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(-) Description

Title :  STRUCTURE OF KIAA1718 JUMONJI DOMAIN IN COMPLEX WITH N-OXALYLGLYCINE
 
Authors :  J. R. Horton, A. K. Upadhyay, H. H. Qi, X. Zhang, Y. Shi, X. Cheng
Date :  29 Nov 09  (Deposition) - 22 Dec 09  (Release) - 09 Feb 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.69
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Jumonji Domain Lysine Demethylase, Metal-Binding, Iron, Nickel Ion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. R. Horton, A. K. Upadhyay, H. H. Qi, X. Zhang, Y. Shi, X. Cheng
Enzymatic And Structural Insights For Substrate Specificity Of A Family Of Jumonji Histone Lysine Demethylases.
Nat. Struct. Mol. Biol. V. 17 38 2010
PubMed-ID: 20023638  |  Reference-DOI: 10.1038/NSMB.1753

(-) Compounds

Molecule 1 - JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 1D
    ChainsA
    EC Number2.-.-.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)CODONPLUS
    Expression System Taxid562
    FragmentRESIDUES 92-488
    GeneJHDM1D, KIAA1718
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1NI2Ligand/IonNICKEL (II) ION
2OGA1Ligand/IonN-OXALYLGLYCINE
3OXY1Ligand/IonOXYGEN MOLECULE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1NI-1Ligand/IonNICKEL (II) ION
2OGA1Ligand/IonN-OXALYLGLYCINE
3OXY1Ligand/IonOXYGEN MOLECULE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1NI-1Ligand/IonNICKEL (II) ION
2OGA2Ligand/IonN-OXALYLGLYCINE
3OXY2Ligand/IonOXYGEN MOLECULE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:282 , ASP A:284 , HIS A:354 , OGA A:5798BINDING SITE FOR RESIDUE NI A 489
2AC2SOFTWARESER A:249 , TRP A:250 , VAL A:251 , PHE A:369 , LEU A:370BINDING SITE FOR RESIDUE NI A 490
3AC3SOFTWAREVAL A:290 , ASN A:368BINDING SITE FOR RESIDUE OXY A 491
4AC4SOFTWAREASN A:224 , ILE A:226 , THR A:279 , HIS A:282 , ASP A:284 , TYR A:292 , LYS A:299 , HIS A:354 , VAL A:356 , NI A:489BINDING SITE FOR RESIDUE OGA A 5798

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3KVB)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3KVB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_049652D392YKDM7A_HUMANPolymorphism5020212AD392Y

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_049652D392YKDM7A_HUMANPolymorphism5020212AD392Y

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_049652D392YKDM7A_HUMANPolymorphism5020212AD392Y

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1JMJCPS51184 JmjC domain profile.KDM7A_HUMAN230-386  1A:230-386
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1JMJCPS51184 JmjC domain profile.KDM7A_HUMAN230-386  1A:230-386
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1JMJCPS51184 JmjC domain profile.KDM7A_HUMAN230-386  2A:230-386

(-) Exons   (0, 0)

(no "Exon" information available for 3KVB)

(-) 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:366
 aligned with KDM7A_HUMAN | Q6ZMT4 from UniProtKB/Swiss-Prot  Length:941

    Alignment length:366
                                   123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473      
          KDM7A_HUMAN   114 PVQAGTRTFIKELRSRVFPSADEIIIKMHGSQLTQRYLEKHGFDVPIMVPKLDDLGLRLPSPTFSVMDVERYVGGDKVIDVIDVARQADSKMTLHNYVKYFMNPNRPKVLNVISLEFSDTKMSELVEVPDIAKKLSWVENYWPDDSVFPKPFVQKYCLMGVQDSYTDFHIDFGGTSVWYHVLWGEKIFYLIKPTDENLARYESWSSSVTQSEVFFGDKVDKCYKCVVKQGHTLFVPTGWIHAVLTSQDCMAFGGNFLHNLNIGMQLRCYEMEKRLKTPDLFKFPFFEAICWFVAKNLLETLKELREDGFQPQTYLVQGVKALHTALKLWMKKELVSEHAFEIPDNVRPGHLIKELSKVIRAIEEEN 479
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhh...hhhhh.ee......hhhhhhhhh....eee...............hhhhhhhhhh...eeeeee.....eeeeehhhhhhhhh.......eeeeeee...hhhhhhh..hhhhhhhhhhhhhh.............eeeee....eeeee.hhhhheeeeeeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee....eeee....eeeeeeeeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Y--------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------JMJC  PDB: A:230-386 UniProt: 230-386                                                                                                                        --------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3kvb A 114 PVQAGTRTFIKELRSRVFPSADEIIIKMHGSQLTQRYLEKHGFDVPIMVPKLDDLGLRLPSPTFSVMDVERYVGGDKVIDVIDVARQADSKMTLHNYVKYFMNPNRPKVLNVISLEFSDTKMSELVEVPDIAKKLSWVENYWPDDSVFPKPFVQKYCLMGVQDSYTDFHIDFGGTSVWYHVLWGEKIFYLIKPTDENLARYESWSSSVTQSEVFFGDKVDKCYKCVVKQGHTLFVPTGWIHAVLTSQDCMAFGGNFLHNLNIGMQLRCYEMEKRLKTPDLFKFPFFEAICWFVAKNLLETLKELREDGFQPQTYLVQGVKALHTALKLWMKKELVSEHAFEIPDNVRPGHLIKELSKVIRAIEEEN 479
                                   123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473      

   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  (0, 0)

(no "SCOP Domain" information available for 3KVB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KVB)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3KVB)

(-) Gene Ontology  (25, 25)

Asymmetric Unit(hide GO term definitions)
Chain A   (KDM7A_HUMAN | Q6ZMT4)
molecular function
    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:0032452    histone demethylase activity    Catalysis of the removal of a methyl group from a histone.
    GO:0071558    histone demethylase activity (H3-K27 specific)    Catalysis of the removal of a methyl group from lysine at position 27 of the histone H3 protein.
    GO:0051864    histone demethylase activity (H3-K36 specific)    Catalysis of the reaction: histone H3 N6-methyl-L-lysine (position 36) + alpha-ketoglutarate + O2 = succinate + CO2 + formaldehyde + lysine. This reaction is the removal of a methyl group from lysine at position 36 of the histone H3 protein.
    GO:0032454    histone demethylase activity (H3-K9 specific)    Catalysis of the reaction: histone H3 N6-methyl-L-lysine (position 9) + alpha-ketoglutarate + O2 = succinate + CO2 + formaldehyde + lysine. This reaction is the removal of a methyl group from lysine at position 9 of the histone H3 protein.
    GO:0035575    histone demethylase activity (H4-K20 specific)    Catalysis of the reaction: histone H4 N6-methyl-L-lysine (position 20) + 2-oxoglutarate + O2 = histone H4 L-lysine (position 20) + succinate + formaldehyde + CO2. This reaction is the removal of a methyl group from lysine at position 20 of the histone H4 protein.
    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:0035064    methylated histone binding    Interacting selectively and non-covalently with a histone in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0071557    histone H3-K27 demethylation    The modification of histone H3 by the removal of a methyl group from lysine at position 27 of the histone.
    GO:0070544    histone H3-K36 demethylation    The modification of histone H3 by the removal of a methyl group from lysine at position 36 of the histone.
    GO:0033169    histone H3-K9 demethylation    The modification of histone H3 by the removal of a methyl group from lysine at position 9 of the histone.
    GO:0035574    histone H4-K20 demethylation    The modification of histone H4 by the removal of a methyl group from lysine at position 20 of the histone.
    GO:0030901    midbrain development    The process whose specific outcome is the progression of the midbrain over time, from its formation to the mature structure. The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles).
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    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:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    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:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        KDM7A_HUMAN | Q6ZMT43kv5 3kv6 3kv9 3kva 3u78

(-) Related Entries Specified in the PDB File

3kv4
3kv5
3kv6
3kv9 STRUCTURE OF KIAA1718 JUMONJI DOMAIN
3kva STRUCTURE OF KIAA1718 JUMONJI DOMAIN IN COMPLEX WITH ALPHA- KETOGLUTARATE