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Protein

PHD finger protein 21A

Gene

PHF21A

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. The BHC complex is recruited at RE1/NRSE sites by REST and acts by deacetylating and demethylating specific sites on histones, thereby acting as a chromatin modifier. In the BHC complex, it may act as a scaffold. Inhibits KDM1A-mediated demethylation of 'Lys-4' of histone H3 in vitro, suggesting a role in demethylation regulation.1 Publication

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi425 – 437A.T hookAdd BLAST13
Zinc fingeri488 – 535PHD-typePROSITE-ProRule annotationAdd BLAST48

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Repressor

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-HSA-3214815. HDACs deacetylate histones.
R-HSA-983231. Factors involved in megakaryocyte development and platelet production.

Names & Taxonomyi

Protein namesi
Recommended name:
PHD finger protein 21A
Alternative name(s):
BHC80a
BRAF35-HDAC complex protein BHC80
Gene namesi
Name:PHF21A
Synonyms:BHC80, KIAA1696
ORF Names:BM-006
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 11

Organism-specific databases

HGNCiHGNC:24156. PHF21A.

Subcellular locationi

GO - Cellular componenti

  • DNA repair complex Source: MGI
  • histone deacetylase complex Source: MGI
  • nucleoplasm Source: Reactome
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi51317.
MalaCardsiPHF21A.
OpenTargetsiENSG00000135365.
Orphaneti52022. Potocki-Shaffer syndrome.
PharmGKBiPA134977844.

Polymorphism and mutation databases

BioMutaiPHF21A.
DMDMi74731224.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002267671 – 680PHD finger protein 21AAdd BLAST680

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki65Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei350PhosphothreonineCombined sources1
Modified residuei444PhosphothreonineCombined sources1
Modified residuei447PhosphoserineCombined sources1

Keywords - PTMi

Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ96BD5.
MaxQBiQ96BD5.
PaxDbiQ96BD5.
PeptideAtlasiQ96BD5.
PRIDEiQ96BD5.

PTM databases

iPTMnetiQ96BD5.
PhosphoSitePlusiQ96BD5.

Expressioni

Tissue specificityi

Highly expressed in brain. Expressed at much lower level in other tissues.1 Publication

Gene expression databases

BgeeiENSG00000135365.
CleanExiHS_PHF21A.
ExpressionAtlasiQ96BD5. baseline and differential.
GenevisibleiQ96BD5. HS.

Organism-specific databases

HPAiHPA023580.

Interactioni

Subunit structurei

Component of a BHC histone deacetylase complex that contains HDAC1, HDAC2, HMG20B/BRAF35, KDM1A, RCOR1/CoREST and PHF21A/BHC80. The BHC complex may also contain ZMYM2, ZNF217, ZMYM3, GSE1 and GTF2I. In the complex, it interacts directly with HDAC1, HDAC2, HMG20B/BRAF35, KDM1A and RCOR1/CoREST.3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
BANPQ8N9N53EBI-745085,EBI-744695
FHL3Q136435EBI-745085,EBI-741101
KRT40Q6A1623EBI-745085,EBI-10171697
NUP62P371985EBI-745085,EBI-347978
TRAF1Q130773EBI-745085,EBI-359224
ZYXQ159423EBI-745085,EBI-444225

GO - Molecular functioni

Protein-protein interaction databases

BioGridi119468. 33 interactors.
DIPiDIP-60252N.
IntActiQ96BD5. 33 interactors.
MINTiMINT-1469147.
STRINGi9606.ENSP00000398824.

Structurei

Secondary structure

1680
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Turni492 – 494Combined sources3
Beta strandi504 – 507Combined sources4
Helixi512 – 514Combined sources3
Beta strandi515 – 517Combined sources3
Helixi530 – 538Combined sources9
Turni539 – 542Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2PUYX-ray1.43A/B486-543[»]
2YQLNMR-A487-535[»]
ProteinModelPortaliQ96BD5.
SMRiQ96BD5.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ96BD5.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni486 – 680Required for transcriptional repressionAdd BLAST195

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili558 – 603Sequence analysisAdd BLAST46

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi4 – 108Gln-richAdd BLAST105

Sequence similaritiesi

Contains 1 A.T hook DNA-binding domain.Curated
Contains 1 PHD-type zinc finger.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri488 – 535PHD-typePROSITE-ProRule annotationAdd BLAST48

Keywords - Domaini

Coiled coil, Zinc-finger

Phylogenomic databases

eggNOGiENOG410IREA. Eukaryota.
ENOG41112YM. LUCA.
GeneTreeiENSGT00530000063984.
HOVERGENiHBG080293.
InParanoidiQ96BD5.
OMAiHHHAQSA.
OrthoDBiEOG091G03CB.
PhylomeDBiQ96BD5.
TreeFamiTF331518.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR019786. Zinc_finger_PHD-type_CS.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR019787. Znf_PHD-finger.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF00628. PHD. 1 hit.
[Graphical view]
SMARTiSM00249. PHD. 1 hit.
[Graphical view]
SUPFAMiSSF57903. SSF57903. 1 hit.
PROSITEiPS01359. ZF_PHD_1. 1 hit.
PS50016. ZF_PHD_2. 1 hit.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q96BD5-1) [UniParc]FASTAAdd to basket

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.

« Hide

        10         20         30         40         50
MELQTLQEAL KVEIQVHQKL VAQMKQDPQN ADLKKQLHEL QAKITALSEK
60 70 80 90 100
QKRVVEQLRK NLIVKQEQPD KFQIQPLPQS ENKLQTAQQQ PLQQLQQQQQ
110 120 130 140 150
YHHHHAQQSA AASPNLTASQ KTVTTASMIT TKTLPLVLKA ATATMPASVV
160 170 180 190 200
GQRPTIAMVT AINSQKAVLS TDVQNTPVNL QTSSKVTGPG AEAVQIVAKN
210 220 230 240 250
TVTLVQATPP QPIKVPQFIP PPRLTPRPNF LPQVRPKPVA QNNIPIAPAP
260 270 280 290 300
PPMLAAPQLI QRPVMLTKFT PTTLPTSQNS IHPVRVVNGQ TATIAKTFPM
310 320 330 340 350
AQLTSIVIAT PGTRLAGPQT VQLSKPSLEK QTVKSHTETD EKQTESRTIT
360 370 380 390 400
PPAAPKPKRE ENPQKLAFMV SLGLVTHDHL EEIQSKRQER KRRTTANPVY
410 420 430 440 450
SGAVFEPERK KSAVTYLNST MHPGTRKRGR PPKYNAVLGF GALTPTSPQS
460 470 480 490 500
SHPDSPENEK TETTFTFPAP VQPVSLPSPT STDGDIHEDF CSVCRKSGQL
510 520 530 540 550
LMCDTCSRVY HLDCLDPPLK TIPKGMWICP RCQDQMLKKE EAIPWPGTLA
560 570 580 590 600
IVHSYIAYKA AKEEEKQKLL KWSSDLKQER EQLEQKVKQL SNSISKCMEM
610 620 630 640 650
KNTILARQKE MHSSLEKVKQ LIRLIHGIDL SKPVDSEATV GAISNGPDCT
660 670 680
PPANAATSTP APSPSSQSCT ANCNQGEETK
Length:680
Mass (Da):74,854
Last modified:December 1, 2001 - v1
Checksum:iC7AF87EB2984A796
GO
Isoform 2 (identifier: Q96BD5-2) [UniParc]FASTAAdd to basket
Also known as: hBHC80-4

The sequence of this isoform differs from the canonical sequence as follows:
     204-204: L → LQ
     429-483: GRPPKYNAVLGFGALTPTSPQSSHPDSPENEKTETTFTFPAPVQPVSLPSPTSTD → ANEEHWPK

Show »
Length:634
Mass (Da):70,210
Checksum:iB1F247CD92D7D411
GO
Isoform 3 (identifier: Q96BD5-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     204-204: L → LQ

Show »
Length:681
Mass (Da):74,982
Checksum:iF95DC57A1D3C0FEC
GO

Sequence cautioni

The sequence AAF64262 differs from that shown. Reason: Frameshift at several positions.Curated
The sequence BAB21787 differs from that shown. Reason: Erroneous initiation.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti447S → P in BAB13839 (PubMed:14702039).Curated1
Sequence conflicti662 – 680PSPSS…GEETK → LCSLPELHSEL (Ref. 7) CuratedAdd BLAST19

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_025515347R → H.2 PublicationsCorresponds to variant rs3736508dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_017448204L → LQ in isoform 2 and isoform 3. 3 Publications1
Alternative sequenceiVSP_017449429 – 483GRPPK…PTSTD → ANEEHWPK in isoform 2. 3 PublicationsAdd BLAST55

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY090777 mRNA. Translation: AAM09095.1.
AB051483 mRNA. Translation: BAB21787.1. Different initiation.
AK021530 mRNA. Translation: BAB13839.1.
AK023258 mRNA. Translation: BAB14492.1.
CH471064 Genomic DNA. Translation: EAW68012.1.
CH471064 Genomic DNA. Translation: EAW68013.1.
CH471064 Genomic DNA. Translation: EAW68015.1.
CH471064 Genomic DNA. Translation: EAW68017.1.
BC015714 mRNA. Translation: AAH15714.1.
BX648236 mRNA. Translation: CAH10542.1.
AF208848 mRNA. Translation: AAF64262.1. Frameshift.
CCDSiCCDS31474.1. [Q96BD5-2]
CCDS44578.1. [Q96BD5-1]
RefSeqiNP_001095272.1. NM_001101802.1. [Q96BD5-1]
NP_057705.3. NM_016621.3. [Q96BD5-2]
XP_005253022.1. XM_005252965.4. [Q96BD5-3]
XP_011518475.1. XM_011520173.2. [Q96BD5-3]
XP_011518476.1. XM_011520174.2. [Q96BD5-3]
XP_011518481.1. XM_011520179.2. [Q96BD5-2]
XP_016873380.1. XM_017017891.1. [Q96BD5-1]
UniGeneiHs.502458.

Genome annotation databases

EnsembliENST00000323180; ENSP00000323152; ENSG00000135365. [Q96BD5-2]
ENST00000418153; ENSP00000398824; ENSG00000135365. [Q96BD5-1]
GeneIDi51317.
KEGGihsa:51317.
UCSCiuc001ncb.5. human. [Q96BD5-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY090777 mRNA. Translation: AAM09095.1.
AB051483 mRNA. Translation: BAB21787.1. Different initiation.
AK021530 mRNA. Translation: BAB13839.1.
AK023258 mRNA. Translation: BAB14492.1.
CH471064 Genomic DNA. Translation: EAW68012.1.
CH471064 Genomic DNA. Translation: EAW68013.1.
CH471064 Genomic DNA. Translation: EAW68015.1.
CH471064 Genomic DNA. Translation: EAW68017.1.
BC015714 mRNA. Translation: AAH15714.1.
BX648236 mRNA. Translation: CAH10542.1.
AF208848 mRNA. Translation: AAF64262.1. Frameshift.
CCDSiCCDS31474.1. [Q96BD5-2]
CCDS44578.1. [Q96BD5-1]
RefSeqiNP_001095272.1. NM_001101802.1. [Q96BD5-1]
NP_057705.3. NM_016621.3. [Q96BD5-2]
XP_005253022.1. XM_005252965.4. [Q96BD5-3]
XP_011518475.1. XM_011520173.2. [Q96BD5-3]
XP_011518476.1. XM_011520174.2. [Q96BD5-3]
XP_011518481.1. XM_011520179.2. [Q96BD5-2]
XP_016873380.1. XM_017017891.1. [Q96BD5-1]
UniGeneiHs.502458.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2PUYX-ray1.43A/B486-543[»]
2YQLNMR-A487-535[»]
ProteinModelPortaliQ96BD5.
SMRiQ96BD5.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi119468. 33 interactors.
DIPiDIP-60252N.
IntActiQ96BD5. 33 interactors.
MINTiMINT-1469147.
STRINGi9606.ENSP00000398824.

PTM databases

iPTMnetiQ96BD5.
PhosphoSitePlusiQ96BD5.

Polymorphism and mutation databases

BioMutaiPHF21A.
DMDMi74731224.

Proteomic databases

EPDiQ96BD5.
MaxQBiQ96BD5.
PaxDbiQ96BD5.
PeptideAtlasiQ96BD5.
PRIDEiQ96BD5.

Protocols and materials databases

DNASUi51317.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000323180; ENSP00000323152; ENSG00000135365. [Q96BD5-2]
ENST00000418153; ENSP00000398824; ENSG00000135365. [Q96BD5-1]
GeneIDi51317.
KEGGihsa:51317.
UCSCiuc001ncb.5. human. [Q96BD5-1]

Organism-specific databases

CTDi51317.
DisGeNETi51317.
GeneCardsiPHF21A.
HGNCiHGNC:24156. PHF21A.
HPAiHPA023580.
MalaCardsiPHF21A.
MIMi608325. gene.
neXtProtiNX_Q96BD5.
OpenTargetsiENSG00000135365.
Orphaneti52022. Potocki-Shaffer syndrome.
PharmGKBiPA134977844.
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IREA. Eukaryota.
ENOG41112YM. LUCA.
GeneTreeiENSGT00530000063984.
HOVERGENiHBG080293.
InParanoidiQ96BD5.
OMAiHHHAQSA.
OrthoDBiEOG091G03CB.
PhylomeDBiQ96BD5.
TreeFamiTF331518.

Enzyme and pathway databases

ReactomeiR-HSA-3214815. HDACs deacetylate histones.
R-HSA-983231. Factors involved in megakaryocyte development and platelet production.

Miscellaneous databases

ChiTaRSiPHF21A. human.
EvolutionaryTraceiQ96BD5.
GeneWikiiPHF21A.
GenomeRNAii51317.
PROiQ96BD5.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000135365.
CleanExiHS_PHF21A.
ExpressionAtlasiQ96BD5. baseline and differential.
GenevisibleiQ96BD5. HS.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR019786. Zinc_finger_PHD-type_CS.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR019787. Znf_PHD-finger.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF00628. PHD. 1 hit.
[Graphical view]
SMARTiSM00249. PHD. 1 hit.
[Graphical view]
SUPFAMiSSF57903. SSF57903. 1 hit.
PROSITEiPS01359. ZF_PHD_1. 1 hit.
PS50016. ZF_PHD_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPF21A_HUMAN
AccessioniPrimary (citable) accession number: Q96BD5
Secondary accession number(s): D3DQP5
, Q6AWA2, Q9C0G7, Q9H8V9, Q9HAK6, Q9NZE9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 7, 2006
Last sequence update: December 1, 2001
Last modified: November 30, 2016
This is version 139 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 11
    Human chromosome 11: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.