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

(-) Description

Title :  S-NITROSYLATED PHD2 (NO EXPOSED) IN COMPLEX WITH FE(II) AND UN9
 
Authors :  R. Chowdhury, M. A. Mcdonough, C. J. Schofield
Date :  18 Dec 10  (Deposition) - 29 Dec 10  (Release) - 22 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Non-Heme, Transcription And Epigenetic Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Chowdhury, E. Flashman, J. Mecinovic, H. B. Kramer, B. M. Kessler, Y. M. Frapart, J. -L. Boucher, I. J. Clifton, M. A. Mcdonough, C. J. Schofield
Studies On The Reaction Of Nitric Oxide With The Hypoxia-Inducible Factor Prolyl Hydroxylase Domain 2 (Egln1)
J. Mol. Biol. V. 410 268 2011
PubMed-ID: 21601578  |  Reference-DOI: 10.1016/J.JMB.2011.04.075
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EGL NINE HOMOLOG 1
    ChainsA
    EC Number1.14.11.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPET28A
    Expression System Vector TypePLASMID
    FragmentCATALYTIC DOMAIN, RESIDUES 181-426
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHYPOXIA-INDUCIBLE FACTOR PROLYL HYDROXYLASE 2, PROLYL HYDROXYLASE DOMAIN-CONTAINING PROTEIN 2, SM-20, HIF-PH2, HIF-PROLYL HYDROXYLASE 2, HPH-2, PHD2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1FE21Ligand/IonFE (II) ION
2SNC1Mod. Amino AcidS-NITROSO-CYSTEINE
3UN92Ligand/IonN-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:313 , ASP A:315 , HIS A:374 , UN9 A:601 , HOH A:2073BINDING SITE FOR RESIDUE FE2 A 501
2AC2SOFTWAREASP A:254 , MET A:299 , TYR A:303 , TYR A:310 , HIS A:313 , ASP A:315 , TYR A:329 , LEU A:343 , HIS A:374 , VAL A:376 , ARG A:383 , ARG A:398 , VAL A:401 , FE2 A:501 , HOH A:2073 , HOH A:2112BINDING SITE FOR RESIDUE UN9 A 601
3AC3SOFTWARETRP A:258 , ASP A:320 , ARG A:322 , PHE A:391 , VAL A:401 , HOH A:2054 , HOH A:2113BINDING SITE FOR RESIDUE UN9 A 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y34)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Y34)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_027371P317REGLN1_HUMANDisease (ECYT3)80358193AP317R
2UniProtVAR_045902R371HEGLN1_HUMANDisease (ECYT3)119476044AR371H

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FE2OG_OXYPS51471 Fe(2+) 2-oxoglutarate dioxygenase domain profile.EGLN1_HUMAN291-392  1A:291-392

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003666411ENSE00001257532chr1:231560790-2315567444047EGLN1_HUMAN1-2972971A:187-297111
1.3ENST000003666413ENSE00001713815chr1:231509845-231509726120EGLN1_HUMAN298-337401A:298-33740
1.4ENST000003666414ENSE00000921387chr1:231506444-231506308137EGLN1_HUMAN338-383461A:338-38346
1.5ENST000003666415ENSE00000921386chr1:231503382-23150331568EGLN1_HUMAN383-406241A:383-40220
1.6bENST000003666416bENSE00001888819chr1:231502221-2314994972725EGLN1_HUMAN406-426210--

(-) 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:216
 aligned with EGLN1_HUMAN | Q9GZT9 from UniProtKB/Swiss-Prot  Length:426

    Alignment length:216
                                   196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396      
          EGLN1_HUMAN   187 PLPALKLALEYIVPCMNKHGICVVDDFLGKETGQQIGDEVRALHDTGKFTDGQLVSQKSDSSKDIRGDKITWIEGKEPGCETIGLLMSSMDDLIRHCNGKLGSYKINGRTKAMVACYPGNGTGYVRHVDNPNGDGRCVTCIYYLNKDWDAKVSGGILRIFPEGKAQFADIEPKFDRLLFFWSDRRNPHEVQPAYATRYAITVWYFDADERARAKVK 402
               SCOP domains d2y34a_ A: automated matches                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------2OG-FeII_Oxy_3-2y34A01 A:298-391                                                              ----------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhheeee....hhhhhhhhhhhhhhhhhh.......eee........ee..eeeee......hhhhhhhhhhhhhhhhh.........eeee..eeeeee......eeee........eeeeeeee.....hhhhhh..eee........eee.....eeeeee......eee......eeeeeeeeeehhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------R-----------------------------------------------------H------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------FE2OG_OXY  PDB: A:291-392 UniProt: 291-392                                                            ---------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:187-297 UniProt: 1-297 [INCOMPLETE]                                                           Exon 1.3  PDB: A:298-337                Exon 1.4  PDB: A:338-383 UniProt: 338-383     ------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.5             Transcript 1 (2)
                 2y34 A 187 PLPALKLALEYIVPCMNKHGICVVDDFLGKETGQQIGDEVRALHDTGKFTDGQLVSQKSDSSKDIRGDKITWIEGKEPGCETIGLLMSSMDDLIRHCNGKLGSYKINGRTKAMVAcYPGNGTGYVRHVDNPNGDGRCVTCIYYLNKDWDAKVSGGILRIFPEGKAQFADIEPKFDRLLFFWSDRRNPHEVQPAYATRYAITVWYFDADERARAKVK 402
                                   196       206       216       226       236       246       256       266       276       286       296     | 306       316       326       336       346       356       366       376       386       396      
                                                                                                                                             302-SNC                                                                                                

   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/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y34)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Cupin (179)

(-) Gene Ontology  (28, 28)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (EGLN1_HUMAN | Q9GZT9)
molecular function
    GO:0031418    L-ascorbic acid binding    Interacting selectively and non-covalently with L-ascorbic acid, (2R)-2-[(1S)-1,2-dihydroxyethyl]-4-hydroxy-5-oxo-2,5-dihydrofuran-3-olate; L-ascorbic acid is vitamin C and has co-factor and anti-oxidant activities in many species.
    GO:0051213    dioxygenase activity    Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    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: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.
    GO:0016706    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors    Catalysis of the reaction: A + 2-oxoglutarate + O2 = B + succinate + CO2. This is an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from 2-oxoglutarate and one other donor, and one atom of oxygen is incorporated into each donor.
    GO:0031545    peptidyl-proline 4-dioxygenase activity    Catalysis of the reaction: peptidyl L-proline + 2-oxoglutarate + O2 = peptidyl trans-4-hydroxy-L-proline + succinate + CO2.
    GO:0031543    peptidyl-proline dioxygenase activity    Catalysis of the reaction: peptidyl L-proline + 2-oxoglutarate + O2 = peptidyl hydroxy-L-proline + succinate + CO2.
    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:0055008    cardiac muscle tissue morphogenesis    The process in which the anatomical structures of cardiac muscle tissue are generated and organized.
    GO:0060347    heart trabecula formation    The process of creating a trabecula in the heart. A trabecula is a tissue element in the form of a small beam, strut or rod.
    GO:0060711    labyrinthine layer development    The process in which the labyrinthine layer of the placenta progresses, from its formation to its mature state.
    GO:0030821    negative regulation of cAMP catabolic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
    GO:0051344    negative regulation of cyclic-nucleotide phosphodiesterase activity    Any process that stops or reduces the rate of cyclic nucleotide phosphodiesterase activity, the catalysis of the reaction: nucleotide 3',5'-cyclic phosphate + H2O = nucleotide 5'-phosphate.
    GO:0043433    negative regulation of sequence-specific DNA binding transcription factor activity    Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
    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:0032364    oxygen homeostasis    A homeostatic process involved in the maintenance of an internal steady state of oxygen within an organism or cell.
    GO:0018401    peptidyl-proline hydroxylation to 4-hydroxy-L-proline    The modification of peptidyl-proline to form 4-hydroxy-L-proline; catalyzed by procollagen-proline,2-oxoglutarate-4-dioxygenase.
    GO:0045765    regulation of angiogenesis    Any process that modulates the frequency, rate or extent of angiogenesis.
    GO:0061418    regulation of transcription from RNA polymerase II promoter in response to hypoxia    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a hypoxia stimulus.
    GO:0001666    response to hypoxia    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 stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0071731    response to nitric oxide    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 nitric oxide stimulus.
    GO:0060412    ventricular septum morphogenesis    The developmental process in which a ventricular septum is generated and organized. A ventricular septum is an anatomical structure that separates the lower chambers (ventricles) of the heart from one another.
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:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    FE2  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SNC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    UN9  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2y34)
 

(-) 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
  2y34
    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
  EGLN1_HUMAN | Q9GZT9
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.14.11.-
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  609820
    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
  EGLN1_HUMAN | Q9GZT9
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        EGLN1_HUMAN | Q9GZT92g19 2g1m 2hbt 2hbu 2y33 3hqr 3hqu 3ouh 3oui 3ouj 4bqw 4bqx 4bqy 4jzr 4kbz 4uwd 5a3u 5l9b 5l9r 5l9v 5la9 5las 5lat 5lb6 5lbb 5lbc 5lbe 5lbf 5v18

(-) Related Entries Specified in the PDB File

2g19 CELLULAR OXYGEN SENSING: CRYSTAL STRUCTURE OF HYPOXIA- INDUCIBLE FACTOR PROLYL HYDROXYLASE (PHD2)
2g1m CELLULAR OXYGEN SENSING: CRYSTAL STRUCTURE OF HYPOXIA- INDUCIBLE FACTOR PROLYL HYDROXYLASE (PHD2)
2hbt CRYSTAL STRUCTURE OF HIF PROLYL HYDROXYLASE EGLN-1 INCOMPLEX WITH A BIOLOGICALLY ACTIVE INHIBITOR
2hbu CRYSTAL STRUCTURE OF HIF PROLYL HYDROXYLASE EGLN-1 INCOMPLEX WITH A BIOLOGICALLY ACTIVE INHIBITOR
2y33 S-NITROSYLATED PHD2 (GSNO SOAKED) IN COMPLEX WITH ZN(II) AND UN9