Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  MOUSE SEPIAPTERIN REDUCTASE COMPLEXED WITH NADP AND SEPIAPTERIN
 
Authors :  G. Auerbach, A. Herrmann, M. Guetlich, M. Fischer, U. Jacob, A. Bacher,
Date :  23 May 97  (Deposition) - 13 Jan 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Oxidoreductase, Sepiapterin Reductase, Tetrahydrobiopterin (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Auerbach, A. Herrmann, M. Gutlich, M. Fischer, U. Jacob, A. Bacher, R. Huber
The 1. 25 A Crystal Structure Of Sepiapterin Reductase Reveals Its Binding Mode To Pterins And Brain Neurotransmitters.
Embo J. V. 16 7219 1997
PubMed-ID: 9405351  |  Reference-DOI: 10.1093/EMBOJ/16.24.7219

(-) Compounds

Molecule 1 - SEPIAPTERIN REDUCTASE
    ChainsA
    EC Number1.1.1.153
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Cellular LocationCYTOSOL
    Expression System Taxid562
    OrganBRAIN
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1BIO1Ligand/IonBIOPTERIN
2NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1BIO2Ligand/IonBIOPTERIN
2NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:15 , SER A:17 , ARG A:18 , GLY A:19 , PHE A:20 , ALA A:42 , ARG A:43 , SER A:44 , ALA A:69 , ASP A:70 , LEU A:71 , ASN A:101 , ALA A:102 , ALA A:103 , LEU A:127 , ILE A:156 , SER A:157 , TYR A:171 , LYS A:175 , PRO A:199 , GLY A:200 , LEU A:202 , ASN A:204 , MET A:206 , GLN A:207 , BIO A:801 , HOH A:813 , HOH A:814 , HOH A:825 , HOH A:867 , HOH A:881 , HOH A:888 , HOH A:910 , HOH A:995 , HOH A:1192BINDING SITE FOR RESIDUE NAP A 800
2AC2SOFTWARESER A:158 , LEU A:159 , TRP A:168 , TYR A:171 , ALA A:198 , GLY A:200 , PRO A:201 , GLN A:207 , ASP A:258 , TYR A:260 , NAP A:800 , HOH A:1157BINDING SITE FOR RESIDUE BIO A 801

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1SEP)

(-) Exons   (0, 0)

(no "Exon" information available for 1SEP)

(-) 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:259
 aligned with SPRE_MOUSE | Q64105 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:259
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252         
           SPRE_MOUSE     3 ADGLGCAVCVLTGASRGFGRALAPQLARLLSPGSVMLVSARSESMLRQLKEELGAQQPDLKVVLAAADLGTEAGVQRLLSAVRELPRPEGLQRLLLINNAATLGDVSKGFLNVNDLAEVNNYWALNLTSMLCLTSGTLNAFQDSPGLSKTVVNISSLCALQPYKGWGLYCAGKAARDMLYQVLAAEEPSVRVLSYAPGPLDNDMQQLARETSKDPELRSKLQKLKSDGALVDCGTSAQKLLGLLQKDTFQSGAHVDFYD 261
               SCOP domains d1sepa_ A: Sepiapterin reductase                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1sepA00 A:3-261 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                 CATH domains
               Pfam domains ------adh_short-1sepA01 A:9-189                                                                                                                                                            ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee.....hhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhh.........eeeeee...........hhh...hhhhhhhhhhh.hhhhhhhhhhhhh.......eeeeeeee.hhh.......hhhhhhhhhhhhhhhhhhhh...eeeeeee......hhhhhhhhh...hhhhhhhhhhhh......hhhhhhhhhhhhhh......eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sep A   3 ADGLGCAVCVLTGASRGFGRALAPQLARLLSPGSVMLVSARSESMLRQLKEELGAQQPDLKVVLAAADLGTEAGVQRLLSAVRELPRPEGLQRLLLINNAATLGDVSKGFLNVNDLAEVNNYWALNLTSMLCLTSGTLNAFQDSPGLSKTVVNISSLCALQPYKGWGLYCAGKAARDMLYQVLAAEEPSVRVLSYAPGPLDNDMQQLARETSKDPELRSKLQKLKSDGALVDCGTSAQKLLGLLQKDTFQSGAHVDFYD 261
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252         

   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  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (19, 19)

Asymmetric Unit(hide GO term definitions)
Chain A   (SPRE_MOUSE | Q64105)
molecular function
    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.
    GO:0004757    sepiapterin reductase activity    Catalysis of the reaction: 7,8-dihydrobiopterin + NADP+ = sepiapterin + NADPH + H+.
biological process
    GO:0006558    L-phenylalanine metabolic process    The chemical reactions and pathways involving L-phenylalanine, the L-enantiomer of 2-amino-3-phenylpropanoic acid, i.e. (2S)-2-amino-3-phenylpropanoic acid.
    GO:0048667    cell morphogenesis involved in neuron differentiation    The process in which the structures of a neuron are generated and organized. This process occurs while the initially relatively unspecialized cell is acquiring the specialized features of a neuron.
    GO:0042417    dopamine metabolic process    The chemical reactions and pathways involving dopamine, a catecholamine neurotransmitter and a metabolic precursor of noradrenaline and adrenaline.
    GO:0006809    nitric oxide biosynthetic process    The chemical reactions and pathways resulting in the formation of nitric oxide, nitrogen monoxide (NO), a colorless gas only slightly soluble in water.
    GO:0042415    norepinephrine metabolic process    The chemical reactions and pathways involving norepinephrine, a hormone secreted by the adrenal medulla, and a neurotransmitter in the sympathetic peripheral nervous system and in some tracts in the central nervous system. It is also the demethylated biosynthetic precursor of epinephrine.
    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:0019889    pteridine metabolic process    The chemical reactions and pathways involving pteridine, pyrazino(2,3-dipyrimidine), the parent structure of pterins and the pteroyl group.
    GO:0040014    regulation of multicellular organism growth    Any process that modulates the frequency, rate or extent of growth of the body of an organism so that it reaches its usual body size.
    GO:0042428    serotonin metabolic process    The chemical reactions and pathways involving serotonin (5-hydroxytryptamine), a monoamine neurotransmitter occurring in the peripheral and central nervous systems, also having hormonal properties.
    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.
    GO:0046146    tetrahydrobiopterin metabolic process    The chemical reactions and pathways involving 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.
    GO:0050882    voluntary musculoskeletal movement    The movement of an organism or part of an organism using mechanoreceptors, the nervous system, striated muscle and/or the skeletal system that can be controlled at will.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    BIO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1sep)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1sep
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SPRE_MOUSE | Q64105
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.1.1.153
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  SPRE_MOUSE | Q64105
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SPRE_MOUSE | Q641051nas 1oaa

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1SEP)