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(-) Description

Title :  PHF2 JUMONJI-NOG-NI(II)
 
Authors :  J. R. Horton, A. K. Upadhyay, H. Hashimoto, X. Zhang, X. Cheng
Date :  06 Dec 10  (Deposition) - 26 Jan 11  (Release) - 29 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.08
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Alpha-Ketoglutarate-Fe2+ Dependent Dioxygenases, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. R. Horton, A. K. Upadhyay, H. Hashimoto, X. Zhang, X. Cheng
Structural Basis For Human Phf2 Jumonji Domain Interaction With Metal Ions.
J. Mol. Biol. V. 406 1 2011
PubMed-ID: 21167174  |  Reference-DOI: 10.1016/J.JMB.2010.12.013

(-) Compounds

Molecule 1 - PHD FINGER PROTEIN 2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PXC870
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: JUMONJI DOMAIN (UNP RESIDUES 60-451)
    Gene: PHF2, KIAA0662
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GRC5

 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  (5, 21)

Asymmetric Unit (5, 21)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2EDO14Ligand/Ion1,2-ETHANEDIOL
3NI2Ligand/IonNICKEL (II) ION
4OGA2Ligand/IonN-OXALYLGLYCINE
5OXY1Ligand/IonOXYGEN MOLECULE
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO5Ligand/Ion1,2-ETHANEDIOL
3NI-1Ligand/IonNICKEL (II) ION
4OGA1Ligand/IonN-OXALYLGLYCINE
5OXY-1Ligand/IonOXYGEN MOLECULE
Biological Unit 2 (3, 11)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO9Ligand/Ion1,2-ETHANEDIOL
3NI-1Ligand/IonNICKEL (II) ION
4OGA1Ligand/IonN-OXALYLGLYCINE
5OXY1Ligand/IonOXYGEN MOLECULE

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:375 , HIS A:425 , PHE A:426 , LYS A:427BINDING SITE FOR RESIDUE EDO A 1
02AC2SOFTWAREARG A:201BINDING SITE FOR RESIDUE EDO A 2
03AC3SOFTWAREHOH A:47 , LEU A:113 , GLY A:134 , LYS A:214BINDING SITE FOR RESIDUE EDO A 7
04AC4SOFTWARETYR A:372 , GLU A:424BINDING SITE FOR RESIDUE EDO A 8
05AC5SOFTWAREPRO A:130 , LYS A:131 , GLN A:311 , ASP B:179BINDING SITE FOR RESIDUE EDO A 10
06AC6SOFTWAREHOH A:24 , SER A:216 , TRP A:217 , VAL A:218 , PHE A:336 , LEU A:337BINDING SITE FOR RESIDUE CL A 3
07AC7SOFTWAREHIS A:249 , ASP A:251 , TYR A:321 , OGA A:453 , HOH A:500BINDING SITE FOR RESIDUE NI A 452
08AC8SOFTWARETHR A:246 , HIS A:249 , ASP A:251 , TYR A:259 , LYS A:266 , TYR A:321 , THR A:323 , HIS A:335 , NI A:452 , HOH A:492BINDING SITE FOR RESIDUE OGA A 453
09AC9SOFTWARETHR B:193 , HIS B:335 , OGA B:453BINDING SITE FOR RESIDUE OXY B 2
10BC1SOFTWAREARG A:107 , VAL A:108 , PRO A:109 , PRO A:130 , ASP B:179 , TYR B:182 , SER B:183BINDING SITE FOR RESIDUE EDO B 3
11BC2SOFTWARELYS B:375 , PHE B:426 , LYS B:427BINDING SITE FOR RESIDUE EDO B 4
12BC3SOFTWAREASP A:297 , GLN A:298 , VAL A:299 , HIS B:425BINDING SITE FOR RESIDUE EDO B 5
13BC4SOFTWARETHR B:234 , LYS B:235BINDING SITE FOR RESIDUE EDO B 6
14BC5SOFTWAREGLY B:110 , LEU B:113 , GLY B:134 , LYS B:214 , HOH B:476BINDING SITE FOR RESIDUE EDO B 9
15BC6SOFTWARESER B:198 , LYS B:230 , LYS B:232 , HOH B:468BINDING SITE FOR RESIDUE EDO B 11
16BC7SOFTWARESER A:275 , HOH B:45 , LEU B:228 , ALA B:229 , ASN B:365BINDING SITE FOR RESIDUE EDO B 12
17BC8SOFTWARELYS A:400 , LYS B:171BINDING SITE FOR RESIDUE EDO B 13
18BC9SOFTWAREASP A:420 , PRO B:273 , SER B:275 , ILE B:278 , MET B:344 , ARG B:347BINDING SITE FOR RESIDUE EDO B 14
19CC1SOFTWARESER B:216 , TRP B:217 , VAL B:218 , PHE B:336 , LEU B:337 , HOH B:488BINDING SITE FOR RESIDUE CL B 452
20CC2SOFTWAREHIS B:249 , ASP B:251 , TYR B:321 , OGA B:453 , HOH B:486BINDING SITE FOR RESIDUE NI B 1
21CC3SOFTWARENI B:1 , OXY B:2 , LEU B:238 , THR B:246 , HIS B:249 , ASP B:251 , TYR B:259 , LYS B:266 , TYR B:321 , THR B:323 , HIS B:335 , HOH B:493BINDING SITE FOR RESIDUE OGA B 453

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Thr A:184 -Asn A:185

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1JMJCPS51184 JmjC domain profile.PHF2_HUMAN197-353
 		  2A:197-353
B:197-353
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1JMJCPS51184 JmjC domain profile.PHF2_HUMAN197-353
 		  1A:197-353
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1JMJCPS51184 JmjC domain profile.PHF2_HUMAN197-353
 		  1-
B:197-353

(-) Exons   (0, 0)

(no "Exon" information available for 3PUS)

(-) 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:365
 aligned with PHF2_HUMAN | O75151 from UniProtKB/Swiss-Prot  Length:1096

    Alignment length:365
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439     
           PHF2_HUMAN    80 KPVQNGSQLFIKELRSRTFPSAEDVVARVPGSQLTLGYMEEHGFTEPILVPKKDGLGLAVPAPTFYVSDVENYVGPERSVDVTDVTKQKDCKMKLKEFVDYYYSTNRKRVLNVTNLEFSDTRMSSFVEPPDIVKKLSWVENYWPDDALLAKPKVTKYCLICVKDSYTDFHIDSGGASAWYHVLKGEKTFYLIRPASANISLYERWRSASNHSEMFFADQVDKCYKCIVKQGQTLFIPSGWIYATLTPVDCLAFAGHFLHSLSVEMQMRAYEVERRLKLGSLTQFPNFETACWYMGKHLLEAFKGSHKSGKQLPPHLVQGAKILNGAFRSWTKKQALAEHEDELPEHFKPSQLIKDLAKEIRLSEN 444
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhh.........ee.hhhhhhhhhhhhhh....eee...............hhhhhhhhhh...eeeeee....eeeeeehhhhhhhhh.......eeeeeee...hhhhhhh..hhhhhhhhhhhhhh.............eeeee...eeeeee.hhhhheeeeeeee.eeeeeee..hhhhhhhhhhhhh..hhhhhhhhhhh...eeeeee...eeee....eeeeee...eeeeeeee....hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------JMJC  PDB: A:197-353 UniProt: 197-353                                                                                                                        ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pus A  80 KPVQNGSQLFIKELRSRTFPSAEDVVARVPGSQLTLGYMEEHGFTEPILVPKKDGLGLAVPAPTFYVSDVENYVGPERSVDVTDVTKQKDCKMKLKEFVDYYYSTNRKRVLNVTNLEFSDTRMSSFVEPPDIVKKLSWVENYWPDDALLAKPKVTKYCLICVKDSYTDFHIDSGGASAWYHVLKGEKTFYLIRPASANISLYERWRSASNHSEMFFADQVDKCYKCIVKQGQTLFIPSGWIYATLTPVDCLAFAGHFLHSLSVEMQMRAYEVERRLKLGSLTQFPNFETACWYMGKHLLEAFKGSHKSGKQLPPHLVQGAKILNGAFRSWTKKQALAEHEDELPEHFKPSQLIKDLAKEIRLSEN 444
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439     


Chain B from PDB  Type:PROTEIN  Length:364
 aligned with PHF2_HUMAN | O75151 from UniProtKB/Swiss-Prot  Length:1096

    Alignment length:364
                                    91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441    
           PHF2_HUMAN    82 VQNGSQLFIKELRSRTFPSAEDVVARVPGSQLTLGYMEEHGFTEPILVPKKDGLGLAVPAPTFYVSDVENYVGPERSVDVTDVTKQKDCKMKLKEFVDYYYSTNRKRVLNVTNLEFSDTRMSSFVEPPDIVKKLSWVENYWPDDALLAKPKVTKYCLICVKDSYTDFHIDSGGASAWYHVLKGEKTFYLIRPASANISLYERWRSASNHSEMFFADQVDKCYKCIVKQGQTLFIPSGWIYATLTPVDCLAFAGHFLHSLSVEMQMRAYEVERRLKLGSLTQFPNFETACWYMGKHLLEAFKGSHKSGKQLPPHLVQGAKILNGAFRSWTKKQALAEHEDELPEHFKPSQLIKDLAKEIRLSENA 445
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------------------------------------------------------------JmjC-3pusB01 B:236-336                                                                               ------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------JmjC-3pusB02 B:236-336                                                                               ------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ....hhhhhhhhh.....hhhhh.ee.hhhhhhhhhhhhhh....eee...............hhhhhhhhhh...eeeeee....eeeeeehhhhhhhhh.......eeeeeee...hhhhhhh..hhhhhhhhhhhhhh.............eeeee...eeeeee.hhhhheeeeeeee.eeeeeee..hhhhhhhhhhhhhh.hhhhhhhhhhh...eeeeee...eeee....eeeeee...eeeeeeee.hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh...hhhhhhhhh....hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------JMJC  PDB: B:197-353 UniProt: 197-353                                                                                                                        -------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pus B  82 VQNGSQLFIKELRSRTFPSAEDVVARVPGSQLTLGYMEEHGFTEPILVPKKDGLGLAVPAPTFYVSDVENYVGPERSVDVTDVTKQKDCKMKLKEFVDYYYSTNRKRVLNVTNLEFSDTRMSSFVEPPDIVKKLSWVENYWPDDALLAKPKVTKYCLICVKDSYTDFHIDSGGASAWYHVLKGEKTFYLIRPASANISLYERWRSASNHSEMFFADQVDKCYKCIVKQGQTLFIPSGWIYATLTPVDCLAFAGHFLHSLSVEMQMRAYEVERRLKLGSLTQFPNFETACWYMGKHLLEAFKGSHKSGKQLPPHLVQGAKILNGAFRSWTKKQALAEHEDELPEHFKPSQLIKDLAKEIRLSENA 445
                                    91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441
   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 3PUS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Cupin (179)
(-)
Family: JmjC (39)
(-)
Homo sapiens (Human) (31)
1aJmjC-3pusB01B:236-336
1bJmjC-3pusB02B:236-336

(-) Gene Ontology  (25, 25)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PHF2_HUMAN | O75151)
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: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: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: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:0003713    transcription coactivator activity    Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    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:0001889    liver development    The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes.
    GO:0061188    negative regulation of chromatin silencing at rDNA    Any process that decreases the rate, frequency, or extent of the repression of transcription of ribosomal DNA by altering the structure of chromatin.
    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:0006482    protein demethylation    The removal of a methyl group, from a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom.
    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:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000775    chromosome, centromeric region    The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
    GO:0000777    condensed chromosome kinetochore    A multisubunit complex that is located at the centromeric region of a condensed chromosome and provides an attachment point for the spindle microtubules.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0000776    kinetochore    A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules.
    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
        PHF2_HUMAN | O75151: 3kqi 3ptr 3pu3 3pu8 3pua

(-) Related Entries Specified in the PDB File

3ptr PHF2 JUMONJI DOMAIN
3pu3 PHF2-NOG
3pu8 PHF2-NOG-FE(II)
3pua PHF2-NOG-NI(II) IN C2 SPACE GROUP