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Q640I9 (KDM2B_XENLA) Reviewed, UniProtKB/Swiss-Prot

Last modified November 16, 2011. Version 57. 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 2B
EC=1.14.11.27
Alternative name(s):
F-box and leucine-rich repeat protein 10
F-box/LRR-repeat protein 10
JmjC domain-containing histone demethylation protein 1B
[Histone-H3]-lysine-36 demethylase 1B
Gene names
Name:kdm2b
Synonyms:fbxl10, jhdm1b
OrganismXenopus laevis (African clawed frog)
Taxonomic identifier8355 [NCBI]
Taxonomic lineageEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Amphibia › Batrachia › Anura › Mesobatrachia › Pipoidea › Pipidae › Xenopodinae › Xenopus › Xenopus

Protein attributes

Sequence length1259 AA.
Sequence statusComplete.
Protein existenceEvidence at transcript level

General annotation (Comments)

Function

Histone demethylase that demethylates 'Lys-4' and 'Lys-36' of histone H3, thereby playing a central role in histone code. Preferentially demethylates trimethylated H3 'Lys-4' and dimethylated H3 'Lys-36' residue while it has weak or no activity for mono- and tri-methylated H3 'Lys-36'. Preferentially binds the transcribed region of ribosomal RNA and represses the transcription of ribosomal RNA genes which inhibits cell growth and proliferation 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 › nucleolus By similarity.

Domain

The JmjC domain mediates demethylation activity. It is also required for repression of ribosomal RNA genes 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 5 LRR (leucine-rich) repeats.

Contains 1 PHD-type zinc finger.

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q640I9-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
Isoform 2 (identifier: Q640I9-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-521: Missing.
     522-539: NLAISGVPVVMWPKKPSK → MALSLSNDDEEYDSEQEQ
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 12591259Lysine-specific demethylase 2B
PRO_0000226786

Regions

Domain147 – 315169JmjC
Domain985 – 103046F-box
Repeat1056 – 108126LRR 1
Repeat1082 – 110524LRR 2
Repeat1145 – 117026LRR 3
Repeat1171 – 120030LRR 4
Repeat1201 – 122525LRR 5
Zinc finger567 – 61347CXXC-type
Zinc finger620 – 68667PHD-type
Coiled coil864 – 89128 Potential
Compositional bias688 – 799112Lys-rich

Sites

Metal binding2111Iron; catalytic By similarity
Metal binding2131Iron; catalytic By similarity
Metal binding2831Iron; catalytic By similarity
Binding site2081Substrate By similarity
Binding site2281Substrate By similarity

Natural variations

Alternative sequence1 – 521521Missing in isoform 2.
VSP_017479
Alternative sequence522 – 53918NLAIS…KKPSK → MALSLSNDDEEYDSEQEQ in isoform 2.
VSP_017480

Experimental info

Sequence conflict9191N → H in AAH73414. Ref.1

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified October 25, 2004. Version 1.
Checksum: 8FAAAE440E4765C3

FASTA1,259144,054
        10         20         30         40         50         60 
MEAKKDSARR LRSIDRTRYA EHEDLSDVED MVSIRGFSLE QKVSCNAYRG NFVRYMEGKD 

        70         80         90        100        110        120 
FTYEYVQREA LQTPLLFSTK EGLGIKMPEQ DFTVRDVKLL VGSRRVVDVM DVNTQKSIDM 

       130        140        150        160        170        180 
SMSQFVRYYE TPEMEREKLY NVISLEFSHT KLERVVKRPT VVDAVDWVDN MWPRHLKEQQ 

       190        200        210        220        230        240 
KESTNVIAEM KYPKVKKYCL MSVKGCYTDF HIDFGGTSVW YHVFRGGKVF WLIPPTGHNL 

       250        260        270        280        290        300 
QLYEEWLLSG KQTDIFLGDR SEGCQRIELK QGQTFFIPSG WIHAVYTPAD SLVFGGNILH 

       310        320        330        340        350        360 
SFNIPMQLRV FEIEDRTRVN AKFRYPFYYE MCWYVLERYV CTLTKRSHLI KEYQRESMIT 

       370        380        390        400        410        420 
DRKPSLDSHS SDSWLEMEEE SCDIHIKEEK GNLVEKPSKQ SGDESSTTNS THSNGKDAAE 

       430        440        450        460        470        480 
KKQKATLMQQ LKRTLSNDSD ESSKSIVHSD FPKTPTGSPA TDMPCKLTHL TEFELKGLKA 

       490        500        510        520        530        540 
LVEKLESLPE NKKCVPEGIE DPQALLEDMK TVLKEHADDD NNLAISGVPV VMWPKKPSKN 

       550        560        570        580        590        600 
RAVGRPKGKI ASSPAVKLSA NRTSAGARRR RTRCRKCEAC LRTECGECHF CKDMKKFGGP 

       610        620        630        640        650        660 
GRMKQSCIMR QCIAPVLPHT AVCLVCGEAG KEDCVEGQEA KFNVMLMECS ICNEIIHPGC 

       670        680        690        700        710        720 
LKTKESDGVV NDELPNCWEC PKCNHAGKTG KVYKQKRGPG FKYASNLPGS LLKEQKVNRD 

       730        740        750        760        770        780 
NKELTEIVKK KVEREETPKQ IPEEQPKKKP TEGIIKKKPE DGHVRKKRKF EKPPDPSVRK 

       790        800        810        820        830        840 
RLKLVKEEKL LRKKRRSWKT PDERAMMAKT LRRIKQEPDD DLTEAAPKAK ESDQSRSSSP 

       850        860        870        880        890        900 
TAGPSTEGSE PKEKKKIRRK RRVSNKELSK ELSKELNQEI QKTESSLASE NHHPIKSEPE 

       910        920        930        940        950        960 
SDNEESKKCI STNGERMHNF SKGLNGTPKE LRHELFPSLK TTPRANNRPP PSLSPPKCMQ 

       970        980        990       1000       1010       1020 
MERHVIRPPP ISPPPDSLPL ANGAAHVMQR EVWMAIFSYL SHRDLCICMR ICRTWNRWCC 

      1030       1040       1050       1060       1070       1080 
DKRLWTQIDL NRCKSITPLM LSGIIRRQPA SLDLSWTNIS KKQLSWLINR LPALRDLNLS 

      1090       1100       1110       1120       1130       1140 
GCSWIAVSAL CSSCCPLLRT LNVQWVEGLK DAQMRDLLSP PTDNRPGQID NRSKLRNITE 

      1150       1160       1170       1180       1190       1200 
LRLAGLDITD ASLRLMIRHM PLLAKLDLSY CNHVTDQSIN LLTAVGTSTR DTLLEMNLSD 

      1210       1220       1230       1240       1250 
CNNVTDQCLT FFKRCGNICL IDLRFCKQVS KESCEQFIAE MSVIVQFGQT EEKLLQKVS

« Hide

Isoform 2 [UniParc].

Checksum: B02819AB1EAB7F99
Show »

FASTA73883,769

References

[1]NIH - Xenopus Gene Collection (XGC) project
Submitted (SEP-2004) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
Tissue: Embryo.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		BC073414 mRNA. Translation: AAH73414.1.
BC082636 mRNA. Translation: AAH82636.1.
RefSeqNP_001085840.1. NM_001092371.1.
UniGeneXl.52422.

3D structure databases

ProteinModelPortalQ640I9.
SMRQ640I9. Positions 35-534.
ModBaseSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID444267.
KEGGxla:444267.

Organism-specific databases

CTD84678.
XenbaseXB-GENE-990512. kdm2b.

Family and domain databases

InterProIPR001810. F-box_dom_cyclin-like.
IPR013129. TF_JmjC.
IPR003347. TF_JmjC_AAH.
IPR002857. Znf_CXXC.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR019787. Znf_PHD-finger.
[Graphical view]
KOK10276.
PfamPF00646. F-box. 1 hit.
PF02373. 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. False negative.
PS50016. ZF_PHD_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameKDM2B_XENLA
AccessionPrimary (citable) accession number: Q640I9
Secondary accession number(s): Q6GNT8
Entry history
Integrated into UniProtKB/Swiss-Prot: March 7, 2006
Last sequence update: October 25, 2004
Last modified: November 16, 2011
This is version 57 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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