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(-) Description

Title :  CEKDM7A FROM C.ELEGANS, COMPLEX WITH H3K4ME3 PEPTIDE, H3K9ME2 PEPTIDE AND NOG
 
Authors :  Y. Yang, L. Hu, P. Wang, H. Hou, C. D. Chen, Y. Xu
Date :  31 May 10  (Deposition) - 30 Jun 10  (Release) - 11 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.31
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Histone, Methylation, Demethylase, Phd, Jmjc, Fe(Ii) And Alpha-Kg (Alpha-Ketoglutarate)-Dependent Dioxygenase Family, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Yang, L. Hu, P. Wang, H. Hou, Y. Lin, Y. Liu, Z. Li, R. Gong, X. Feng, L. Zhou, W. Zhang, Y. Dong, H. Yang, H. Lin, Y. Wang, C. D. Chen, Y. Xu
Structural Insights Into A Dual-Specificity Histone Demethylase Cekdm7A From Caenorhabditis Elegans
Cell Res. V. 20 886 2010
PubMed-ID: 20567261  |  Reference-DOI: 10.1038/CR.2010.86

(-) Compounds

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN
    Chains: A
    EC Number: 1.14.11.27
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: PHD DOMAIN, UNP RESIDUES 201-724
    Gene: F29B9.2
    Organism Scientific: CAENORHABDITIS ELEGANS
    Organism Taxid: 6239
    Synonym: LYSINE DEMETHYLASE
 
Molecule 2 - HISTONE H3 PEPTIDE
    Chains: B
    Engineered: YES
    Fragment: JMJC DOMAIN, UNP RESIDUES 2-16
    Organism Scientific: CAENORHABDITIS ELEGANS
    Organism Taxid: 6239
    Other Details: H3K4ME3
    Other Details - Source: CHEMICAL SYNTHESIS, PURCHASED FROM A COMPANY
    Synthetic: YES
 
Molecule 3 - HISTONE H3 PEPTIDE
    Chains: C
    Engineered: YES
    Fragment: JMJC DOMAIN, UNP RESIDUES 2-18
    Organism Scientific: CAENORHABDITIS ELEGANS
    Organism Taxid: 6239
    Other Details: H3K9ME2
    Other Details - Source: CHEMICAL SYNTHESIS, PURCHASED FROM A COMPANY
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 6)

Asymmetric/Biological Unit (5, 6)
No.NameCountTypeFull Name
1FE21Ligand/IonFE (II) ION
2M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
3MLY1Mod. Amino AcidN-DIMETHYL-LYSINE
4OGA1Ligand/IonN-OXALYLGLYCINE
5ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREOGA A:4 , HOH A:7 , HIS A:495 , ASP A:497 , HIS A:567BINDING SITE FOR RESIDUE FE2 A 1
2AC2SOFTWARECYS A:198 , CYS A:201 , HIS A:252 , CYS A:255BINDING SITE FOR RESIDUE ZN A 2
3AC3SOFTWARECYS A:244 , CYS A:247 , CYS A:271 , CYS A:274BINDING SITE FOR RESIDUE ZN A 3
4AC4SOFTWAREFE2 A:1 , HOH A:7 , HOH A:33 , ASN A:421 , LEU A:423 , THR A:492 , HIS A:495 , ASP A:497 , TYR A:505 , LYS A:512 , HIS A:567 , VAL A:569 , MLY C:9BINDING SITE FOR RESIDUE OGA A 4

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3N9O)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3N9O)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3N9O)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_PHD_1PS01359 Zinc finger PHD-type signature.KDM7_CAEEL211-287  1A:198-274
2JMJCPS51184 JmjC domain profile.KDM7_CAEEL441-612  1A:428-599

(-) Exons   (0, 0)

(no "Exon" information available for 3N9O)

(-) 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:483
 aligned with KDM7_CAEEL | Q9GYI0 from UniProtKB/Swiss-Prot  Length:910

    Alignment length:512
                                   214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714  
           KDM7_CAEEL   205 PKESDRCGGCGKFTHEDDLIALEEEKKKEKEKPLMSKKKSHHHKKNDFQWIGCDSCQTWYHFLCSGLEQFEYYLYEKFFCPKCVPHTGHSIRYKVVAPHRYRWYSPNEKHLGIEVGSKTWIEDFITRENTVPSPTDDEVCIVEDGYEFRREFEKLGGADNWGKVFMVKDMDGLNMTMPKPGFDLEDVVKIMGSDYEVDTIDVYNQSTYSMKLDTFRKLFRDTKNRPLLYNFLSLEFSDNNEMKEIAKPPRFVQEISMVNRLWPDVSGAEYIKLLQREEYLPEDQRPKVEQFCLAGMAGSYTDFHVDFGGSSVYYHILKGEKIFYIAAPTEQNFAAYQAHETSPDTTTWFGDIANGAVKRVVIKEGQTLLIPAGWIHAVLTPVDSLVFGGNFLHLGNLEMQMRVYHLENAIRKEIRSEEKFYFPNFELLHWMYMRNVLLEKITEANQEGSDMREQEKNIWTASQIMKAEMERWMDRELRLGPEKNAILPTDDKNKIMISVRKQIEIQTKIQNA 716
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------JmjC-3n9oA01 A:482-582                                                                               ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh...........--------------------------.....eeee......eee.hhh..hhhhh..eee.............ee............hhhhh.......hhhhhhhhhhhhhhh.......eeeeeehhhhhhhhhhhhhhhhh..eeeeee.............hhhhhhhhhh...eeeeee....eeeeeehhhhhhhhhh.......eeeeeee.....hhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhh....hhhhh.....eeeee...eeeeee.hhhhheeeeeeeeeeeeeeee..hhhhhhhhhhhhhh.....hhhhhh....eeeeee...eeee....eeeeeeeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh..---..hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------ZF_PHD_1  PDB: A:198-274 UniProt: 211-287                                    ---------------------------------------------------------------------------------------------------------------------------------------------------------JMJC  PDB: A:428-599 UniProt: 441-612                                                                                                                                       -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n9o A 192 PKESDRCGGCGKFTHED--------------------------KKNDFQWIGCDSCQTWYHFLCSGLEQFEYYLYEKFFCPKCVPHTGHSIRYKVVAPHRYRWYSPNEKHLGIEVGSKTWIEDFITRENTVPSPTDDEVCIVEDGYEFRREFEKLGGADNWGKVFMVKDMDGLNMTMPKPGFDLEDVVKIMGSDYEVDTIDVYNQSTYSMKLDTFRKLFRDTKNRPLLYNFLSLEFSDNNEMKEIAKPPRFVQEISMVNRLWPDVSGAEYIKLLQREEYLPEDQRPKVEQFCLAGMAGSYTDFHVDFGGSSVYYHILKGEKIFYIAAPTEQNFAAYQAHETSPDTTTWFGDIANGAVKRVVIKEGQTLLIPAGWIHAVLTPVDSLVFGGNFLHLGNLEMQMRVYHLENAIRKEIRSEEKFYFPNFELLHWMYMRNVLLEKITEANQEGSDMREQEKNIWTASQIMKAEMERWMDRELRLGPE---ILPTDDKNKIMISVRKQIEIQTKIQNA 703
                                   201      |  -         -         -   |   241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671 |   | 681       691       701  
                                          208                        235                                                                                                                                                                                                                                                                                                                                                                                                                                                   673 677                          


Chain B from PDB  Type:PROTEIN  Length:6
 aligned with H3_CAEEL | P08898 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:6
             H3_CAEEL     2 ARTKQT   7
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ..eee. Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 3n9o B   1 ARTkQT   6
                               |  
                               |  
                               4-M3L


Chain C from PDB  Type:PROTEIN  Length:8
 aligned with H3_CAEEL | P08898 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:8
             H3_CAEEL     5 KQTARKST  12
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 3n9o C   4 KQTARkST  11
                                 |  
                                 9-MLY
   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 3N9O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3N9O)

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (18, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (KDM7_CAEEL | Q9GYI0)
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:0042393    histone binding    Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
    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: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: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: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: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: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:0040012    regulation of locomotion    Any process that modulates the frequency, rate or extent of locomotion of a cell or organism.
    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: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.

Chain B,C   (H3_CAEEL | P08898)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000786    nucleosome    A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
    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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  KDM7_CAEEL | Q9GYI0
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  1.14.11.27
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 Related Entries

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

UniProtKB/Swiss-Prot
        H3_CAEEL | P08898: 3n9l 3n9n 3n9p 3n9q
        KDM7_CAEEL | Q9GYI0: 3n9l 3n9m 3n9n 3n9p 3n9q 3puq 3pur

(-) Related Entries Specified in the PDB File

3n9l LYSINE DEMETHYLASE WITH HISTONE H3(K4ME3) AND NOG
3n9m APO LYSINE DEMETHYLASE
3n9n LYSINE DEMETHYLASE WITH HISTONE H3(K4ME3K9ME2) AND NOG
3n9p LYSINE DEMETHYLASE WITH HISTONE H3(K4ME3K27ME2) AND NOG
3n9q LYSINE DEMETHYLASE WITH HISTONE H3(K4ME3) AND HISTONE H3(K27ME2) AND NOG