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(-) Description

Title :  HIF PROLYL HYDROXYLASE 2 (PHD2/ EGLN1) IN COMPLEX WITH MN(II) AND N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE (IOX3/UN9)
 
Authors :  R. Chowdhury, C. J. Schofield
Date :  03 Jun 13  (Deposition) - 19 Jun 13  (Release) - 13 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.79
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, 2-Oxoglutarate, Dioxygenase, Egln, Oxygenase, Dna-Binding, Transcription, Dsbh, Facial Triad, Asparaginyl/ Aspartyl Hydroxylase, Transcription And Epigenetic Regulation, Signaling, Development, Cell Structure, Ard, Beta-Hydroxylation, Transcription Activator/Inhibitor, S-Nitrosylation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Chowdhury, J. I. Candela-Lena, M. C. Chan, D. J. Greenald, K. K. Yeoh Y. Tian, M. A. Mcdonough, A. Tumber, N. R. Rose, A. Conejo-Garcia, M. Demetriades, S. Mathavan, A. Kawamura, M. K. Lee, F. Van Eeden, C. W. Pugh, P. J. Ratcliffe, C. J. Schofield
Selective Small Molecule Probes For The Hypoxia Inducible Factor (Hif) Prolyl Hydroxylases.
Acs Chem. Biol. V. 8 1488 2013
PubMed-ID: 23683440  |  Reference-DOI: 10.1021/CB400088Q

(-) 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, HIF-PH2, HIF-PROLYL HYDROXYLASE 2, HPH-2, PROLYL HYDROXYLASE DOMAIN-CONTAINING PROTEIN 2, PHD2, SM-20

 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
1MN1Ligand/IonMANGANESE (II) ION
2UN91Ligand/IonN-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:313 , ASP A:315 , HIS A:374 , UN9 A:601 , HOH A:2078BINDING SITE FOR RESIDUE MN A 501
2AC2SOFTWAREASP A:254 , ILE A:256 , 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 , MN A:501 , HOH A:2121BINDING SITE FOR RESIDUE UN9 A 601

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:201 -A:208

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4BQX)

 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:188-297110
1.3ENST000003666413ENSE00001713815chr1:231509845-231509726120EGLN1_HUMAN298-337401A:298-33740
1.4ENST000003666414ENSE00000921387chr1:231506444-231506308137EGLN1_HUMAN338-383461A:338-38346
1.5ENST000003666415ENSE00000921386chr1:231503382-23150331568EGLN1_HUMAN383-406241A:383-40422
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:217
 aligned with EGLN1_HUMAN | Q9GZT9 from UniProtKB/Swiss-Prot  Length:426

    Alignment length:217
                                   197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       
          EGLN1_HUMAN   188 LPALKLALEYIVPCMNKHGICVVDDFLGKETGQQIGDEVRALHDTGKFTDGQLVSQKSDSSKDIRGDKITWIEGKEPGCETIGLLMSSMDDLIRHCNGKLGSYKINGRTKAMVACYPGNGTGYVRHVDNPNGDGRCVTCIYYLNKDWDAKVSGGILRIFPEGKAQFADIEPKFDRLLFFWSDRRNPHEVQPAYATRYAITVWYFDADERARAKVKYL 404
               SCOP domains d4bqxa_ A: automated matches                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhheeee....hhhhhhhhhhhhhhhhhh.......eee........ee..eeeee......hhhhhhhhhhhhhhhhh.........eeee..eeeeee......eeee........eeeeeeee.....hhhhhh..eee........eee.....eeeeee......eee......eeeeeeeeeehhhhhhhhhhh. 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:188-297 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 [INCOMPLETE]  Transcript 1 (2)
                 4bqx A 188 LPALKLALEYIVPCMNKHGICVVDDFLGKETGQQIGDEVRALHDTGKFTDGQLVSQKSDSSKDIRGDKITWIEGKEPGCETIGLLMSSMDDLIRHCNGKLGSYKINGRTKAMVACYPGNGTGYVRHVDNPNGDGRCVTCIYYLNKDWDAKVSGGILRIFPEGKAQFADIEPKFDRLLFFWSDRRNPHEVQPAYATRYAITVWYFDADERARAKVKYL 404
                                   197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       

   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 4BQX)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4BQX)

(-) 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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        EGLN1_HUMAN | Q9GZT92g19 2g1m 2hbt 2hbu 2y33 2y34 3hqr 3hqu 3ouh 3oui 3ouj 4bqw 4bqy 4jzr 4kbz 4uwd 5a3u 5l9b 5l9r 5l9v 5la9 5las 5lat 5lb6 5lbb 5lbc 5lbe 5lbf 5v18

(-) Related Entries Specified in the PDB File

4bqw HIF PROLYL HYDROXYLASE 2 (PHD2/ EGLN1) IN COMPLEX WITH MN(II) AND 2-(4-HYDROXY-2-OXO-1,2- DIHYDROQUINOLINE-3-CARBOXAMIDO)ACETIC ACID
4bqy HIF PROLYL HYDROXYLASE 2 (PHD2/ EGLN1) IN COMPLEX WITH FE(II) AND N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL) CARBONYL]ALANINE