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Q5U263 (KDM2A_XENTR) Reviewed, UniProtKB/Swiss-Prot

Last modified November 16, 2011. Version 60. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (1) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
Lysine-specific demethylase 2A
EC=1.14.11.27
Alternative name(s):
F-box and leucine-rich repeat protein 11
F-box/LRR-repeat protein 11
JmjC domain-containing histone demethylation protein 1A
[Histone-H3]-lysine-36 demethylase 1A
Gene names
Name:kdm2a
Synonyms:fbxl11, jhdm1a
OrganismXenopus tropicalis (Western clawed frog) (Silurana tropicalis)
Taxonomic identifier8364 [NCBI]
Taxonomic lineageEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Amphibia › Batrachia › Anura › Mesobatrachia › Pipoidea › Pipidae › Xenopodinae › Xenopus › Silurana

Protein attributes

Sequence length1146 AA.
Sequence statusComplete.
Protein existenceEvidence at transcript level

General annotation (Comments)

Function

Histone demethylase that specifically demethylates 'Lys-36' of histone H3, thereby playing a central role in histone code. Preferentially demethylates dimethylated H3 'Lys-36' residue while it has weak or no activity for mono- and tri-methylated H3 'Lys-36'. May also recognize and bind to some phosphorylated proteins and promote their ubiquitination and degradation. Required to maintain the heterochromatic state. Associates with centromeres and represses transcription of small non-coding RNAs that are encoded by the clusters of satellite repeats at the centromere. Required to sustain centromeric integrity and genomic stability, particularly during mitosis By similarity.

Catalytic activity

Protein N6,N(6)-dimethyl-L-lysine + 2-oxoglutarate + O2 = protein N(6)-methyl-L-lysine + succinate + formaldehyde + CO2.

Protein N(6)-methyl-L-lysine + 2-oxoglutarate + O2 = protein L-lysine + succinate + formaldehyde + CO2.

Cofactor

Binds 1 Fe2+ ion per subunit By similarity.

Subcellular location

Nucleus › nucleoplasm By similarity.

Domain

The JmjC domain mediates demethylation activity and is required for satellite silencing By similarity.

The CXXC zinc finger preferentially recognizes nonmethylated CpG DNA, and binding is blocked when the CpG DNA is methylated By similarity.

Sequence similarities

Belongs to the JHDM1 histone demethylase family.

Contains 1 CXXC-type zinc finger.

Contains 1 F-box domain.

Contains 1 JmjC domain.

Contains 6 LRR (leucine-rich) repeats.

Contains 1 PHD-type zinc finger.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 11461146Lysine-specific demethylase 2A
PRO_0000226787

Regions

Domain146 – 314169JmjC
Domain874 – 91946F-box
Repeat945 – 96622LRR 1
Repeat968 – 99427LRR 2
Repeat1032 – 105726LRR 3
Repeat1058 – 108730LRR 4
Repeat1088 – 111225LRR 5
Repeat1113 – 113826LRR 6
Zinc finger585 – 63147CXXC-type
Zinc finger638 – 69962PHD-type

Sites

Metal binding2101Iron; catalytic By similarity
Metal binding2121Iron; catalytic By similarity
Metal binding2821Iron; catalytic By similarity
Binding site2071Substrate By similarity
Binding site2271Substrate By similarity

Sequences

Sequence LengthMass (Da)Tools
Q5U263 [UniParc].

Last modified December 7, 2004. Version 1.
Checksum: C2812F2A5FD45816

FASTA1,146131,750
        10         20         30         40         50         60 
MEEEQLRYSR RLRHTLRRRY EDDGISDDEI EGKRTFDLEE KLRSSKYNSN FITYMEGKDF 

        70         80         90        100        110        120 
NMKFIQEGGL RDPIIFTKSE GLGIKMPDPN FSVNDVKMFV GSRRVVDVMD VGTQKGIEMT 

       130        140        150        160        170        180 
MAQWAKYYET PEEEREKLYN VISLEFSHTK LENLVQRPTT VDQIDWVDNI WPRHLKDRQT 

       190        200        210        220        230        240 
ESTNVIQEMQ YPKVQKYCLM SVRGCYTDFH VDFGGTSVWY HILRGGKVFW LIPPTDQNLE 

       250        260        270        280        290        300 
LYENWLLSGK QGDVFLGDRV TECQRIELKQ GYTFVIPSGW IHAVYTPQDT LVFGGNFLHS 

       310        320        330        340        350        360 
FNIPMQLRIY SIEDRTRVPT KFRYPFYYEM CWYVLERYVY CMMRRSHLTK EFQRESLSID 

       370        380        390        400        410        420 
LELNGRQRPD TPSSSSSSSS SGLSSSSDND DSSDQDWEEE EGLRKRERDR CRVERELQRK 

       430        440        450        460        470        480 
RNRDRQQRDQ ERDRHGRTER IIIHTLPASL RPLTPPPSLP LPTPDSPPST SPFLTWFEVE 

       490        500        510        520        530        540 
GLRCLVLKLE SLPPLKKCLP DGIHDPEALI FDIKRLLEDH AHDPPELALT GVPIIQWPKR 

       550        560        570        580        590        600 
SQYKVHLRPK IQFTKPHTMR PASRHSTAPP RTSGTPSGTT ASSGARRRRV RCRKCQACVQ 

       610        620        630        640        650        660 
RECGTCHYCK DMKKFGGPGR MKQSCVLRQC LAPRLPHSVT CALCGEVDQT NDTQDFERKL 

       670        680        690        700        710        720 
MECSVCNEIV HPGCLEMDGE GLLSDELPNY WECPKCYEGQ KHTVEANHDR ILLHSKRKAA 

       730        740        750        760        770        780 
DNYESSHYYP AKVLRPPLGQ SPPSPPLLLL PPSPSSAPPT PPSAQTQVPL ASREERAKRR 

       790        800        810        820        830        840 
QLAREKENHP TGCDQSEGDR LRLRGPYLTV TLQRPPKELS STSIVPKLQA ITPNPRQPIR 

       850        860        870        880        890        900 
AAPLHQDEER EEEEEEEEEE EETENVMLGQ RKDSTSMQKD VWLSVFHYLT HEELCICMRV 

       910        920        930        940        950        960 
CKAWYKWGCD KRLWSRIDVS RCKSLVPQAL SGIIKRQPIY LDLSWTNVSK KQLIWLINRL 

       970        980        990       1000       1010       1020 
PGLKDLILAG CTWSAVSALA SCSCPLLRTL DLRWTVGIKD TQIRDLLTPA SDKSGHDSRS 

      1030       1040       1050       1060       1070       1080 
KLRLLTDLRL SGLDISDVTL RLIIRHCPLL SKLDLSHCPL LSDQSVNLLT AVGSSTRGTL 

      1090       1100       1110       1120       1130       1140 
THIHLAGCKG VTDESLLYLR RATNLSLIDL HGCKQVTRGA CEEFISDLSV STLYCLSDDK 


LIQRIS

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References

[1]NIH - Xenopus Gene Collection (XGC) project
Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Tissue: Embryo.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		BC086264 mRNA. Translation: AAH86264.1.
RefSeqNP_001011176.1. NM_001011176.1.
UniGeneStr.11178.

3D structure databases

ProteinModelPortalQ5U263.
SMRQ5U263. Positions 32-538.
ModBaseSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID496596.
KEGGxtr:496596.

Organism-specific databases

CTD22992.
XenbaseXB-GENE-5900838. kdm2a.

Phylogenomic databases

eggNOGveNOG07492.
GeneTreeENSGT00550000074396.
InParanoidQ5U263.
OrthoDBEOG4TF0JF.

Gene expression databases

BgeeQ5U263.

Family and domain databases

InterProIPR013129. TF_JmjC.
IPR003347. TF_JmjC_AAH.
IPR019786. Zinc_finger_PHD-type_CS.
IPR002857. Znf_CXXC.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR019787. Znf_PHD-finger.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
Gene3DG3DSA:3.30.40.10. Znf_RING/FYVE/PHD. 1 hit.
KOK10276.
PfamPF02373. JmjC. 1 hit.
PF02008. zf-CXXC. 1 hit.
[Graphical view]
SMARTSM00558. JmjC. 1 hit.
SM00249. PHD. 1 hit.
[Graphical view]
SUPFAMSSF57903. FYVE_PHD_ZnF. 1 hit.
PROSITEPS50181. FBOX. False negative.
PS51184. JMJC. 1 hit.
PS51058. ZF_CXXC. 1 hit.
PS01359. ZF_PHD_1. 1 hit.
PS50016. ZF_PHD_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameKDM2A_XENTR
AccessionPrimary (citable) accession number: Q5U263
Entry history
Integrated into UniProtKB/Swiss-Prot: March 7, 2006
Last sequence update: December 7, 2004
Last modified: November 16, 2011
This is version 60 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

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