CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-001124
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Lysine-specific demethylase PHF2 
Protein Synonyms/Alias
 GRC5; PHD finger protein 2 
Gene Name
 PHF2 
Gene Synonyms/Alias
 KIAA0662 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
175KDCKMKLKEFVDYYYubiquitination[1]
412AFRSWTKKQALAEHEubiquitination[2, 3]
427DELPEHFKPSQLIKDubiquitination[1, 2, 3]
720VLPTPVTKPKLDSAAacetylation[3, 4]
Reference
 [1] A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles.
 Wagner SA, Beli P, Weinert BT, Nielsen ML, Cox J, Mann M, Choudhary C.
 Mol Cell Proteomics. 2011 Oct;10(10):M111.013284. [PMID: 21890473]
 [2] Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments.
 Udeshi ND, Svinkina T, Mertins P, Kuhn E, Mani DR, Qiao JW, Carr SA.
 Mol Cell Proteomics. 2013 Mar;12(3):825-31. [PMID: 23266961]
 [3] Integrated proteomic analysis of post-translational modifications by serial enrichment.
 Mertins P, Qiao JW, Patel J, Udeshi ND, Clauser KR, Mani DR, Burgess MW, Gillette MA, Jaffe JD, Carr SA.
 Nat Methods. 2013 Jul;10(7):634-7. [PMID: 23749302]
 [4] Proteomic investigations of lysine acetylation identify diverse substrates of mitochondrial deacetylase sirt3.
 Sol EM, Wagner SA, Weinert BT, Kumar A, Kim HS, Deng CX, Choudhary C.
 PLoS One. 2012;7(12):e50545. [PMID: 23236377] 
Functional Description
 Lysine demethylase that demethylates both histones and non-histone proteins. Enzymatically inactive by itself, and becomes active following phosphorylation by PKA: forms a complex with ARID5B and mediates demethylation of methylated ARID5B. Demethylation of ARID5B leads to target the PHF2-ARID5B complex to target promoters, where PHF2 mediates demethylation of dimethylated 'Lys-9' of histone H3 (H3K9me2), followed by transcription activation of target genes. The PHF2-ARID5B complex acts as a coactivator of HNF4A in liver. PHF2 is recruited to trimethylated 'Lys-4' of histone H3 (H3K4me3) at rDNA promoters and promotes expression of rDNA. 
Sequence Annotation
 DOMAIN 197 353 JmjC.
 ZN_FING 5 56 PHD-type.
 METAL 249 249 Iron; catalytic.
 METAL 251 251 Iron; catalytic.
 METAL 321 321 Iron; catalytic.
 BINDING 193 193 Alpha-ketoglutarate.
 BINDING 246 246 Alpha-ketoglutarate.
 BINDING 259 259 Alpha-ketoglutarate.
 BINDING 266 266 Alpha-ketoglutarate.
 BINDING 321 321 Alpha-ketoglutarate.
 BINDING 323 323 Alpha-ketoglutarate.
 MOD_RES 458 458 Phosphoserine (By similarity).
 MOD_RES 459 459 Phosphoserine (By similarity).
 MOD_RES 474 474 Phosphoserine.
 MOD_RES 479 479 Phosphothreonine.
 MOD_RES 539 539 Phosphoserine.
 MOD_RES 681 681 Phosphoserine (By similarity).
 MOD_RES 705 705 Phosphoserine.
 MOD_RES 738 738 Phosphoserine (By similarity).
 MOD_RES 882 882 Phosphoserine.
 MOD_RES 1056 1056 Phosphoserine; by PKA.  
Keyword
 3D-structure; Activator; Chromatin regulator; Complete proteome; Dioxygenase; Iron; Metal-binding; Nucleus; Oxidoreductase; Phosphoprotein; Polymorphism; Reference proteome; Transcription; Transcription regulation; Zinc; Zinc-finger. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 1096 AA 
Protein Sequence
MATVPVYCVC RLPYDVTRFM IECDACKDWF HGSCVGVEEE EAPDIDIYHC PNCEKTHGKS 60
TLKKKRTWHK HGPGQAPDVK PVQNGSQLFI KELRSRTFPS AEDVVARVPG SQLTLGYMEE 120
HGFTEPILVP KKDGLGLAVP APTFYVSDVE NYVGPERSVD VTDVTKQKDC KMKLKEFVDY 180
YYSTNRKRVL NVTNLEFSDT RMSSFVEPPD IVKKLSWVEN YWPDDALLAK PKVTKYCLIC 240
VKDSYTDFHI DSGGASAWYH VLKGEKTFYL IRPASANISL YERWRSASNH SEMFFADQVD 300
KCYKCIVKQG QTLFIPSGWI YATLTPVDCL AFAGHFLHSL SVEMQMRAYE VERRLKLGSL 360
TQFPNFETAC WYMGKHLLEA FKGSHKSGKQ LPPHLVQGAK ILNGAFRSWT KKQALAEHED 420
ELPEHFKPSQ LIKDLAKEIR LSENASKAVR PEVNTVASSD EVCDGDREKE EPPSPIEATP 480
PQSLLEKVSK KKTPKTVKMP KPSKIPKPPK PPKPPRPPKT LKLKDGGKKK GKKSRESASP 540
TIPNLDLLEA HTKEALTKME PPKKGKATKS VLSVPNKDVV HMQNDVERLE IREQTKSKSE 600
AKWKYKNSKP DSLLKMEEEQ KLEKSPLAGN KDNKFSFSFS NKKLLGSKAL RPPTSPGVFG 660
ALQNFKEDKP KPVRDEYEYV SDDGELKIDE FPIRRKKNAP KRDLSFLLDK KAVLPTPVTK 720
PKLDSAAYKS DDSSDEGSLH IDTDTKPGRN ARVKKESGSS AAGILDLLQA SEEVGALEYN 780
PSSQPPASPS TQEAIQGMLS MANLQASDSC LQTTWGAGQA KGSSLAAHGA RKNGGGSGKS 840
AGKRLLKRAA KNSVDLDDYE EEQDHLDACF KDSDYVYPSL ESDEDNPIFK SRSKKRKGSD 900
DAPYSPTARV GPSVPRQDRP VREGTRVASI ETGLAAAAAK LSQQEEQKSK KKKSAKRKLT 960
PNTTSPSTST SISAGTTSTS TTPASTTPAS TTPASTSTAS SQASQEGSSP EPPPESHSSS 1020
LADHEYTAAG TFTGAQAGRT SQPMAPGVFL TQRRPSASSP NNNTAAKGKR TKKGMATAKQ 1080
RLGKILKIHR NGKLLL 1096 
Gene Ontology
 GO:0005730; C:nucleolus; IDA:UniProtKB.
 GO:0032454; F:histone demethylase activity (H3-K9 specific); IDA:UniProtKB.
 GO:0005506; F:iron ion binding; IDA:UniProtKB.
 GO:0035064; F:methylated histone residue binding; IDA:UniProtKB.
 GO:0016702; F:oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen; IEA:UniProtKB-KW.
 GO:0008270; F:zinc ion binding; IDA:UniProtKB.
 GO:0001889; P:liver development; TAS:UniProtKB.
 GO:0061188; P:negative regulation of chromatin silencing at rDNA; IMP:UniProtKB.
 GO:0006351; P:transcription, DNA-dependent; IEA:UniProtKB-KW. 
Interpro
 IPR003347; JmjC_dom.
 IPR019786; Zinc_finger_PHD-type_CS.
 IPR011011; Znf_FYVE_PHD.
 IPR001965; Znf_PHD.
 IPR019787; Znf_PHD-finger.
 IPR013083; Znf_RING/FYVE/PHD. 
Pfam
 PF02373; JmjC
 PF00628; PHD 
SMART
 SM00558; JmjC
 SM00249; PHD 
PROSITE
 PS51184; JMJC
 PS01359; ZF_PHD_1
 PS50016; ZF_PHD_2 
PRINTS