Any process that decreases the frequency, rate or extent of lipase activity, the hydrolysis of a lipid or phospholipid.
    GO:0043602    nitrate catabolic process    The chemical reactions and pathways resulting in the breakdown of nitrates, inorganic or organic salts and esters of nitric acid.
    GO:0046210    nitric oxide catabolic process    The chemical reactions and pathways resulting in the breakdown of nitric oxide, nitrogen monoxide (NO), a colorless gas only slightly soluble in water.
    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.
    GO:0045542    positive regulation of cholesterol biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of cholesterol.
    GO:0032332    positive regulation of chondrocyte differentiation    Any process that activates or increases the frequency, rate or extent of chondrocyte differentiation.
    GO:0032770    positive regulation of monooxygenase activity    Any process that activates or increases the activity of a monooxygenase.
    GO:0045880    positive regulation of smoothened signaling pathway    Any process that activates or increases the frequency, rate or extent of smoothened signaling.
    GO:0090031    positive regulation of steroid hormone biosynthetic process    Any process that increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroid hormones,compounds with a 1, 2, cyclopentanoperhydrophenanthrene nucleus that act as hormones.
    GO:0090181    regulation of cholesterol metabolic process    Any process that modulates the rate, frequency, or extent of cholesterol metabolism, the chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones.
    GO:0003420    regulation of growth plate cartilage chondrocyte proliferation    Any process that modulates the rate, frequency, or extent of the multiplication or reproduction of chondrocytes in a growing endochondral bone, resulting in the expansion of a cell population.
    GO:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0007584    response to nutrient    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nutrient stimulus.
cellular component
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NCPR_RAT | P003881amo 1j9z 1ja0 1ja1 3es9 3ojw 3wkt 4y7c 4y9r 4y9u 4yaf 4yal 4yao 4yau 4yaw

(-) Related Entries Specified in the PDB File

3ojw NADP+ FREE