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(-) Description

Title :  CRYSTAL STRUCTURE OF NADPH-CYTOCHROME P450 REDUCTASE (FAD/NADPH DOMAIN AND R457H MUTANT)
 
Authors :  C. Xia, C. Marohnic, S. P. Panda, B. S. Masters, J. -J. P. Kim
Date :  22 Jan 11  (Deposition) - 17 Aug 11  (Release) - 31 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Nadph-Cytochrome P450 Reductase, Flavoprotein, Antley-Bixler Syndrome, Fad, Nadph, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Xia, S. P. Panda, C. C. Marohnic, P. Martasek, B. S. Masters, J. J. Kim
Structural Basis For Human Nadph-Cytochrome P450 Oxidoreductase Deficiency.
Proc. Natl. Acad. Sci. Usa V. 108 13486 2011
PubMed-ID: 21808038  |  Reference-DOI: 10.1073/PNAS.1106632108

(-) Compounds

Molecule 1 - NADPH--CYTOCHROME P450 REDUCTASE
    ChainsA
    EC Number1.6.2.4
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET_CYPORDELTA244
    Expression System StrainJM109(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentFAD/NADPH DOMAIN (UNP RESIDUES 241-677)
    GenePOR, CYPOR
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCPR, P450R

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

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

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:1 , HOH A:5 , HOH A:14 , HOH A:23 , HOH A:27 , HOH A:31 , HOH A:81 , HOH A:91 , HIS A:322 , ARG A:427 , HIS A:457 , TYR A:458 , TYR A:459 , SER A:460 , CYS A:475 , ALA A:476 , VAL A:477 , VAL A:479 , TYR A:481 , GLY A:491 , VAL A:492 , ALA A:493 , THR A:494 , ARG A:517 , TRP A:679BINDING SITE FOR RESIDUE FAD A 752
2AC2SOFTWAREHOH A:6 , HOH A:19 , HOH A:70 , HOH A:156 , HOH A:194 , ARG A:301 , PRO A:536 , GLY A:537 , THR A:538 , CYS A:569 , ARG A:570 , SER A:599 , ARG A:600 , LYS A:605 , TYR A:607 , GLN A:609 , ASN A:637 , MET A:638 , ASP A:641 , HOH A:764 , HOH A:883 , HOH A:890BINDING SITE FOR RESIDUE NAP A 753

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:277 -Pro A:278
2Cys A:366 -Pro A:367

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (9, 9)

Asymmetric/Biological Unit (9, 9)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_047886D252NNCPR_HUMANPolymorphism  ---AD255N
2UniProtVAR_021155A284PNCPR_HUMANDisease (DISPORD)  ---AA287P
3UniProtVAR_021156R454HNCPR_HUMANDisease (DISPORD)  ---AH457H
4UniProtVAR_021157V489ENCPR_HUMANDisease (ABS1)  ---AV492E
5UniProtVAR_004617A500VNCPR_HUMANPolymorphism1057868AV503V
6UniProtVAR_004618R551QNCPR_HUMANPolymorphism  ---AR554Q
7UniProtVAR_021158C566YNCPR_HUMANDisease (DISPORD)  ---AC569Y
8UniProtVAR_021159Y575CNCPR_HUMANDisease (ABS1)  ---AY578C
9UniProtVAR_021160V605FNCPR_HUMANDisease (DISPORD)  ---AV608F

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FAD_FRPS51384 Ferredoxin reductase-type FAD binding domain profile.NCPR_HUMAN279-521  1A:282-524

(-) Exons   (0, 0)

(no "Exon" information available for 3QFT)

(-) 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:433
 aligned with NCPR_HUMAN | P16435 from UniProtKB/Swiss-Prot  Length:677

    Alignment length:435
                                   252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672     
           NCPR_HUMAN   243 RQYELVVHTDIDAAKVYMGEMGRLKSYENQKPPFDAKNPFLAAVTTNRKLNQGTERHLMHLELDISDSKIRYESGDHVAVYPANDSALVNQLGKILGADLDVVMSLNNLDEESNKKHPFPCPTSYRTALTYYLDITNPPRTNVLYELAQYASEPSEQELLRKMASSSGEGKELYLSWVVEARRHILAILQDCPSLRPPIDHLCELLPRLQARYYSIASSSKVHPNSVHICAVVVEYETKAGRINKGVATNWLRAKEPAGENGGRALVPMFVRKSQFRLPFKATTPVIMVGPGTGVAPFIGFIQERAWLRQQGKEVGETLLYYGCRRSDEDYLYREELAQFHRDGALTQLNVAFSREQSHKVYVQHLLKQDREHLWKLIEGGAHIYVCGDARNMARDVQNTFYDIVAELGAMEHAQAVDYIKKLMTKGRYSLDVWS 677
               SCOP domains d3qfta1 A:246-521 automated matches                                                                                                                                                                                                                                                 d3qfta2 A:522-680 automated matches                                                                                                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....hhhhh.......................eeeeeeeeee........eeeeeee............eeee....hhhhhhhhhhhhh.....eeeeee..............eehhhhhhhh.......hhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhh.....hhhhhhhhh.....hhhhhhhhh.....eeee..........eeeeeee..eee.....eeehhhhhhhhh....--.....eeeeeee.............eeee.hhhhhhhhhhhhhhhhhhhhhh.....eeeeeee........hhhhhhhhhhh....eeeeee........hhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------N-------------------------------P-------------------------------------------------------------------------------------------------------------------------------------------------------------------------H----------------------------------E----------V--------------------------------------------------Q--------------Y--------C-----------------------------F------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------FAD_FR  PDB: A:282-524 UniProt: 279-521                                                                                                                                                                                                            ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qft A 246 RQYELVVHTDIDAAKVYMGEMGRLKSYENQKPPFDAKNPFLAAVTTNRKLNQGTERHLMHLELDISDSKIRYESGDHVAVYPANDSALVNQLGKILGADLDVVMSLNNLDEESNKKHPFPCPTSYRTALTYYLDITNPPRTNVLYELAQYASEPSEQELLRKMASSSGEGKELYLSWVVEARRHILAILQDCPSLRPPIDHLCELLPRLQAHYYSIASSSKVHPNSVHICAVVVEYETKAGRINKGVATNWLRAKEPV--NGGRALVPMFVRKSQFRLPFKATTPVIMVGPGTGVAPFIGFIQERAWLRQQGKEVGETLLYYGCRRSDEDYLYREELAQFHRDGALTQLNVAFSREQSHKVYVQHLLKQDREHLWKLIEGGAHIYVCGDARNMARDVQNTFYDIVAELGAMEHAQAVDYIKKLMTKGRYSLDVWS 680
                                   255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       | -|      515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675     
                                                                                                                                                                                                                                                                                           503  |                                                                                                                                                                              
                                                                                                                                                                                                                                                                                              506                                                                                                                                                                              

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (44, 44)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NCPR_HUMAN | P16435)
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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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.
    GO:0006805    xenobiotic metabolic process    The chemical reactions and pathways involving a xenobiotic compound, a compound foreign to living organisms. Used of chemical compounds, e.g. a xenobiotic chemical, such as a pesticide.
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_HUMAN | P164351b1c 3fjo 3qe2 3qfc 3qfr 3qfs 5emn 5fa6

(-) Related Entries Specified in the PDB File

3qe2 FULL-LENGTH WILD TYPE
3qfc FULL-LENGTH V492E MUTANT
3qfr FULL-LENGTH R457H MUTANT
3qfs FAD/NADPH DOMAIN WILD TYPE