Reviewed,
UniProtKB/Swiss-Prot Q13029 (PRDM2_HUMAN)
Last modified
November 3, 2009.
Version 101.
History...
Clusters with 100%,
90%,
50% identity |
Documents (6) |
Third-party data |
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Names and origin
| Protein names | Recommended name: PR domain zinc finger protein 2 EC=2.1.1.43 Alternative name(s): PR domain-containing protein 2 Retinoblastoma protein-interacting zinc finger protein Zinc finger protein RIZ MTE-binding protein MTB-ZF GATA-3-binding protein G3B Lysine N-methyltransferase 8 | ||||
| Gene names |
| ||||
| Organism | Homo sapiens (Human) [Complete proteome] | ||||
| Taxonomic identifier | 9606 [NCBI] | ||||
| Taxonomic lineage | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo |
Protein attributes
| Sequence length | 1718 AA. |
| Sequence status | Complete. |
| Sequence processing | The displayed sequence is not processed. |
| Protein existence | Evidence at protein level. |
General annotation (Comments)
| Function | S-adenosyl-L-methionine-dependent histone methyltransferase that specifically methylates 'Lys-9' of histone H3. May function as a DNA-binding transcription factor. Binds to the macrophage-specific TPA-responsive element (MTE) of the HMOX1 (heme oxygenase 1) gene and may act as a transcriptional activator of this gene. Ref.6 |
| Catalytic activity | S-adenosyl-L-methionine + histone L-lysine = S-adenosyl-L-homocysteine + histone N(6)-methyl-L-lysine. |
| Subunit structure | Binds to the retinoblastoma protein (RB). Interacts with GATA3. Ref.4 Ref.10 |
| Subcellular location | |
| Tissue specificity | Highly expressed in retinoblastoma cell lines and in brain tumors. Also expressed in a number of other cell lines and in brain, heart, skeletal muscle, liver and spleen. Isoform 1 is expressed in testis at much higher level than isoform 3. Ref.2 Ref.5 |
| Sequence similarities | Contains 8 C2H2-type zinc fingers. Contains 1 SET domain. |
Ontologies
Alternative products
| This entry describes 3 isoforms produced by alternative splicing and alternative initiation. [Align] [Select] | ||||||
| Isoform 1 (identifier: Q13029-1) Also known as: RIZ1; 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: Q13029-2) Also known as: MTB-Zf; The sequence of this isoform differs from the canonical sequence as follows: 1679-1682: SYSL → RNFL 1683-1718: Missing. | ||||||
| Note: No experimental confirmation available. | ||||||
| Isoform 3 (identifier: Q13029-3) Also known as: RIZ2; The sequence of this isoform differs from the canonical sequence as follows: 1-201: Missing. | ||||||
| Note: Produced by alternative initiation at Met-202 of isoform 1. |
Sequence annotation (Features)
| Feature key | Position(s) | Length | Description | Graphical view | Feature identifier | ||||||||||||||||||||||||||||||||
Molecule processing | |||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Chain | 1 – 1718 | 1718 | PR domain zinc finger protein 2 | PRO_0000041634 | |||||||||||||||||||||||||||||||||
Regions | |||||||||||||||||||||||||||||||||||||
| Domain | 27 – 145 | 119 | SET | ||||||||||||||||||||||||||||||||||
| Zinc finger | 360 – 382 | 23 | C2H2-type 1 | ||||||||||||||||||||||||||||||||||
| Zinc finger | 390 – 412 | 23 | C2H2-type 2 | ||||||||||||||||||||||||||||||||||
| Zinc finger | 483 – 506 | 24 | C2H2-type 3 | ||||||||||||||||||||||||||||||||||
| Zinc finger | 1134 – 1156 | 23 | C2H2-type 4 | ||||||||||||||||||||||||||||||||||
| Zinc finger | 1162 – 1185 | 24 | C2H2-type 5 | ||||||||||||||||||||||||||||||||||
| Zinc finger | 1191 – 1214 | 24 | C2H2-type 6 | ||||||||||||||||||||||||||||||||||
| Zinc finger | 1333 – 1355 | 23 | C2H2-type 7; atypical | ||||||||||||||||||||||||||||||||||
| Zinc finger | 1455 – 1478 | 24 | C2H2-type 8; atypical | ||||||||||||||||||||||||||||||||||
| Region | 294 – 316 | 23 | Retinoblastoma protein binding | ||||||||||||||||||||||||||||||||||
| Motif | 970 – 979 | 10 | SH3-binding Potential | ||||||||||||||||||||||||||||||||||
| Motif | 985 – 998 | 14 | SH3-binding Potential | ||||||||||||||||||||||||||||||||||
| Motif | 1028 – 1052 | 25 | SH3-binding Potential | ||||||||||||||||||||||||||||||||||
| Compositional bias | 268 – 296 | 29 | Asp/Glu-rich (acidic) | ||||||||||||||||||||||||||||||||||
| Compositional bias | 933 – 1049 | 117 | Pro-rich | ||||||||||||||||||||||||||||||||||
| Compositional bias | 1052 – 1074 | 23 | Poly-Ser | ||||||||||||||||||||||||||||||||||
| Compositional bias | 1361 – 1447 | 87 | Arg/Lys-rich (basic) | ||||||||||||||||||||||||||||||||||
Amino acid modifications | |||||||||||||||||||||||||||||||||||||
| Modified residue | 641 | 1 | Phosphothreonine Ref.8 | ||||||||||||||||||||||||||||||||||
| Modified residue | 643 | 1 | Phosphoserine Ref.8 Ref.7 | ||||||||||||||||||||||||||||||||||
| Modified residue | 739 | 1 | Phosphoserine Ref.9 | ||||||||||||||||||||||||||||||||||
| Modified residue | 743 | 1 | Phosphoserine Ref.9 | ||||||||||||||||||||||||||||||||||
Natural variations | |||||||||||||||||||||||||||||||||||||
| Alternative sequence | 1 – 201 | 201 | Missing in isoform 3. | VSP_018974 | |||||||||||||||||||||||||||||||||
| Alternative sequence | 1679 – 1682 | 4 | SYSL → RNFL in isoform 2. | VSP_006927 | |||||||||||||||||||||||||||||||||
| Alternative sequence | 1683 – 1718 | 36 | Missing in isoform 2. | VSP_006928 | |||||||||||||||||||||||||||||||||
| Natural variant | 283 | 1 | D → E: dbSNP rs2076324. | VAR_052929 | |||||||||||||||||||||||||||||||||
| Natural variant | 450 | 1 | S → N: dbSNP rs17350795. | VAR_052930 | |||||||||||||||||||||||||||||||||
Experimental info | |||||||||||||||||||||||||||||||||||||
| Mutagenesis | 106 | 1 | C → Y: Reduced histone methyltransferase activity. Ref.6 | ||||||||||||||||||||||||||||||||||
| Mutagenesis | 159 | 1 | A → V: Reduced histone methyltransferase activity. Ref.6 | ||||||||||||||||||||||||||||||||||
| Mutagenesis | 188 | 1 | I → V: Loss of histone methyltransferase activity. Ref.6 | ||||||||||||||||||||||||||||||||||
| Sequence conflict | 164 | 1 | S → T in AAA87023. Ref.4 | ||||||||||||||||||||||||||||||||||
| Sequence conflict | 196 | 1 | D → S in AAA87023. Ref.4 | ||||||||||||||||||||||||||||||||||
| Sequence conflict | 200 | 1 | A → G in AAA87023. Ref.4 | ||||||||||||||||||||||||||||||||||
| Sequence conflict | 276 – 293 | 18 | EDEEE…LEDEG → VGGGGGVVVVVSWKARGE in AAA87023. Ref.4 | ||||||||||||||||||||||||||||||||||
| Sequence conflict | 307 – 318 | 12 | EPEIR…EKPED → SQKYGVMRSQKI in AAA87023. Ref.4 | ||||||||||||||||||||||||||||||||||
| Sequence conflict | 336 – 337 | 2 | EV → DL in AAA87023. Ref.4 | ||||||||||||||||||||||||||||||||||
| Sequence conflict | 371 | 1 | T → I in AAA87023. Ref.4 | ||||||||||||||||||||||||||||||||||
| Sequence conflict | 466 – 467 | 2 | DT → VS in AAA87023. Ref.4 | ||||||||||||||||||||||||||||||||||
| Sequence conflict | 534 – 550 | 17 | TQNVY…EEGEA → PRTCMYQAQSRRGRGSR in AAA87023. Ref.4 | ||||||||||||||||||||||||||||||||||
| Sequence conflict | 703 | 1 | P → PP Ref.1 | ||||||||||||||||||||||||||||||||||
| Sequence conflict | 703 | 1 | P → PP Ref.5 | ||||||||||||||||||||||||||||||||||
Secondary structure | |||||||||||||||||||||||||||||||||||||
Helix Strand Turn | |||||||||||||||||||||||||||||||||||||
| Beta strand | 5 – 7 | 3 | |||||||||||||||||||||||||||||||||||
| Helix | 15 – 17 | 3 | |||||||||||||||||||||||||||||||||||
| Helix | 20 – 24 | 5 | |||||||||||||||||||||||||||||||||||
| Beta strand | 30 – 34 | 5 | |||||||||||||||||||||||||||||||||||
| Beta strand | 41 – 48 | 8 | |||||||||||||||||||||||||||||||||||
| Beta strand | 62 – 64 | 3 | |||||||||||||||||||||||||||||||||||
| Helix | 66 – 68 | 3 | |||||||||||||||||||||||||||||||||||
| Beta strand | 72 – 80 | 9 | |||||||||||||||||||||||||||||||||||
| Turn | 81 – 83 | 3 | |||||||||||||||||||||||||||||||||||
| Beta strand | 84 – 89 | 6 | |||||||||||||||||||||||||||||||||||
| Helix | 93 – 95 | 3 | |||||||||||||||||||||||||||||||||||
| Helix | 98 – 101 | 4 | |||||||||||||||||||||||||||||||||||
| Beta strand | 113 – 118 | 6 | |||||||||||||||||||||||||||||||||||
| Beta strand | 121 – 128 | 8 | |||||||||||||||||||||||||||||||||||
| Helix | 149 – 158 | 10 | |||||||||||||||||||||||||||||||||||
Sequences
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References
| « Hide 'large scale' references | |
| [1] | "The retinoblastoma protein binds to RIZ, a zinc-finger protein that shares an epitope with the adenovirus E1A protein." Buyse I.M., Shao G., Huang S. Proc. Natl. Acad. Sci. U.S.A. 92:4467-4471(1995) [PubMed: 7538672] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), SUBCELLULAR LOCATION. Tissue: Fetal brain and Retinoblastoma. |
| [2] | "The retinoblastoma interacting zinc finger gene RIZ produces a PR domain-lacking product through an internal promoter." Liu L., Shao G., Steele-Perkins G., Huang S. J. Biol. Chem. 272:2984-2991(1997) [PubMed: 9006946] [Abstract] Cited for: NUCLEOTIDE SEQUENCE (ISOFORMS 1 AND 3), ALTERNATIVE INITIATION, TISSUE SPECIFICITY, SUBCELLULAR LOCATION. |
| [3] | "The DNA sequence and biological annotation of human chromosome 1." Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K. Bentley D.R.Nature 441:315-321(2006) [PubMed: 16710414] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. |
| [4] | "Identification and cloning of the G3B cDNA encoding a 3' segment of a protein binding to GATA-3." Shapiro V.S., Lee P., Winoto A. Gene 163:329-330(1995) [PubMed: 7590293] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 159-550, INTERACTION WITH GATA3. |
| [5] | "cDNA cloning of a novel protein containing two zinc-finger domains that may function as a transcription factor for the human heme-oxygenase-1 gene." Muraosa Y., Takahashi K., Yoshizawa M., Shibahara S. Eur. J. Biochem. 235:471-479(1996) [PubMed: 8654390] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 202-1718 (ISOFORM 2), TISSUE SPECIFICITY. |
| [6] | "Inactivation of a histone methyltransferase by mutations in human cancers." Kim K.-C., Geng L., Huang S. Cancer Res. 63:7619-7623(2003) [PubMed: 14633678] [Abstract] Cited for: FUNCTION, MUTAGENESIS OF CYS-106; ALA-159 AND ILE-188, SUBCELLULAR LOCATION. |
| [7] | "Large-scale characterization of HeLa cell nuclear phosphoproteins." Beausoleil S.A., Jedrychowski M., Schwartz D., Elias J.E., Villen J., Li J., Cohn M.A., Cantley L.C., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 101:12130-12135(2004) [PubMed: 15302935] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-643, MASS SPECTROMETRY. Tissue: Epithelium. |
| [8] | "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks." Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M. Cell 127:635-648(2006) [PubMed: 17081983] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-641 AND SER-643, MASS SPECTROMETRY. Tissue: Epithelium. |
| [9] | "Combining protein-based IMAC, peptide-based IMAC, and MudPIT for efficient phosphoproteomic analysis." Cantin G.T., Yi W., Lu B., Park S.K., Xu T., Lee J.-D., Yates J.R. III J. Proteome Res. 7:1346-1351(2008) [PubMed: 18220336] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-739 AND SER-743, MASS SPECTROMETRY. |
| [10] | "Structural studies of the SET domain from RIZ1 tumor suppressor." Briknarova K., Zhou X., Satterthwait A., Hoyt D.W., Ely K.R., Huang S. Biochem. Biophys. Res. Commun. 366:807-813(2008) [PubMed: 18082620] [Abstract] Cited for: STRUCTURE BY NMR OF 1-161, INTERACTION WITH HISTONE H3. |
| [11] | "The crystal structure of methyltransferase domain of human PR domain-containing protein 2." Structural genomics consortium (SGC) Submitted (AUG-2007) to the PDB data bank Cited for: X-RAY CRYSTALLOGRAPHY (1.79 ANGSTROMS) OF 2-148. |
| + | Additional computationally mapped references. |
Cross-references
Sequence databases | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| U17838 mRNA. Translation: AAC50820.2. AL031277, AL583942 Genomic DNA. Translation: CAI19343.1. AL583942, AL031277 Genomic DNA. Translation: CAH70943.1. U23736 mRNA. Translation: AAA87023.1. D45132 mRNA. Translation: BAA08110.1. Different initiation. | |||||||||||||||||||
| IPI | IPI00016780. IPI00219556. IPI00759628. | ||||||||||||||||||
| PIR | I38902. | ||||||||||||||||||
| RefSeq | NP_001007258.1. NP_036363.2. NP_056950.2. | ||||||||||||||||||
| UniGene | Hs.371823 | ||||||||||||||||||
3D structure databases | |||||||||||||||||||
| |||||||||||||||||||
| ModBase | Search... | ||||||||||||||||||
Protein-protein interaction databases | |||||||||||||||||||
| DIP | DIP:428N. | ||||||||||||||||||
| STRING | Q13029. | ||||||||||||||||||
PTM databases | |||||||||||||||||||
| PhosphoSite | Q13029. | ||||||||||||||||||
Proteomic databases | |||||||||||||||||||
| PRIDE | Q13029. | ||||||||||||||||||
Genome annotation databases | |||||||||||||||||||
| Ensembl | ENST00000235372; ENSP00000235372; ENSG00000116731; Homo sapiens. [Genome view] ENST00000311066; ENSP00000312352; ENSG00000116731; Homo sapiens. [Genome view] ENST00000343137; ENSP00000341621; ENSG00000116731; Homo sapiens. [Genome view] ENST00000376048; ENSP00000365216; ENSG00000116731; Homo sapiens. [Genome view] ENST00000400800; ENSP00000383603; ENSG00000116731; Homo sapiens. [Genome view] ENST00000400801; ENSP00000383604; ENSG00000116731; Homo sapiens. [Genome view] ENST00000400802; ENSP00000383605; ENSG00000116731; Homo sapiens. [Genome view] ENST00000400803; ENSP00000383606; ENSG00000116731; Homo sapiens. [Genome view] ENST00000407521; ENSP00000384430; ENSG00000116731; Homo sapiens. [Genome view] ENST00000413440; ENSP00000411103; ENSG00000116731; Homo sapiens. [Genome view] ENST00000431014; ENSP00000388735; ENSG00000116731; Homo sapiens. [Genome view] | ||||||||||||||||||
| GeneID | 7799. | ||||||||||||||||||
| KEGG | hsa:7799. | ||||||||||||||||||
| UCSC | uc001avh.1. human. uc001avi.1. human. | ||||||||||||||||||
Organism-specific databases | |||||||||||||||||||
| CTD | 7799. | ||||||||||||||||||
| GeneCards | GC01P013899. | ||||||||||||||||||
| HGNC | HGNC:9347. PRDM2. | ||||||||||||||||||
| HPA | HPA005809. | ||||||||||||||||||
| MIM | 601196. gene. | ||||||||||||||||||
| PharmGKB | PA33715. | ||||||||||||||||||
| GenAtlas | Search... | ||||||||||||||||||
Phylogenomic databases | |||||||||||||||||||
| HOGENOM | Q13029. | ||||||||||||||||||
| HOVERGEN | Q13029. | ||||||||||||||||||
| OMA | KELHPCK. | ||||||||||||||||||
Gene expression databases | |||||||||||||||||||
| ArrayExpress | Q13029. | ||||||||||||||||||
| Bgee | Q13029. | ||||||||||||||||||
| CleanEx | HS_PRDM2. | ||||||||||||||||||
| Genevestigator | Q13029. | ||||||||||||||||||
| GermOnline | ENSG00000116731. Homo sapiens. | ||||||||||||||||||
Family and domain databases | |||||||||||||||||||
| InterPro | IPR009170. RIZ_retinblastoma-bd_prot. IPR001214. SET. IPR007087. Znf_C2H2. IPR015880. Znf_C2H2-like. [Graphical view] | ||||||||||||||||||
| Pfam | PF00856. SET. 1 hit. PF00096. zf-C2H2. 5 hits. [Graphical view] | ||||||||||||||||||
| PIRSF | PIRSF002395. RIZ_SET. 1 hit. | ||||||||||||||||||
| SMART | SM00317. SET. 1 hit. SM00355. ZnF_C2H2. 8 hits. [Graphical view] | ||||||||||||||||||
| PROSITE | PS50280. SET. 1 hit. PS00028. ZINC_FINGER_C2H2_1. 6 hits. PS50157. ZINC_FINGER_C2H2_2. 7 hits. [Graphical view] | ||||||||||||||||||
| ProtoNet | Search... | ||||||||||||||||||
Other Resources | |||||||||||||||||||
| NextBio | 30170. | ||||||||||||||||||
| SOURCE | Search... | ||||||||||||||||||
Entry information
| Entry name | PRDM2_HUMAN | ||||||||
| Accession | Primary (citable) accession number: Q13029 Secondary accession number(s): Q13149, Q14550, Q5VUL9 | ||||||||
| Entry history |
| ||||||||
| Entry status | Reviewed (UniProtKB/Swiss-Prot) | ||||||||
| Annotation project | HPI (Human Proteome Initiative) | ||||||||
| Disclaimer | Any 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. | ||||||||
Relevant documents
| Human chromosome 1 Human chromosome 1: entries, gene names and cross-references to MIM |
| Human entries with polymorphisms or disease mutations List of human entries with polymorphisms or disease mutations |
| Human polymorphisms and disease mutations Index of human polymorphisms and disease mutations |
| MIM cross-references Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot |
| PDB cross-references Index of Protein Data Bank (PDB) cross-references |
| SIMILARITY comments Index of protein domains and families |

Clusters with


