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(-) Description

Title :  CRYSTAL STRUCTURE OF RAT LIVER DIHYDROPTERIDINE REDUCTASE
 
Authors :  K. I. Varughese, M. M. Skinner, J. M. Whiteley, D. A. Matthews, N. H. Xuon
Date :  30 Mar 92  (Deposition) - 15 Jul 93  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Oxidoreductase(Acting On Nadh Or Nadph) (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. I. Varughese, M. M. Skinner, J. M. Whiteley, D. A. Matthews, N. H. Xuong
Crystal Structure Of Rat Liver Dihydropteridine Reductase.
Proc. Natl. Acad. Sci. Usa V. 89 6080 1992
PubMed-ID: 1631094  |  Reference-DOI: 10.1073/PNAS.89.13.6080

(-) Compounds

Molecule 1 - DIHYDROPTERIDINE REDUCTASE
    ChainsA
    EC Number1.6.99.10
    EngineeredYES
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:12 , ARG A:15 , GLY A:16 , ALA A:17 , LEU A:18 , ASP A:37 , VAL A:38 , VAL A:50 , GLN A:59 , LYS A:69 , VAL A:82 , ALA A:83 , GLY A:84 , GLY A:85 , LYS A:105 , GLN A:106 , THR A:110 , ALA A:131 , TYR A:146 , LYS A:150 , VAL A:179 , THR A:180 , LEU A:181 , ASN A:186 , HOH A:245 , HOH A:248 , HOH A:254 , HOH A:275 , HOH A:279 , HOH A:300 , HOH A:308BINDING SITE FOR RESIDUE NAD A 241

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1DHR)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1DHR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1DHR)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADH_SHORTPS00061 Short-chain dehydrogenases/reductases family signature.DHPR_RAT134-162  1A:133-161
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADH_SHORTPS00061 Short-chain dehydrogenases/reductases family signature.DHPR_RAT134-162  2A:133-161

(-) Exons   (7, 7)

Asymmetric Unit (7, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000043851ENSRNOE00000030853chr14:70741985-70742143159DHPR_RAT1-32321A:5-3127
1.2ENSRNOT000000043852ENSRNOE00000030907chr14:70744499-7074459193DHPR_RAT33-63311A:32-6231
1.3ENSRNOT000000043853ENSRNOE00000030939chr14:70746515-7074661197DHPR_RAT64-96331A:63-9533
1.4ENSRNOT000000043854ENSRNOE00000030977chr14:70747481-70747621141DHPR_RAT96-143481A:95-14248
1.5ENSRNOT000000043855ENSRNOE00000031006chr14:70750300-70750408109DHPR_RAT143-179371A:142-17837
1.6ENSRNOT000000043856ENSRNOE00000031035chr14:70751781-7075186484DHPR_RAT179-207291A:178-20629
1.7ENSRNOT000000043857ENSRNOE00000031064chr14:70754973-70755600628DHPR_RAT207-241351A:206-24035

(-) Sequences/Alignments

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:236
 aligned with DHPR_RAT | P11348 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:236
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235      
             DHPR_RAT     6 EARRVLVYGGRGALGSRCVQAFRARNWWVASIDVVENEEASASVIVKMTDSFTEQADQVTAEVGKLLGDQKVDAILCVAGGWAGGNAKSKSLFKNCDLMWKQSIWTSTISSHLATKHLKEGGLLTLAGAKAALDGTPGMIGYGMAKGAVHQLCQSLAGKNSGMPSGAAAIAVLPVTLDTPMNRKSMPEADFSSWTPLEFLVETFHDWITGNKRPNSGSLIQVVTTDGKTELTPAYF 241
               SCOP domains d1dhra_ A: Dihydropteridin reductase (pteridine reductase)                                                                                                                                                                                   SCOP domains
               CATH domains 1dhrA00 A:5-240 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) ..eeeeee....hhhhhhhhhhhh...eeeeee.......eeeeee.....hhhhhhhhhhhhhhhh.....eeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee..hhhh......hhhhhhhhhhhhhhhhhh..........------------hhhhhh-----hhh---hhhhhhhhhhhh.........eeeeeeee...eeeeee.. Sec.struct. author (1)
     Sec.struct. author (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------eeeeeeeeeeeeeeeeeeeeeeeeeeeee---------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: A:133-161    ------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:5-31      Exon 1.2  PDB: A:32-62         Exon 1.3  PDB: A:63-95           ----------------------------------------------Exon 1.5  PDB: A:142-178             ---------------------------Exon 1.7  PDB: A:206-240            Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------Exon 1.4  PDB: A:95-142 UniProt: 96-143         -----------------------------------Exon 1.6  PDB: A:178-206     ---------------------------------- Transcript 1 (2)
                 1dhr A   5 EARRVLVYGGRGALGSRCVQAFRARNWWVASIDVVENEEASASVIVKMTDSFTEQADQVTAEVGKLLGDQKVDAILCVAGGWAGGNAKSKSLFKNCDLMWKQSIWTSTISSHLATKHLKEGGLLTLAGAKAALDGTPGMIGYGMAKGAVHQLCQSLAGKNSGMPSGAAAIAVLPVTLDTPMNRKSMPEADFSSWTPLEFLVETFHDWITGNKRPNSGSLIQVVTTDGKTELTPAYF 240
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234      

   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  (1, 1)

Asymmetric Unit

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1DHR)

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)
Chain A   (DHPR_RAT | P11348)
molecular function
    GO:0004155    6,7-dihydropteridine reductase activity    Catalysis of the reaction: NADP+ + 5,6,7,8-tetrahydropteridine = NADPH + H+ + 6,7-dihydropteridine.
    GO:0070404    NADH binding    Interacting selectively and non-covalently with the reduced form, NADH, of nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions.
    GO:0070402    NADPH binding    Interacting selectively and non-covalently with the reduced form, NADPH, of nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0006559    L-phenylalanine catabolic process    The chemical reactions and pathways resulting in the breakdown of phenylalanine, 2-amino-3-phenylpropanoic acid.
    GO:0035690    cellular response to drug    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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0001889    liver development    The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes.
    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:0010044    response to aluminum ion    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 an aluminum ion stimulus.
    GO:0033762    response to glucagon    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 glucagon stimulus.
    GO:0010288    response to lead ion    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 lead ion stimulus.
    GO:0006729    tetrahydrobiopterin biosynthetic process    The chemical reactions and pathways resulting in the formation of tetrahydrobiopterin, the reduced form of biopterin (2-amino-4-hydroxy-6-(1,2-dihydroxypropyl)-pteridine). It functions as a hydroxylation coenzyme, e.g. in the conversion of phenylalanine to tyrosine.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.

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