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(-) Description

Title :  CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY
 
Authors :  M. Vollmar, C. Gileadi, L. Shrestha, S. Goubin, C. Johansson, T. Krojer J. W. Raynor, A. Bradley, F. Von Delft, C. H. Arrowsmith, C. Bountra, A U. Oppermann
Date :  31 Jan 13  (Deposition) - 27 Feb 13  (Release) - 20 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. J. Walport, R. J. Hopkinson, M. Vollmar, S. K. Madden, C. Gileadi, U. Oppermann, C. J. Schofield, C. Johansson
Human Uty(Kdm6C) Is A Male-Specific Nepsilon-Methyl Lysyl Demethylase.
J. Biol. Chem. V. 289 18302 2014
PubMed-ID: 24798337  |  Reference-DOI: 10.1074/JBC.M114.555052

(-) Compounds

Molecule 1 - HISTONE DEMETHYLASE UTY
    Chains: A, B
    EC Number: 1.14.11.-
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PFB-CT10HF-LIC
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: JMJC DOMAIN, RESIDUES 878-1347
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: UBIQUITOUSLY-TRANSCRIBED TPR PROTEIN ON THE Y CHROMOSOME, UBIQUITOUSLY-TRANSCRIBED Y CHROMOSOME TETRATRICOPEPTIDE REPEAT PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 20)

Asymmetric Unit (4, 20)
No.NameCountTypeFull Name
1AKG2Ligand/Ion2-OXOGLUTARIC ACID
2EDO14Ligand/Ion1,2-ETHANEDIOL
3FE22Ligand/IonFE (II) ION
4ZN2Ligand/IonZINC ION
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1AKG1Ligand/Ion2-OXOGLUTARIC ACID
2EDO8Ligand/Ion1,2-ETHANEDIOL
3FE21Ligand/IonFE (II) ION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 8)
No.NameCountTypeFull Name
1AKG1Ligand/Ion2-OXOGLUTARIC ACID
2EDO6Ligand/Ion1,2-ETHANEDIOL
3FE21Ligand/IonFE (II) ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:1084 , THR A:1090 , HIS A:1093 , GLU A:1095 , SER A:1101 , ASN A:1103 , HIS A:1173 , ALA A:1185 , HOH A:2135 , HOH A:2140 , EDO A:2351 , FE2 A:4001BINDING SITE FOR RESIDUE AKG A4000
02AC2SOFTWAREHIS A:1093 , GLU A:1095 , HIS A:1173 , HOH A:2140 , AKG A:4000BINDING SITE FOR RESIDUE FE2 A4001
03AC3SOFTWARECYS A:1278 , CYS A:1281 , CYS A:1305 , CYS A:1308BINDING SITE FOR RESIDUE ZN A4002
04AC4SOFTWARELYS B:1084 , THR B:1090 , HIS B:1093 , GLU B:1095 , SER B:1101 , ASN B:1103 , TRP B:1113 , HIS B:1173 , ALA B:1185 , HOH B:2115 , HOH B:2121 , EDO B:2350 , FE2 B:4001BINDING SITE FOR RESIDUE AKG B4000
05AC5SOFTWAREHIS B:1093 , GLU B:1095 , HIS B:1173 , HOH B:2121 , AKG B:4000BINDING SITE FOR RESIDUE FE2 B4001
06AC6SOFTWARECYS B:1278 , CYS B:1281 , CYS B:1305 , CYS B:1308BINDING SITE FOR RESIDUE ZN B4002
07AC7SOFTWAREILE A:967 , TRP A:968 , ARG A:969 , ASN A:1131BINDING SITE FOR RESIDUE EDO A2345
08AC8SOFTWAREILE B:967 , TRP B:968 , ARG B:969 , LEU B:1133 , HOH B:2261BINDING SITE FOR RESIDUE EDO B2345
09AC9SOFTWARETHR A:908 , CYS A:1100 , ASN A:1168 , PRO A:1190 , THR A:1192 , CYS A:1194BINDING SITE FOR RESIDUE EDO A2346
10BC1SOFTWARESER A:932 , THR A:933 , GLN A:986 , PRO A:1108 , HOH A:2040 , EDO A:2348 , EDO A:2349BINDING SITE FOR RESIDUE EDO A2347
11BC2SOFTWAREGLN B:986 , PHE B:990 , HOH B:2068 , EDO B:2347BINDING SITE FOR RESIDUE EDO B2346
12BC3SOFTWARETHR B:933 , GLN B:986 , GLY B:1107 , PRO B:1108 , ASN B:1182 , EDO B:2346BINDING SITE FOR RESIDUE EDO B2347
13BC4SOFTWAREGLN A:986 , PHE A:990 , PRO A:1108 , HOH A:2076 , EDO A:2347BINDING SITE FOR RESIDUE EDO A2348
14BC5SOFTWARELYS A:895 , VAL B:1123 , ASP B:1126 , ALA B:1150BINDING SITE FOR RESIDUE EDO B2348
15BC6SOFTWARELEU A:928 , GLY A:929 , SER A:932 , ILE A:1106 , EDO A:2347BINDING SITE FOR RESIDUE EDO A2349
16BC7SOFTWAREHIS A:1267 , HIS A:1276 , TYR A:1301BINDING SITE FOR RESIDUE EDO A2350
17BC8SOFTWAREHIS B:1267 , GLU B:1273 , HIS B:1276 , TYR B:1301 , VAL B:1303BINDING SITE FOR RESIDUE EDO B2349
18BC9SOFTWAREGLY A:1075 , GLN A:1080 , TYR A:1082 , GLU A:1095 , SER A:1101 , TRP A:1186 , ASN A:1187 , HOH A:2133 , HOH A:2140 , AKG A:4000BINDING SITE FOR RESIDUE EDO A2351
19CC1SOFTWAREGLY B:1075 , GLN B:1080 , TYR B:1082 , GLU B:1095 , SER B:1101 , ALA B:1185 , ASN B:1187 , HOH B:2114 , HOH B:2121 , AKG B:4000BINDING SITE FOR RESIDUE EDO B2350
20CC2SOFTWARETYR A:891 , LEU A:892 , GLU A:893 , ARG A:918 , GLN B:991BINDING SITE FOR RESIDUE EDO A2352

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:1024 -Pro A:1025
2Gly A:1107 -Pro A:1108
3Gly B:1107 -Pro B:1108

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1JMJCPS51184 JmjC domain profile.UTY_HUMAN1042-1205
 		  2A:1042-1205
B:1042-1205
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1JMJCPS51184 JmjC domain profile.UTY_HUMAN1042-1205
 		  1A:1042-1205
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1JMJCPS51184 JmjC domain profile.UTY_HUMAN1042-1205
 		  1-
B:1042-1205

(-) Exons   (0, 0)

(no "Exon" information available for 3ZLI)

(-) 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:443
 aligned with UTY_HUMAN | O14607 from UniProtKB/Swiss-Prot  Length:1347

    Alignment length:466
                                   889       899       909       919       929       939       949       959       969       979       989       999      1009      1019      1029      1039      1049      1059      1069      1079      1089      1099      1109      1119      1129      1139      1149      1159      1169      1179      1189      1199      1209      1219      1229      1239      1249      1259      1269      1279      1289      1299      1309      1319      1329      1339      
           UTY_HUMAN    880 KDKLNPPTPSIYLENKRDAFFPPLHQFCTNPKNPVTVIRGLAGALKLDLGLFSTKTLVEANNEHMVEVRTQLLQPADENWDPTGTKKIWRCESNRSHTTIAKYAQYQASSFQESLREENEKRTQHKDHSDNESTSSENSGRRRKGPFKTIKFGTNIDLSDNKKWKLQLHELTKLPAFARVVSAGNLLTHVGHTILGMNTVQLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFVVPEDYWGVLNDFCEKNNLNFLMSSWWPNLEDLYEANVPVYRFIQRPGDLVWINAGTVHWVQAVGWCNNIAWNVGPLTACQYKLAVERYEWNKLKSVKSPVPMVHLSWNMARNIKVSDPKLFEMIKYCLLKILKQYQTLREALVAAGKEVIWHGRTNDEPAHYCSICEVEVFNLLFVTNESNTQKTYIVHCHDCARKTSKSLENFVVLEQYKMEDLIQVYDQFTLALSLSS 1345
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh....eee..hhhhhhhhhhhhhhhh....eeeeehhhhhhh.hhhhhhhhhhhhhh...eeeeeeee....................eeeeeeehhhhhhhhhhhhhhhhhhhh.-----------------------.....eeeeeeeee......hhhhhhhhh..hhhhh.....hhhhhh..........eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhh...........hhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.........ee......ee..eeeeehhhhhh......hhhhhhhhh.....eeeee..hhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------JMJC  PDB: A:1042-1205 UniProt: 1042-1205                                                                                                                           -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3zli A  880 KDKLNPPTPSIYLENKRDAFFPPLHQFCTNPKNPVTVIRGLAGALKLDLGLFSTKTLVEANNEHMVEVRTQLLQPADENWDPTGTKKIWRCESNRSHTTIAKYAQYQASSFQESLREENE-----------------------KGPFKTIKFGTNIDLSDNKKWKLQLHELTKLPAFARVVSAGNLLTHVGHTILGMNTVQLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFVVPEDYWGVLNDFCEKNNLNFLMSSWWPNLEDLYEANVPVYRFIQRPGDLVWINAGTVHWVQAVGWCNNIAWNVGPLTACQYKLAVERYEWNKLKSVKSPVPMVHLSWNMARNIKVSDPKLFEMIKYCLLKILKQYQTLREALVAAGKEVIWHGRTNDEPAHYCSICEVEVFNLLFVTNESNTQKTYIVHCHDCARKTSKSLENFVVLEQYKMEDLIQVYDQFTLALSLSS 1345
                                   889       899       909       919       929       939       949       959       969       979       989       999         -         -   |  1029      1039      1049      1059      1069      1079      1089      1099      1109      1119      1129      1139      1149      1159      1169      1179      1189      1199      1209      1219      1229      1239      1249      1259      1269      1279      1289      1299      1309      1319      1329      1339      
                                                                                                                                                 999                    1023                                                                                                                                                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:439
 aligned with UTY_HUMAN | O14607 from UniProtKB/Swiss-Prot  Length:1347

    Alignment length:465
                                   890       900       910       920       930       940       950       960       970       980       990      1000      1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210      1220      1230      1240      1250      1260      1270      1280      1290      1300      1310      1320      1330      1340     
           UTY_HUMAN    881 DKLNPPTPSIYLENKRDAFFPPLHQFCTNPKNPVTVIRGLAGALKLDLGLFSTKTLVEANNEHMVEVRTQLLQPADENWDPTGTKKIWRCESNRSHTTIAKYAQYQASSFQESLREENEKRTQHKDHSDNESTSSENSGRRRKGPFKTIKFGTNIDLSDNKKWKLQLHELTKLPAFARVVSAGNLLTHVGHTILGMNTVQLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFVVPEDYWGVLNDFCEKNNLNFLMSSWWPNLEDLYEANVPVYRFIQRPGDLVWINAGTVHWVQAVGWCNNIAWNVGPLTACQYKLAVERYEWNKLKSVKSPVPMVHLSWNMARNIKVSDPKLFEMIKYCLLKILKQYQTLREALVAAGKEVIWHGRTNDEPAHYCSICEVEVFNLLFVTNESNTQKTYIVHCHDCARKTSKSLENFVVLEQYKMEDLIQVYDQFTLALSLSS 1345
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee..hhhhhhhhhhhhhhhh....eeeeehhhhhhh.hhhhhhhhhhhhhh...eeeeeeee.....................eeeeeehhhhhhhhhhhhhhhhhhhh.--------------------------..eeeeeeeee......hhhhhhhhh..hhhhh.....hhhhhh..........eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhh...........hhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.........ee......ee..eeeeehhhhhh......hhhhhhhhh.....eeeee..hhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------JMJC  PDB: B:1042-1205 UniProt: 1042-1205                                                                                                                           -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3zli B  881 DKLNPPTPSIYLENKRDAFFPPLHQFCTNPKNPVTVIRGLAGALKLDLGLFSTKTLVEANNEHMVEVRTQLLQPADENWDPTGTKKIWRCESNRSHTTIAKYAQYQASSFQESLREENE--------------------------FKTIKFGTNIDLSDNKKWKLQLHELTKLPAFARVVSAGNLLTHVGHTILGMNTVQLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFVVPEDYWGVLNDFCEKNNLNFLMSSWWPNLEDLYEANVPVYRFIQRPGDLVWINAGTVHWVQAVGWCNNIAWNVGPLTACQYKLAVERYEWNKLKSVKSPVPMVHLSWNMARNIKVSDPKLFEMIKYCLLKILKQYQTLREALVAAGKEVIWHGRTNDEPAHYCSICEVEVFNLLFVTNESNTQKTYIVHCHDCARKTSKSLENFVVLEQYKMEDLIQVYDQFTLALSLSS 1345
                                   890       900       910       920       930       940       950       960       970       980       990        |-         -         -     |1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210      1220      1230      1240      1250      1260      1270      1280      1290      1300      1310      1320      1330      1340     
                                                                                                                                                999                       1026
   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 3ZLI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (UTY_HUMAN | O14607)
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: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.
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: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:0010468    regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
cellular component
    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
        UTY_HUMAN | O14607: 3zpo 4uf0 5a1l 5fxv 5fxw 5fxx 5fxz 5fy0 5fy1 5fy7 5fym

(-) Related Entries Specified in the PDB File

3zpo CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY WITH BOUND GSK J1