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(-) Description

Title :  FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH S-2-HYDROXYGLUTARATE
 
Authors :  R. Chowdhury, I. J. Clifton, C. J. Schofield
Date :  18 Mar 11  (Deposition) - 30 Mar 11  (Release) - 11 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.28
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Oxidoreductase, Non-Heme Iron, Dioxygenase, Metal-Binding, Transcription, Helix-Loop-Helix-Beta, Dsbh, Facial Triad, Asparaginyl/ Aspartyl Hydroxylase, Ankyrin Repeat Domain, Ard, Beta-Hydroxylation, Transcription Activator/Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Chowdhury, K. K. Yeoh, Y. M. Tian, L. Hillringhaus, E. A. Bagg, N. R. Rose, I. K. Leung, X. S. Li, E. C. Woon, M. Yang, M. A. Mcdonough, O. N. King, I. J. Clifton, R. J. Klose, T. D. Claridge, P. J. Ratcliffe, C. J. Schofield, A. Kawamura
The Oncometabolite 2-Hydroxyglutarate Inhibits Histone Lysine Demethylases.
Embo Rep. V. 12 463 2011
PubMed-ID: 21460794  |  Reference-DOI: 10.1038/EMBOR.2011.43

(-) Compounds

Molecule 1 - HYPOXIA-INDUCIBLE FACTOR 1-ALPHA INHIBITOR
    ChainsA
    EC Number1.14.11.16
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPET28A
    Expression System Vector TypePLASMID
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymFACTOR INHIBITING HIF, FACTOR INHIBITING HIF-1, FIH-1, HYPOXIA-INDUCIBLE FACTOR ASPARAGINE HYDROXYLASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric Unit (4, 9)
No.NameCountTypeFull Name
1FE1Ligand/IonFE (III) ION
2GOL2Ligand/IonGLYCEROL
3S2G2Ligand/Ion(2S)-2-HYDROXYPENTANEDIOIC ACID
4SO44Ligand/IonSULFATE ION
Biological Unit 1 (3, 16)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2GOL4Ligand/IonGLYCEROL
3S2G4Ligand/Ion(2S)-2-HYDROXYPENTANEDIOIC ACID
4SO48Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:199 , ASP A:201 , HIS A:279 , S2G A:601 , GOL A:604BINDING SITE FOR RESIDUE FE A 501
2AC2SOFTWARETYR A:145 , THR A:196 , HIS A:199 , ASP A:201 , ASN A:205 , PHE A:207 , LYS A:214 , HIS A:279 , ILE A:281 , ASN A:294 , TRP A:296 , FE A:501 , GOL A:604BINDING SITE FOR RESIDUE S2G A 601
3AC3SOFTWAREGLN A:148 , THR A:149BINDING SITE FOR RESIDUE S2G A 602
4AC4SOFTWARELYS A:99 , TYR A:230 , SER A:240 , GLN A:241 , ASP A:243BINDING SITE FOR RESIDUE GOL A 603
5AC5SOFTWAREGLN A:147 , HIS A:199 , ASP A:201 , TRP A:296 , FE A:501 , S2G A:601BINDING SITE FOR RESIDUE GOL A 604
6AC6SOFTWAREASP A:222 , LYS A:311 , ALA A:312 , HOH A:2081 , HOH A:2082 , HOH A:2083BINDING SITE FOR RESIDUE SO4 A 901
7AC7SOFTWAREARG A:138 , GLY A:140 , GLU A:141 , GLU A:142BINDING SITE FOR RESIDUE SO4 A 902
8AC8SOFTWARELYS A:107 , ARG A:320 , LYS A:324BINDING SITE FOR RESIDUE SO4 A 903
9AC9SOFTWAREARG A:143 , GLU A:192 , GLY A:193 , LEU A:285 , ASN A:286BINDING SITE FOR RESIDUE SO4 A 905

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Tyr A:308 -Pro A:309

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_051028P41AHIF1N_HUMANPolymorphism2295778AP41A

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_051028P41AHIF1N_HUMANPolymorphism2295778AP41A

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1JMJCPS51184 JmjC domain profile.HIF1N_HUMAN142-312  1A:142-312
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1JMJCPS51184 JmjC domain profile.HIF1N_HUMAN142-312  2A:142-312

(-) Exons   (8, 8)

Asymmetric Unit (8, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2bENST000002991632bENSE00001695622chr10:102295616-102295892277HIF1N_HUMAN1-59591A:1-5959
1.3bENST000002991633bENSE00001100126chr10:102296168-102296418251HIF1N_HUMAN60-143841A:60-14384
1.4bENST000002991634bENSE00001100124chr10:102300391-102300539149HIF1N_HUMAN143-193511A:143-19351
1.5aENST000002991635aENSE00001100127chr10:102304708-102304853146HIF1N_HUMAN193-241491A:193-24149
1.6bENST000002991636bENSE00001100128chr10:102305700-102305806107HIF1N_HUMAN242-277361A:242-27736
1.7ENST000002991637ENSE00001100132chr10:102306275-10230633864HIF1N_HUMAN277-298221A:277-29822
1.8bENST000002991638bENSE00001100130chr10:102306897-102307007111HIF1N_HUMAN299-335371A:299-33537
1.9bENST000002991639bENSE00001212367chr10:102307850-1023097631914HIF1N_HUMAN336-349141A:336-34914

(-) 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:349
 aligned with HIF1N_HUMAN | Q9NWT6 from UniProtKB/Swiss-Prot  Length:349

    Alignment length:349
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340         
          HIF1N_HUMAN     1 MAATAAEAVASGSGEPREEAGALGPAWDESQLRSYSFPTRPIPRLSQSDPRAEELIENEEPVVLTDTNLVYPALKWDLEYLQENIGNGDFSVYSASTHKFLYYDEKKMANFQNFKPRSNREEMKFHEFVEKLQDIQQRGGEERLYLQQTLNDTVGRKIVMDFLGFNWNWINKQQGKRGWGQLTSNLLLIGMEGNVTPAHYDEQQNFFAQIKGYKRCILFPPDQFECLYPYPVHHPCDRQSQVDFDNPDYERFPNFQNVVGYETVVGPGDVLYIPMYWWHHIESLLNGGITITVNFWYKGAPTPKRIEYPLKAHQKVAIMRNIEKMLGEALGNPQEVGPLLNTMIKGRYN 349
               SCOP domains d2ydea_ A: Hypoxia-inducible factor HIF ihhibitor (FIH1)                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------------------------------Cupin_8-2ydeA01 A:48-302                                                                                                                                                                                                                                       ----------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh........hhhhh....hhhhh......eee..ee...hhhhhhhhhh...eee.....hhhhhhhhhhhhhhhh...eeeeeee........hhhhh.........eeeeeeehhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhh.hhhhhhhhhhhhh...eee.eeeee....eeeee....eeeeeeee..eeeeeehhhhhhhhh.......................hhhhhhh.eeeeee....eeee....eeeeee......eeeeeeee.............hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------JMJC  PDB: A:142-312 UniProt: 142-312                                                                                                                                      ------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: A:1-59 UniProt: 1-59                       Exon 1.3b  PDB: A:60-143 UniProt: 60-143                                            -------------------------------------------------Exon 1.5a  PDB: A:193-241 UniProt: 193-241       Exon 1.6b  PDB: A:242-277           ---------------------Exon 1.8b  PDB: A:299-335            Exon 1.9b      Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------------------------------------Exon 1.4b  PDB: A:143-193 UniProt: 143-193         -----------------------------------------------------------------------------------Exon 1.7              --------------------------------------------------- Transcript 1 (2)
                 2yde A   1 MAATAAEAVASGSGEPREEAGALGPAWDESQLRSYSFPTRPIPRLSQSDPRAEELIENEEPVVLTDTNLVYPALKWDLEYLQENIGNGDFSVYSASTHKFLYYDEKKMANFQNFKPRSNREEMKFHEFVEKLQDIQQRGGEERLYLQQTLNDTVGRKIVMDFLGFNWNWINKQQGKRGWGQLTSNLLLIGMEGNVTPAHYDEQQNFFAQIKGYKRCILFPPDQFECLYPYPVHHPCDRQSQVDFDNPDYERFPNFQNVVGYETVVGPGDVLYIPMYWWHHIESLLNGGITITVNFWYKGAPTPKRIEYPLKAHQKVAIMRNIEKMLGEALGNPQEVGPLLNTMIKGRYN 349
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340         

   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  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Cupin (179)

(-) Gene Ontology  (32, 32)

Asymmetric Unit(hide GO term definitions)
Chain A   (HIF1N_HUMAN | Q9NWT6)
molecular function
    GO:0051059    NF-kappaB binding    Interacting selectively and non-covalently with NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters.
    GO:0005112    Notch binding    Interacting selectively and non-covalently with the Notch (N) protein, a surface receptor.
    GO:0071532    ankyrin repeat binding    Interacting selectively and non-covalently with an ankyrin repeat of a protein. Ankyrin repeats are tandemly repeated modules of about 33 amino acids; each repeat folds into a helix-loop-helix structure with a beta-hairpin/loop region projecting out from the helices at a 90-degree angle, and repeats stack to form an L-shaped structure.
    GO:0031406    carboxylic acid binding    Interacting selectively and non-covalently with a carboxylic acid, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
    GO:0048037    cofactor binding    Interacting selectively and non-covalently with a cofactor, a substance that is required for the activity of an enzyme or other protein. Cofactors may be inorganic, such as the metal atoms zinc, iron, and copper in certain forms, or organic, in which case they are referred to as coenzymes. Cofactors may either be bound tightly to active sites or bind loosely with the substrate.
    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: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: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:0019826    oxygen sensor activity    Interacting selectively and non-covalently with and responding, e.g. by conformational change, to changes in the cellular level of oxygen (O2).
    GO:0036140    peptidyl-asparagine 3-dioxygenase activity    Catalysis of the reaction: peptidyl L-asparagine + 2-oxoglutarate + O2 = peptidyl 3-hydroxy-L-asparagine + succinate + CO2.
    GO:0036139    peptidyl-histidine dioxygenase activity    Catalysis of the reaction: peptidyl L-histidine + 2-oxoglutarate + O2 = peptidyl hydroxy-L-histidine + 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).
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0045746    negative regulation of Notch signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of the Notch signaling pathway.
    GO:0061428    negative regulation of transcription from RNA polymerase II promoter in response to hypoxia    Any process that decreases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a hypoxia stimulus.
    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:0042265    peptidyl-asparagine hydroxylation    The hydroxylation of peptidyl-asparagine to form peptidyl-hydroxyasparagine.
    GO:0042264    peptidyl-aspartic acid hydroxylation    The hydroxylation of peptidyl-aspartic acid to form peptidyl-hydroxyaspartic acid.
    GO:0036138    peptidyl-histidine hydroxylation    The hydroxylation of peptidyl-histidine to form peptidyl-hydroxyhistidine.
    GO:0045663    positive regulation of myoblast differentiation    Any process that activates or increases the frequency, rate or extent of myoblast differentiation. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers.
    GO:2001214    positive regulation of vasculogenesis    Any process that activates or increases the frequency, rate or extent of vasculogenesis.
    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:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
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:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HIF1N_HUMAN | Q9NWT61h2k 1h2l 1h2m 1h2n 1iz3 1mze 1mzf 1yci 2cgn 2cgo 2ilm 2w0x 2wa3 2wa4 2xum 2y0i 2yc0 3d8c 3kcx 3kcy 3od4 3p3n 3p3p 4ai8 4b7e 4b7k 4bio 4jaa 4nr1 4z1v 4z2w 5jwk 5jwl 5jwp

(-) Related Entries Specified in the PDB File

1h2k FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH HIF-1 ALPHA FRAGMENT PEPTIDE
1h2l FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH HIF-1 ALPHA FRAGMENT PEPTIDE
1h2m FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH HIF-1 ALPHA FRAGMENT PEPTIDE
1h2n FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH HIF-1 ALPHA FRAGMENT PEPTIDE
1iz3 DIMERIC STRUCTURE OF FIH (FACTOR INHIBITING HIF)
1mze HUMAN FACTOR INHIBITING HIF (FIH1)
1mzf HUMAN FACTOR INHIBITING HIF (FIH1) IN COMPLEX WITH 2- OXOGLUTARATE
1yci FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH N-( CARBOXYCARBONYL)-D-PHENYLALANINE
2cgn FACTOR INHIBITING HIF-1 ALPHA WITH SUCCINATE
2cgo FACTOR INHIBITING HIF-1 ALPHA WITH FUMARATE
2w0x FACTOR INHIBITING HIF-1 ALPHA WITH PYRIDINE 2,4 DICARBOXYLIC ACID
2wa3 FACTOR INHIBITING HIF-1 ALPHA WITH 2-(3-HYDROXYPHENYL )-2-OXOACETIC ACID
2wa4 FACTOR INHIBITING HIF-1 ALPHA WITH N,3- DIHYDROXYBENZAMIDE
2xum FACTOR INHIBITING HIF (FIH) Q239H MUTANT IN COMPLEX WITH ZN(II), NOG AND ASP-SUBSTRATE PEPTIDE (20-MER)
2y0i FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH TANKYRASE-2 (TNKS2) FRAGMENT PEPTIDE (21-MER)
2yc0 FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH R-2- HYDROXYGLUTARATE