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Protein

PR domain-containing protein 11

Gene

PRDM11

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

Functioni

May be involved in transcription regulation.1 Publication

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

S-adenosyl-L-methionine

Names & Taxonomyi

Protein namesi
Recommended name:
PR domain-containing protein 11 (EC:2.1.1.-)
Gene namesi
Name:PRDM11
Synonyms:PFM8
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 11

Organism-specific databases

HGNCiHGNC:13996. PRDM11.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA33709.

Polymorphism and mutation databases

DMDMi308153475.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 511511PR domain-containing protein 11PRO_0000047768Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei63 – 631PhosphoserineCombined sources
Cross-linki214 – 214Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources

Keywords - PTMi

Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiQ9NQV5.
PaxDbiQ9NQV5.
PRIDEiQ9NQV5.

PTM databases

iPTMnetiQ9NQV5.
PhosphoSiteiQ9NQV5.

Expressioni

Tissue specificityi

Highly expressed in lung, including bronchial epithelial cells and airway smooth muscle cells, as well as in peripheral blood mononuclear cells. In tonsils, expressed in B-cell types, including naive B-cells, centroblasts, centrocytes and memory B-cells (at protein level). In benign hyperplastic lymph nodes, expressed in germinal center cells in both the dark and light zones, as well as in scattered cells in the mantle zone and the interfollicular area (at protein level).2 Publications

Developmental stagei

Differential expressed during pseudoglandular and canalicular stages of lung development.1 Publication

Gene expression databases

BgeeiQ9NQV5.
CleanExiHS_PRDM11.
ExpressionAtlasiQ9NQV5. baseline and differential.
GenevisibleiQ9NQV5. HS.

Organism-specific databases

HPAiHPA057072.

Interactioni

Protein-protein interaction databases

STRINGi9606.ENSP00000263765.

Structurei

Secondary structure

1
511
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi108 – 1103Combined sources
Turni111 – 1144Combined sources
Beta strandi115 – 1217Combined sources
Turni122 – 1243Combined sources
Beta strandi128 – 1303Combined sources
Helixi142 – 1454Combined sources
Beta strandi151 – 1555Combined sources
Beta strandi161 – 1655Combined sources
Beta strandi174 – 1763Combined sources
Beta strandi181 – 1844Combined sources
Beta strandi194 – 1985Combined sources
Beta strandi204 – 2085Combined sources
Turni212 – 2143Combined sources
Helixi217 – 2204Combined sources
Turni227 – 2293Combined sources
Beta strandi232 – 2376Combined sources
Beta strandi240 – 2478Combined sources
Beta strandi256 – 2594Combined sources
Helixi261 – 2677Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3RAYX-ray1.73A79-314[»]
ProteinModelPortaliQ9NQV5.
SMRiQ9NQV5. Positions 106-269.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini149 – 260112SETPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the class V-like SAM-binding methyltransferase superfamily.PROSITE-ProRule annotation
Contains 1 SET domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiENOG410IN44. Eukaryota.
ENOG410ZHQ1. LUCA.
GeneTreeiENSGT00830000128341.
HOGENOMiHOG000231445.
HOVERGENiHBG053665.
InParanoidiQ9NQV5.
OMAiWMRYVII.
OrthoDBiEOG7XPZ5F.
PhylomeDBiQ9NQV5.
TreeFamiTF316279.

Family and domain databases

InterProiIPR001214. SET_dom.
[Graphical view]
PfamiPF00856. SET. 1 hit.
[Graphical view]
PROSITEiPS50280. SET. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9NQV5-1) [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
MLKMAEPIAS LMIVECRACL RCSPLFLYQR EKDRMTENMK ECLAQTNAAV
60 70 80 90 100
GDMVTVVKTE VCSPLRDQEY GQPCSRRPDS SAMEVEPKKL KGKRDLIVPK
110 120 130 140 150
SFQQVDFWFC ESCQEYFVDE CPNHGPPVFV SDTPVPVGIP DRAALTIPQG
160 170 180 190 200
MEVVKDTSGE SDVRCVNEVI PKGHIFGPYE GQISTQDKSA GFFSWLIVDK
210 220 230 240 250
NNRYKSIDGS DETKANWMRY VVISREEREQ NLLAFQHSER IYFRACRDIR
260 270 280 290 300
PGEWLRVWYS EDYMKRLHSM SQETIHRNLA RGEKRLQREK SEQVLDNPED
310 320 330 340 350
LRGPIHLSVL RQGKSPYKRG FDEGDVHPQA KKKKIDLIFK DVLEASLESA
360 370 380 390 400
KVEAHQLALS TSLVIRKVPK YQDDAYSQCA TTMTHGVQNI GQTQGEGDWK
410 420 430 440 450
VPQGVSKEPG QLEDEEEEPS SFKADSPAEA SLASDPHELP TTSFCPNCIR
460 470 480 490 500
LKKKVRELQA ELDMLKSGKL PEPPVLPPQV LELPEFSDPA GKLVWMRLLS
510
EGRVRSGLCG G
Length:511
Mass (Da):57,863
Last modified:October 5, 2010 - v2
Checksum:i81DCAA502315EA5B
GO
Isoform 2 (identifier: Q9NQV5-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-34: Missing.

Note: No experimental confirmation available.
Show »
Length:477
Mass (Da):53,865
Checksum:i70133F1E616A817D
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti48 – 481A → V in BAC04425 (PubMed:14702039).Curated
Sequence conflicti58 – 6710KTEVCSPLRD → NPS in AAF87244 (Ref. 1) Curated
Sequence conflicti214 – 2141K → E in AAF87244 (Ref. 1) Curated

Polymorphismi

A genome-wide association analysis shows PRDM11 association with forced vital capacity (FVC), a spirometric measure of pulmonary function, that reflects lung volume and is used to diagnose and monitor lung diseases.1 Publication

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti200 – 2001K → E in a patient with diffuse large B-cell lymphoma; unknown pathological significance. 1 Publication
Corresponds to variant rs139870847 [ dbSNP | Ensembl ].
VAR_073689
Natural varianti285 – 2851R → S in a patient with diffuse large B-cell lymphoma; unknown pathological significance. 1 Publication
VAR_073690

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 3434Missing in isoform 2. 1 PublicationVSP_039836Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF275818 mRNA. Translation: AAF87244.1.
AK094792 mRNA. Translation: BAC04425.1.
AC103681 Genomic DNA. No translation available.
CCDSiCCDS58130.1. [Q9NQV5-2]
RefSeqiNP_001243624.1. NM_001256695.1.
NP_001243625.1. NM_001256696.1. [Q9NQV5-2]
XP_011518533.1. XM_011520231.1. [Q9NQV5-2]
UniGeneiHs.178715.

Genome annotation databases

EnsembliENST00000424263; ENSP00000394314; ENSG00000019485. [Q9NQV5-2]
ENST00000530656; ENSP00000435976; ENSG00000019485. [Q9NQV5-1]
GeneIDi56981.
KEGGihsa:56981.
UCSCiuc031qaa.2. human. [Q9NQV5-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF275818 mRNA. Translation: AAF87244.1.
AK094792 mRNA. Translation: BAC04425.1.
AC103681 Genomic DNA. No translation available.
CCDSiCCDS58130.1. [Q9NQV5-2]
RefSeqiNP_001243624.1. NM_001256695.1.
NP_001243625.1. NM_001256696.1. [Q9NQV5-2]
XP_011518533.1. XM_011520231.1. [Q9NQV5-2]
UniGeneiHs.178715.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3RAYX-ray1.73A79-314[»]
ProteinModelPortaliQ9NQV5.
SMRiQ9NQV5. Positions 106-269.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi9606.ENSP00000263765.

PTM databases

iPTMnetiQ9NQV5.
PhosphoSiteiQ9NQV5.

Polymorphism and mutation databases

DMDMi308153475.

Proteomic databases

MaxQBiQ9NQV5.
PaxDbiQ9NQV5.
PRIDEiQ9NQV5.

Protocols and materials databases

DNASUi56981.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000424263; ENSP00000394314; ENSG00000019485. [Q9NQV5-2]
ENST00000530656; ENSP00000435976; ENSG00000019485. [Q9NQV5-1]
GeneIDi56981.
KEGGihsa:56981.
UCSCiuc031qaa.2. human. [Q9NQV5-1]

Organism-specific databases

CTDi56981.
GeneCardsiPRDM11.
HGNCiHGNC:13996. PRDM11.
HPAiHPA057072.
MIMi616347. gene.
neXtProtiNX_Q9NQV5.
PharmGKBiPA33709.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IN44. Eukaryota.
ENOG410ZHQ1. LUCA.
GeneTreeiENSGT00830000128341.
HOGENOMiHOG000231445.
HOVERGENiHBG053665.
InParanoidiQ9NQV5.
OMAiWMRYVII.
OrthoDBiEOG7XPZ5F.
PhylomeDBiQ9NQV5.
TreeFamiTF316279.

Miscellaneous databases

GenomeRNAii56981.
NextBioi62653.
PROiQ9NQV5.
SOURCEiSearch...

Gene expression databases

BgeeiQ9NQV5.
CleanExiHS_PRDM11.
ExpressionAtlasiQ9NQV5. baseline and differential.
GenevisibleiQ9NQV5. HS.

Family and domain databases

InterProiIPR001214. SET_dom.
[Graphical view]
PfamiPF00856. SET. 1 hit.
[Graphical view]
PROSITEiPS50280. SET. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "A family of novel PR-domain (PRDM) genes as candidate tumor suppressors."
    Yang X.-H., Huang S.
    Submitted (JUN-2000) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
  2. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
    Tissue: Brain.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-63, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  5. "Genome-wide association analysis identifies six new loci associated with forced vital capacity."
    Loth D.W., Artigas M.S., Gharib S.A., Wain L.V., Franceschini N., Koch B., Pottinger T.D., Smith A.V., Duan Q., Oldmeadow C., Lee M.K., Strachan D.P., James A.L., Huffman J.E., Vitart V., Ramasamy A., Wareham N.J., Kaprio J.
    , Wang X.Q., Trochet H., Kaehoenen M., Flexeder C., Albrecht E., Lopez L.M., de Jong K., Thyagarajan B., Alves A.C., Enroth S., Omenaas E., Joshi P.K., Fall T., Vinuela A., Launer L.J., Loehr L.R., Fornage M., Li G., Wilk J.B., Tang W., Manichaikul A., Lahousse L., Harris T.B., North K.E., Rudnicka A.R., Hui J., Gu X., Lumley T., Wright A.F., Hastie N.D., Campbell S., Kumar R., Pin I., Scott R.A., Pietilaeinen K.H., Surakka I., Liu Y., Holliday E.G., Schulz H., Heinrich J., Davies G., Vonk J.M., Wojczynski M., Pouta A., Johansson A., Wild S.H., Ingelsson E., Rivadeneira F., Voelzke H., Hysi P.G., Eiriksdottir G., Morrison A.C., Rotter J.I., Gao W., Postma D.S., White W.B., Rich S.S., Hofman A., Aspelund T., Couper D., Smith L.J., Psaty B.M., Lohman K., Burchard E.G., Uitterlinden A.G., Garcia M., Joubert B.R., McArdle W.L., Musk A.B., Hansel N., Heckbert S.R., Zgaga L., van Meurs J.B., Navarro P., Rudan I., Oh Y.M., Redline S., Jarvis D.L., Zhao J.H., Rantanen T., O'Connor G.T., Ripatti S., Scott R.J., Karrasch S., Grallert H., Gaddis N.C., Starr J.M., Wijmenga C., Minster R.L., Lederer D.J., Pekkanen J., Gyllensten U., Campbell H., Morris A.P., Glaeser S., Hammond C.J., Burkart K.M., Beilby J., Kritchevsky S.B., Gudnason V., Hancock D.B., Williams O.D., Polasek O., Zemunik T., Kolcic I., Petrini M.F., Wjst M., Kim W.J., Porteous D.J., Scotland G., Smith B.H., Viljanen A., Helioevaara M., Attia J.R., Sayers I., Hampel R., Gieger C., Deary I.J., Boezen H.M., Newman A., Jarvelin M.R., Wilson J.F., Lind L., Stricker B.H., Teumer A., Spector T.D., Melen E., Peters M.J., Lange L.A., Barr R.G., Bracke K.R., Verhamme F.M., Sung J., Hiemstra P.S., Cassano P.A., Sood A., Hayward C., Dupuis J., Hall I.P., Brusselle G.G., Tobin M.D., London S.J.
    Nat. Genet. 46:669-677(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: TISSUE SPECIFICITY, POLYMORPHISM, DEVELOPMENTAL STAGE.
  6. "Uncovering global SUMOylation signaling networks in a site-specific manner."
    Hendriks I.A., D'Souza R.C., Yang B., Verlaan-de Vries M., Mann M., Vertegaal A.C.
    Nat. Struct. Mol. Biol. 21:927-936(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-214, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  7. Cited for: FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, VARIANTS GLU-200 AND SER-285.
  8. "Crystal structure of methyltransferase domain of human PR domain-containing protein 11."
    Structural genomics consortium (SGC)
    Submitted (APR-2011) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (1.73 ANGSTROMS) OF 79-314.

Entry informationi

Entry nameiPRD11_HUMAN
AccessioniPrimary (citable) accession number: Q9NQV5
Secondary accession number(s): Q8N9F1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 8, 2002
Last sequence update: October 5, 2010
Last modified: May 11, 2016
This is version 103 of the entry and version 2 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.