Lysine-specific demethylase 2B - Xenopus laevis (African clawed frog)

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Alternative products

Sequence annotation (Features)

Sequences

References

Cross-references

Entry information

Relevant documents

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Alternative products

Sequence annotation (Features)

Sequences

References

Cross-references

Entry information

Relevant documents

Molecule processing

Regions

Sites

Natural variations

Experimental info

Molecule processing

Regions

Sites

Natural variations

Experimental info

Sequence databases

3D structure databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Sequence

>sp|Q640I9|KDM2B_XENLA Lysine-specific demethylase 2B OS=Xenopus laevis GN=kdm2b PE=2 SV=1 MEAKKDSARRLRSIDRTRYAEHEDLSDVEDMVSIRGFSLEQKVSCNAYRGNFVRYMEGKD FTYEYVQREALQTPLLFSTKEGLGIKMPEQDFTVRDVKLLVGSRRVVDVMDVNTQKSIDM SMSQFVRYYETPEMEREKLYNVISLEFSHTKLERVVKRPTVVDAVDWVDNMWPRHLKEQQ KESTNVIAEMKYPKVKKYCLMSVKGCYTDFHIDFGGTSVWYHVFRGGKVFWLIPPTGHNL QLYEEWLLSGKQTDIFLGDRSEGCQRIELKQGQTFFIPSGWIHAVYTPADSLVFGGNILH SFNIPMQLRVFEIEDRTRVNAKFRYPFYYEMCWYVLERYVCTLTKRSHLIKEYQRESMIT DRKPSLDSHSSDSWLEMEEESCDIHIKEEKGNLVEKPSKQSGDESSTTNSTHSNGKDAAE KKQKATLMQQLKRTLSNDSDESSKSIVHSDFPKTPTGSPATDMPCKLTHLTEFELKGLKA LVEKLESLPENKKCVPEGIEDPQALLEDMKTVLKEHADDDNNLAISGVPVVMWPKKPSKN RAVGRPKGKIASSPAVKLSANRTSAGARRRRTRCRKCEACLRTECGECHFCKDMKKFGGP GRMKQSCIMRQCIAPVLPHTAVCLVCGEAGKEDCVEGQEAKFNVMLMECSICNEIIHPGC LKTKESDGVVNDELPNCWECPKCNHAGKTGKVYKQKRGPGFKYASNLPGSLLKEQKVNRD NKELTEIVKKKVEREETPKQIPEEQPKKKPTEGIIKKKPEDGHVRKKRKFEKPPDPSVRK RLKLVKEEKLLRKKRRSWKTPDERAMMAKTLRRIKQEPDDDLTEAAPKAKESDQSRSSSP TAGPSTEGSEPKEKKKIRRKRRVSNKELSKELSKELNQEIQKTESSLASENHHPIKSEPE SDNEESKKCISTNGERMHNFSKGLNGTPKELRHELFPSLKTTPRANNRPPPSLSPPKCMQ MERHVIRPPPISPPPDSLPLANGAAHVMQREVWMAIFSYLSHRDLCICMRICRTWNRWCC DKRLWTQIDLNRCKSITPLMLSGIIRRQPASLDLSWTNISKKQLSWLINRLPALRDLNLS GCSWIAVSALCSSCCPLLRTLNVQWVEGLKDAQMRDLLSPPTDNRPGQIDNRSKLRNITE LRLAGLDITDASLRLMIRHMPLLAKLDLSYCNHVTDQSINLLTAVGTSTRDTLLEMNLSD CNNVTDQCLTFFKRCGNICLIDLRFCKQVSKESCEQFIAEMSVIVQFGQTEEKLLQKVS

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Reviewed, UniProtKB/Swiss-Prot Q640I9 (KDM2B_XENLA)

Last modified June 16, 2009. Version 39. History...

Clusters with 100%, 90%, 50% identity |

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Alternative products · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Protein names

Recommended name:
    Lysine-specific demethylase 2B
    EC=1.14.11.27
Alternative name(s):
    JmjC domain-containing histone demethylation protein 1B
    [Histone-H3]-lysine-36 demethylase 1B
    F-box and leucine-rich repeat protein 10
    F-box/LRR-repeat protein 10

Gene names

Name:	kdm2b
Synonyms:	fbxl10, jhdm1b

Organism

Xenopus laevis (African clawed frog)

Taxonomic identifier

8355 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Amphibia › Batrachia › Anura › Mesobatrachia › Pipoidea › Pipidae › Xenopodinae › Xenopus › Xenopus

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Sequence length	1259 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at transcript level.

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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 4 LRR (leucine-rich) repeats. Contains 1 PHD-type zinc finger.

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Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing
Domain	Coiled coil Leucine-rich repeat Repeat Zinc-finger
Ligand	Iron Metal-binding RNA-binding Zinc rRNA-binding
Molecular function	Chromatin regulator Dioxygenase Oxidoreductase Repressor
PTM	Phosphoprotein
Gene Ontology (GO)
Biological process	chromatin modification Inferred from electronic annotation. Source: UniProtKB-KW oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW transcription Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	DNA binding Inferred from electronic annotation. Source: InterPro histone demethylase activity (H3-K36 specific) Inferred from electronic annotation. Source: EC iron ion binding Inferred from electronic annotation. Source: UniProtKB-KW oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen Inferred from electronic annotation. Source: UniProtKB-KW protein binding Inferred from electronic annotation. Source: InterPro zinc ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

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Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Chain

1 – 1259

1259

Lysine-specific demethylase 2B

PRO_0000226786

Domain

147 – 315

169

JmjC

Domain

985 – 1030

F-box

Repeat

1071 – 1094

LRR 1

Repeat

1135 – 1158

LRR 2

Repeat

1192 – 1216

LRR 3

Repeat

1217 – 1259

LRR 4

Zinc finger

567 – 613

CXXC-type

Zinc finger

620 – 686

PHD-type

Coiled coil

864 – 891

Potential

Compositional bias

688 – 799

112

Lys-rich

Metal binding

211

Iron; catalytic By similarity

Metal binding

213

Iron; catalytic By similarity

Metal binding

283

Iron; catalytic By similarity

Binding site

208

Substrate By similarity

Binding site

228

Substrate By similarity

Alternative sequence

1 – 521

521

Missing in isoform 2.

VSP_017479

Alternative sequence

522 – 539

NLAIS…KKPSK → MALSLSNDDEEYDSEQEQ in isoform 2.

VSP_017480

Sequence conflict

919

N → H in AAH73414. Ref.1

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Sequence		Length	Mass (Da)
Isoform 1 [UniParc]. Last modified October 25, 2004. Version 1. Checksum: 8FAAAE440E4765C3 Show »	FASTA	1,259	144,054
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. Checksum: B02819AB1EAB7F99 Show »	FASTA	738	83,769
10 20 30 40 50 60 MALSLSNDDE EYDSEQEQNR AVGRPKGKIA SSPAVKLSAN RTSAGARRRR TRCRKCEACL 70 80 90 100 110 120 RTECGECHFC KDMKKFGGPG RMKQSCIMRQ CIAPVLPHTA VCLVCGEAGK EDCVEGQEAK 130 140 150 160 170 180 FNVMLMECSI CNEIIHPGCL KTKESDGVVN DELPNCWECP KCNHAGKTGK VYKQKRGPGF 190 200 210 220 230 240 KYASNLPGSL LKEQKVNRDN KELTEIVKKK VEREETPKQI PEEQPKKKPT EGIIKKKPED 250 260 270 280 290 300 GHVRKKRKFE KPPDPSVRKR LKLVKEEKLL RKKRRSWKTP DERAMMAKTL RRIKQEPDDD 310 320 330 340 350 360 LTEAAPKAKE SDQSRSSSPT AGPSTEGSEP KEKKKIRRKR RVSNKELSKE LSKELNQEIQ 370 380 390 400 410 420 KTESSLASEN HHPIKSEPES DNEESKKCIS TNGERMHNFS KGLNGTPKEL RHELFPSLKT 430 440 450 460 470 480 TPRANNRPPP SLSPPKCMQM ERHVIRPPPI SPPPDSLPLA NGAAHVMQRE VWMAIFSYLS 490 500 510 520 530 540 HRDLCICMRI CRTWNRWCCD KRLWTQIDLN RCKSITPLML SGIIRRQPAS LDLSWTNISK 550 560 570 580 590 600 KQLSWLINRL PALRDLNLSG CSWIAVSALC SSCCPLLRTL NVQWVEGLKD AQMRDLLSPP 610 620 630 640 650 660 TDNRPGQIDN RSKLRNITEL RLAGLDITDA SLRLMIRHMP LLAKLDLSYC NHVTDQSINL 670 680 690 700 710 720 LTAVGTSTRD TLLEMNLSDC NNVTDQCLTF FKRCGNICLI DLRFCKQVSK ESCEQFIAEM 730 SVIVQFGQTE EKLLQKVS « Hide

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[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.

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Sequence databases
	BC073414 mRNA. Translation: AAH73414.1. BC082636 mRNA. Translation: AAH82636.1.
RefSeq	NP_001085840.1.
UniGene	Xl.52422
3D structure databases
SMR	Q640I9. Positions 35-361.
ModBase	Search...
Genome annotation databases
GeneID	444267.
KEGG	xla:444267.
Organism-specific databases
Xenbase	XB-FEAT-990505. kdm2b.
Phylogenomic databases
HOVERGEN	Q640I9.
Enzyme and pathway databases
BRENDA	1.14.11.27. 648.
Family and domain databases
InterPro	IPR001810. F-box. IPR013129. TF_JmjC. IPR003347. TF_JmjC_AAH. IPR019786. Zinc_finger_PHD-type_CS. IPR002857. Znf_CXXC. IPR001965. Znf_PHD. IPR019787. Znf_PHD-finger. [Graphical view]
Pfam	PF00646. F-box. 1 hit. PF02373. JmjC. 1 hit. PF02008. zf-CXXC. 1 hit. [Graphical view]
SMART	SM00558. JmjC. 1 hit. SM00249. PHD. 1 hit. [Graphical view]
PROSITE	PS50181. 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]
ProtoNet	Search...

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Entry name

KDM2B_XENLA

Accession

Primary (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:	June 16, 2009
This is version 39 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

Xenopus annotation project

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SIMILARITY comments

Index of protein domains and families

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.