Reviewed, UniProtKB/Swiss-Prot Q13029 (PRDM2_HUMAN)

Names and origin

Protein names

Recommended name:
    PR domain zinc finger protein 2
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

Name:	PRDM2
Synonyms:	KMT8, RIZ

Organism

Homo sapiens (Human)

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	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.
Subunit structure	Binds to the retinoblastoma protein (RB). Interacts with GATA3.
Subcellular location	Nucleus.
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.
Sequence similarities	Contains 8 C2H2-type zinc fingers. Contains 1 SET domain.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Coding sequence diversity	Alternative initiation Alternative splicing
Domain	Repeat Zinc-finger
Ligand	DNA-binding Metal-binding Zinc
Molecular function	Activator
PTM	Phosphoprotein
Technical term	3D-structure
Gene Ontology (GO)
Biological process	regulation of transcription, DNA-dependent Ref.4 Ref.5 Non-traceable author statement. Source: UniProtKB
Cellular component	Golgi apparatus Inferred from direct assay. Source: HPA nucleus Ref.1 Ref.4 Non-traceable author statement. Source: UniProtKB
Molecular function	transcription factor activity Ref.4 Ref.5 Non-traceable author statement. Source: UniProtKB zinc ion binding Ref.1 Non-traceable author statement. Source: UniProtKB
Complete GO annotation...

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.

Notes: 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.

Notes: 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

Modified residue

643

1

Phosphoserine

Modified residue

739

1

Phosphoserine

Modified residue

743

1

Phosphoserine

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

Experimental info

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 Ref.5

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

1718

Helix Strand Turn

Details...

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

	Sequence		Length	Mass (Da)
	Isoform 1 (RIZ1) [UniParc]. Last modified December 21, 2004. Version 3. Checksum: 536BD68667AFE433	FASTA	1,718	188,915
	10 20 30 40 50 60 MNQNTTEPVA ATETLAEVPE HVLRGLPEEV RLFPSAVDKT RIGVWATKPI LKGKKFGPFV 70 80 90 100 110 120 GDKKKRSQVK NNVYMWEVYY PNLGWMCIDA TDPEKGNWLR YVNWACSGEE QNLFPLEINR 130 140 150 160 170 180 AIYYKTLKPI APGEELLVWY NGEDNPEIAA AIEEERASAR SKRSSPKSRK GKKKSQENKN 190 200 210 220 230 240 KGNKIQDIQL KTSEPDFTSA NMRDSAEGPK EDEEKPSASA LEQPATLQEV ASQEVPPELA 250 260 270 280 290 300 TPAPAWEPQP EPDERLEAAA CEVNDLGEEE EEEEEEDEEE EEDDDDDELE DEGEEEASMP 310 320 330 340 350 360 NENSVKEPEI RCDEKPEDLL EEPKTTSEET LEDCSEVTPA MQIPRTKEEA NGDVFETFMF 370 380 390 400 410 420 PCQHCERKFT TKQGLERHMH IHISTVNHAF KCKYCGKAFG TQINRRRHER RHEAGLKRKP 430 440 450 460 470 480 SQTLQPSEDL ADGKASGENV ASKDDSSPPS LGPDCLIMNS EKASQDTINS SVVEENGEVK 490 500 510 520 530 540 ELHPCKYCKK VFGTHTNMRR HQRRVHERHL IPKGVRRKGG LEEPQPPAEQ AQATQNVYVP 550 560 570 580 590 600 STEPEEEGEA DDVYIMDISS NISENLNYYI DGKIQTNNNT SNCDVIEMES ASADLYGINC 610 620 630 640 650 660 LLTPVTVEIT QNIKTTQVPV TEDLPKEPLG STNSEAKKRR TASPPALPKI KAETDSDPMV 670 680 690 700 710 720 PSCSLSLPLS ISTTEAVSFH KEKSVYLSSK LKQLLQTQDK LTPAGISATE IAKLGPVCVS 730 740 750 760 770 780 APASMLPVTS SRFKRRTSSP PSSPQHSPAL RDFGKPSDGK AAWTDAGLTS KKSKLESHSD 790 800 810 820 830 840 SPAWSLSGRD ERETVSPPCF DEYKMSKEWT ASSAFSSVCN QQPLDLSSGV KQKAEGTGKT 850 860 870 880 890 900 PVQWESVLDL SVHKKHCSDS EGKEFKESHS VQPTCSAVKK RKPTTCMLQK VLLNEYNGID 910 920 930 940 950 960 LPVENPADGT RSPSPCKSLE AQPDPDLGPG SGFPAPTVES TPDVCPSSPA LQTPSLSSGQ 970 980 990 1000 1010 1020 LPPLLIPTDP SSPPPCPPVL TVATPPPPLL PTVPLPAPSS SASPHPCPSP LSNATAQSPL 1030 1040 1050 1060 1070 1080 PILSPTVSPS PSPIPPVEPL MSAASPGPPT LSSSSSSSSS SSSFSSSSSS SSPSPPPLSA 1090 1100 1110 1120 1130 1140 ISSVVSSGDN LEASLPMISF KQEELENEGL KPREEPQSAA EQDVVVQETF NKNFVCNVCE 1150 1160 1170 1180 1190 1200 SPFLSIKDLT KHLSIHAEEW PFKCEFCVQL FKDKTDLSEH RFLLHGVGNI FVCSVCKKEF 1210 1220 1230 1240 1250 1260 AFLCNLQQHQ RDLHPDKVCT HHEFESGTLR PQNFTDPSKA HVEHMQSLPE DPLETSKEEE 1270 1280 1290 1300 1310 1320 ELNDSSEELY TTIKIMASGI KTKDPDVRLG LNQHYPSFKP PPFQYHHRNP MGIGVTATNF 1330 1340 1350 1360 1370 1380 TTHNIPQTFT TAIRCTKCGK GVDNMPELHK HILACASASD KKRYTPKKNP VPLKQTVQPK 1390 1400 1410 1420 1430 1440 NGVVVLDNSG KNAFRRMGQP KRLNFSVELS KMSSNKLKLN ALKKKNQLVQ KAILQKNKSA 1450 1460 1470 1480 1490 1500 KQKADLKNAC ESSSHICPYC NREFTYIGSL NKHAAFSCPK KPLSPPKKKV SHSSKKGGHS 1510 1520 1530 1540 1550 1560 SPASSDKNSN SNHRRRTADA EIKMQSMQTP LGKTRARSSG PTQVPLPSSS FRSKQNVKFA 1570 1580 1590 1600 1610 1620 ASVKSKKPSS SSLRNSSPIR MAKITHVEGK KPKAVAKNHS AQLSSKTSRS LHVRVQKSKA 1630 1640 1650 1660 1670 1680 VLQSKSTLAS KKRTDRFNIK SRERSGGPVT RSLQLAAAAD LSENKREDGS AKQELKDFSY 1690 1700 1710 SLRLASRCSP PAAPYITRQY RKVKAPAAAQ FQGPFFKE
	Isoform 2 (MTB-Zf) [UniParc]. Checksum: F353A6402F93712D		1,682	184,961
	10 20 30 40 50 60 MNQNTTEPVA ATETLAEVPE HVLRGLPEEV RLFPSAVDKT RIGVWATKPI LKGKKFGPFV 70 80 90 100 110 120 GDKKKRSQVK NNVYMWEVYY PNLGWMCIDA TDPEKGNWLR YVNWACSGEE QNLFPLEINR 130 140 150 160 170 180 AIYYKTLKPI APGEELLVWY NGEDNPEIAA AIEEERASAR SKRSSPKSRK GKKKSQENKN 190 200 210 220 230 240 KGNKIQDIQL KTSEPDFTSA NMRDSAEGPK EDEEKPSASA LEQPATLQEV ASQEVPPELA 250 260 270 280 290 300 TPAPAWEPQP EPDERLEAAA CEVNDLGEEE EEEEEEDEEE EEDDDDDELE DEGEEEASMP 310 320 330 340 350 360 NENSVKEPEI RCDEKPEDLL EEPKTTSEET LEDCSEVTPA MQIPRTKEEA NGDVFETFMF 370 380 390 400 410 420 PCQHCERKFT TKQGLERHMH IHISTVNHAF KCKYCGKAFG TQINRRRHER RHEAGLKRKP 430 440 450 460 470 480 SQTLQPSEDL ADGKASGENV ASKDDSSPPS LGPDCLIMNS EKASQDTINS SVVEENGEVK 490 500 510 520 530 540 ELHPCKYCKK VFGTHTNMRR HQRRVHERHL IPKGVRRKGG LEEPQPPAEQ AQATQNVYVP 550 560 570 580 590 600 STEPEEEGEA DDVYIMDISS NISENLNYYI DGKIQTNNNT SNCDVIEMES ASADLYGINC 610 620 630 640 650 660 LLTPVTVEIT QNIKTTQVPV TEDLPKEPLG STNSEAKKRR TASPPALPKI KAETDSDPMV 670 680 690 700 710 720 PSCSLSLPLS ISTTEAVSFH KEKSVYLSSK LKQLLQTQDK LTPAGISATE IAKLGPVCVS 730 740 750 760 770 780 APASMLPVTS SRFKRRTSSP PSSPQHSPAL RDFGKPSDGK AAWTDAGLTS KKSKLESHSD 790 800 810 820 830 840 SPAWSLSGRD ERETVSPPCF DEYKMSKEWT ASSAFSSVCN QQPLDLSSGV KQKAEGTGKT 850 860 870 880 890 900 PVQWESVLDL SVHKKHCSDS EGKEFKESHS VQPTCSAVKK RKPTTCMLQK VLLNEYNGID 910 920 930 940 950 960 LPVENPADGT RSPSPCKSLE AQPDPDLGPG SGFPAPTVES TPDVCPSSPA LQTPSLSSGQ 970 980 990 1000 1010 1020 LPPLLIPTDP SSPPPCPPVL TVATPPPPLL PTVPLPAPSS SASPHPCPSP LSNATAQSPL 1030 1040 1050 1060 1070 1080 PILSPTVSPS PSPIPPVEPL MSAASPGPPT LSSSSSSSSS SSSFSSSSSS SSPSPPPLSA 1090 1100 1110 1120 1130 1140 ISSVVSSGDN LEASLPMISF KQEELENEGL KPREEPQSAA EQDVVVQETF NKNFVCNVCE 1150 1160 1170 1180 1190 1200 SPFLSIKDLT KHLSIHAEEW PFKCEFCVQL FKDKTDLSEH RFLLHGVGNI FVCSVCKKEF 1210 1220 1230 1240 1250 1260 AFLCNLQQHQ RDLHPDKVCT HHEFESGTLR PQNFTDPSKA HVEHMQSLPE DPLETSKEEE 1270 1280 1290 1300 1310 1320 ELNDSSEELY TTIKIMASGI KTKDPDVRLG LNQHYPSFKP PPFQYHHRNP MGIGVTATNF 1330 1340 1350 1360 1370 1380 TTHNIPQTFT TAIRCTKCGK GVDNMPELHK HILACASASD KKRYTPKKNP VPLKQTVQPK 1390 1400 1410 1420 1430 1440 NGVVVLDNSG KNAFRRMGQP KRLNFSVELS KMSSNKLKLN ALKKKNQLVQ KAILQKNKSA 1450 1460 1470 1480 1490 1500 KQKADLKNAC ESSSHICPYC NREFTYIGSL NKHAAFSCPK KPLSPPKKKV SHSSKKGGHS 1510 1520 1530 1540 1550 1560 SPASSDKNSN SNHRRRTADA EIKMQSMQTP LGKTRARSSG PTQVPLPSSS FRSKQNVKFA 1570 1580 1590 1600 1610 1620 ASVKSKKPSS SSLRNSSPIR MAKITHVEGK KPKAVAKNHS AQLSSKTSRS LHVRVQKSKA 1630 1640 1650 1660 1670 1680 VLQSKSTLAS KKRTDRFNIK SRERSGGPVT RSLQLAAAAD LSENKREDGS AKQELKDFRN FL
	Isoform 3 (RIZ2) [UniParc]. Checksum: 2AB9A94179532CE7		1,517	166,061
	10 20 30 40 50 60 MRDSAEGPKE DEEKPSASAL EQPATLQEVA SQEVPPELAT PAPAWEPQPE PDERLEAAAC 70 80 90 100 110 120 EVNDLGEEEE EEEEEDEEEE EDDDDDELED EGEEEASMPN ENSVKEPEIR CDEKPEDLLE 130 140 150 160 170 180 EPKTTSEETL EDCSEVTPAM QIPRTKEEAN GDVFETFMFP CQHCERKFTT KQGLERHMHI 190 200 210 220 230 240 HISTVNHAFK CKYCGKAFGT QINRRRHERR HEAGLKRKPS QTLQPSEDLA DGKASGENVA 250 260 270 280 290 300 SKDDSSPPSL GPDCLIMNSE KASQDTINSS VVEENGEVKE LHPCKYCKKV FGTHTNMRRH 310 320 330 340 350 360 QRRVHERHLI PKGVRRKGGL EEPQPPAEQA QATQNVYVPS TEPEEEGEAD DVYIMDISSN 370 380 390 400 410 420 ISENLNYYID GKIQTNNNTS NCDVIEMESA SADLYGINCL LTPVTVEITQ NIKTTQVPVT 430 440 450 460 470 480 EDLPKEPLGS TNSEAKKRRT ASPPALPKIK AETDSDPMVP SCSLSLPLSI STTEAVSFHK 490 500 510 520 530 540 EKSVYLSSKL KQLLQTQDKL TPAGISATEI AKLGPVCVSA PASMLPVTSS RFKRRTSSPP 550 560 570 580 590 600 SSPQHSPALR DFGKPSDGKA AWTDAGLTSK KSKLESHSDS PAWSLSGRDE RETVSPPCFD 610 620 630 640 650 660 EYKMSKEWTA SSAFSSVCNQ QPLDLSSGVK QKAEGTGKTP VQWESVLDLS VHKKHCSDSE 670 680 690 700 710 720 GKEFKESHSV QPTCSAVKKR KPTTCMLQKV LLNEYNGIDL PVENPADGTR SPSPCKSLEA 730 740 750 760 770 780 QPDPDLGPGS GFPAPTVEST PDVCPSSPAL QTPSLSSGQL PPLLIPTDPS SPPPCPPVLT 790 800 810 820 830 840 VATPPPPLLP TVPLPAPSSS ASPHPCPSPL SNATAQSPLP ILSPTVSPSP SPIPPVEPLM 850 860 870 880 890 900 SAASPGPPTL SSSSSSSSSS SSFSSSSSSS SPSPPPLSAI SSVVSSGDNL EASLPMISFK 910 920 930 940 950 960 QEELENEGLK PREEPQSAAE QDVVVQETFN KNFVCNVCES PFLSIKDLTK HLSIHAEEWP 970 980 990 1000 1010 1020 FKCEFCVQLF KDKTDLSEHR FLLHGVGNIF VCSVCKKEFA FLCNLQQHQR DLHPDKVCTH 1030 1040 1050 1060 1070 1080 HEFESGTLRP QNFTDPSKAH VEHMQSLPED PLETSKEEEE LNDSSEELYT TIKIMASGIK 1090 1100 1110 1120 1130 1140 TKDPDVRLGL NQHYPSFKPP PFQYHHRNPM GIGVTATNFT THNIPQTFTT AIRCTKCGKG 1150 1160 1170 1180 1190 1200 VDNMPELHKH ILACASASDK KRYTPKKNPV PLKQTVQPKN GVVVLDNSGK NAFRRMGQPK 1210 1220 1230 1240 1250 1260 RLNFSVELSK MSSNKLKLNA LKKKNQLVQK AILQKNKSAK QKADLKNACE SSSHICPYCN 1270 1280 1290 1300 1310 1320 REFTYIGSLN KHAAFSCPKK PLSPPKKKVS HSSKKGGHSS PASSDKNSNS NHRRRTADAE 1330 1340 1350 1360 1370 1380 IKMQSMQTPL GKTRARSSGP TQVPLPSSSF RSKQNVKFAA SVKSKKPSSS SLRNSSPIRM 1390 1400 1410 1420 1430 1440 AKITHVEGKK PKAVAKNHSA QLSSKTSRSL HVRVQKSKAV LQSKSTLASK KRTDRFNIKS 1450 1460 1470 1480 1490 1500 RERSGGPVTR SLQLAAAADL SENKREDGSA KQELKDFSYS LRLASRCSPP AAPYITRQYR 1510 KVKAPAAAQF QGPFFKE

References

	« Hide 'large scale' referencesShow '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. , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S.,