Reviewed, UniProtKB/Swiss-Prot Q13950 (RUNX2_HUMAN)

Names and origin

Protein names

Recommended name:
    Runt-related transcription factor 2
Alternative name(s):
    Core-binding factor subunit alpha-1
      Short name=CBF-alpha-1
    Acute myeloid leukemia 3 protein
    Oncogene AML-3
    Polyomavirus enhancer-binding protein 2 alpha A subunit
      Short name=PEBP2-alpha A
      Short name=PEA2-alpha A
    SL3-3 enhancer factor 1 alpha A subunit
    SL3/AKV core-binding factor alpha A subunit
    Osteoblast-specific transcription factor 2
      Short name=OSF-2

Gene names

Name:	RUNX2
Synonyms:	AML3, CBFA1, OSF2, PEBP2A

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	521 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Transcription factor involved in osteoblastic differentiation and skeletal morphogenesis. Essential for the maturation of osteoblasts and both intramembranous and endochondral ossification. CBF binds to the core site, 5'-PYGPYGGT-3', of a number of enhancers and promoters, including murine leukemia virus, polyomavirus enhancer, T-cell receptor enhancers, osteocalcin, osteopontin, bone sialoprotein, alpha 1(I) collagen, LCK, IL-3 and GM-CSF promoters By similarity. Inhibits MYST4-dependent transcriptional activation.
Subunit structure	Heterodimer of an alpha and a beta subunit. Interacts with HIVEP3 By similarity. The alpha subunit binds DNA as a monomer and through the Runt domain. DNA-binding is increased by heterodimerization. Interacts with G22P1 (Ku70) and XRCC5 (Ku80). Interacts with MYST3 and MYST4.
Subcellular location	Nucleus.
Tissue specificity	Specifically expressed in osteoblasts.
Domain	A proline/serine/threonine rich region at the C-terminus is necessary for transcriptional activation of target genes and contains the phosphorylation sites.
Post-translational modification	Phosphorylated; probably by MAP kinases (MAPK) By similarity. Isoform 3 is phosphorylated on Ser-340.
Involvement in disease	Defects in RUNX2 are the cause of cleidocranial dysplasia (CCD) [MIM:119600]. CCD is an autosomal dominant skeletal disorder with high penetrance and variable expressivity. It is due to defective endochondral and intramembranous bone formation. Typical features include hypoplasia/aplasia of clavicles, patent fontanelles, wormian bones (additional cranial plates caused by abnormal ossification of the calvaria), supernumerary teeth, short stature, and other skeletal changes. In some cases defects in RUNX2 are exclusively associated with dental anomalies.
Sequence similarities	Contains 1 Runt domain.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing Polymorphism
Disease	Disease mutation
Ligand	DNA-binding
PTM	Phosphoprotein
Gene Ontology (GO)
Biological process	negative regulation of transcription Ref.7 Inferred from direct assay. Source: UniProtKB osteoblast differentiation Traceable author statement. Source: UniProtKB
Cellular component	nucleus Inferred from electronic annotation. Source: InterPro
Molecular function	ATP binding Inferred from electronic annotation. Source: InterPro RNA polymerase II transcription factor activity Traceable author statement. Source: ProtInc protein binding Ref.6 Ref.7 Inferred from physical interaction. Source: UniProtKB transcription activator activity Ref.7 Inferred from direct assay. Source: UniProtKB transcription factor activity Ref.1 Non-traceable author statement. Source: ProtInc
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
SMAD6	O43541	2	EBI-976402,EBI-976374
SMURF1	Q9HCE7	1	EBI-976402,EBI-976466

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q13950-1)

Also known as: Cbfa1a;

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: Q13950-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-19: MASNSLFSTVTPCQQNFFW → MRIPV

Isoform 3 (identifier: Q13950-3)

Also known as: Cbfa1b;

The sequence of this isoform differs from the canonical sequence as follows:
     341-362: Missing.

Notes: Phosphorylated on Ser-340.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 521	521	Runt-related transcription factor 2		PRO_0000174659
Regions
	Domain	101 – 229	129	Runt
	Region	336 – 439	104	Interaction with MYST3 By similarity
	Region	374 – 468	95	Interaction with MYST4
	Compositional bias	49 – 71	23	Poly-Gln
	Compositional bias	73 – 89	17	Poly-Ala
	Compositional bias	237 – 521	285	Pro/Ser/Thr-rich
Natural variations
	Alternative sequence	1 – 19	19	MASNS…QNFFW → MRIPV in isoform 2.		VSP_005937
	Alternative sequence	341 – 362	22	Missing in isoform 3.		VSP_005938
	Natural variant	78 – 83	6	Missing		VAR_012131
	Natural variant	84	1	A → AAAAAAAAAAA in CCD associated with brachydactyly of hands and feet.		VAR_012130
	Natural variant	113	1	L → R in CCD.		VAR_012132
	Natural variant	118	1	S → R in CCD.		VAR_012133
	Natural variant	121	1	F → C in CCD.		VAR_012134
	Natural variant	123	1	C → R in CCD.		VAR_012135
	Natural variant	133	1	Missing in CCD.		VAR_012136
	Natural variant	169	1	R → Q in CCD.		VAR_012137
	Natural variant	175	1	M → R in CCD; abolishes DNA binding.		VAR_012138
	Natural variant	190	1	R → Q in CCD; abolishes DNA binding.		VAR_012139
	Natural variant	190	1	R → W in CCD.		VAR_012140
	Natural variant	191	1	S → N in CCD; abolishes DNA binding.		VAR_012141
	Natural variant	193	1	R → C in CCD.		VAR_012142
	Natural variant	197	1	F → S in CCD; abolishes DNA binding.		VAR_012143
	Natural variant	199	1	L → F in CCD; abolishes DNA binding.		VAR_012144
	Natural variant	200	1	T → A in CCD; mild; associated also with isolated dental anomalies; normal DNA binding.		VAR_012145
	Natural variant	205	1	T → R in CCD.		VAR_012146
	Natural variant	209	1	Q → R in CCD.		VAR_012147
	Natural variant	225	1	R → Q in CCD; interferes with nuclear localization; abolishes DNA binding.		VAR_012148
	Natural variant	225	1	R → W in CCD; interferes with nuclear localization.		VAR_012149
	Natural variant	511	1	G → S in CCD; could be a polymorphism.		VAR_012150
Experimental info
	Sequence conflict	16	1	N → S in AAC77441. Ref.4

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 (Cbfa1a) [UniParc]. Last modified November 2, 2001. Version 2. Checksum: 44C4F3867D6F3EB1	FASTA	521	56,648
	10 20 30 40 50 60 MASNSLFSTV TPCQQNFFWD PSTSRRFSPP SSSLQPGKMS DVSPVVAAQQ QQQQQQQQQQ 70 80 90 100 110 120 QQQQQQQQQQ QEAAAAAAAA AAAAAAAAAV PRLRPPHDNR TMVEIIADHP AELVRTDSPN 130 140 150 160 170 180 FLCSVLPSHW RCNKTLPVAF KVVALGEVPD GTVVTVMAGN DENYSAELRN ASAVMKNQVA 190 200 210 220 230 240 RFNDLRFVGR SGRGKSFTLT ITVFTNPPQV ATYHRAIKVT VDGPREPRRH RQKLDDSKPS 250 260 270 280 290 300 LFSDRLSDLG RIPHPSMRVG VPPQNPRPSL NSAPSPFNPQ GQSQITDPRQ AQSSPPWSYD 310 320 330 340 350 360 QSYPSYLSQM TSPSIHSTTP LSSTRGTGLP AITDVPRRIS DDDTATSDFC LWPSTLSKKS 370 380 390 400 410 420 QAGASELGPF SDPRQFPSIS SLTESRFSNP RMHYPATFTY TPPVTSGMSL GMSATTHYHT 430 440 450 460 470 480 YLPPPYPGSS QSQSGPFQTS STPYLYYGTS SGSYQFPMVP GGDRSPSRML PPCTTTSNGS 490 500 510 520 TLLNPNLPNQ NDGVDADGSH SSSPTVLNSS GRMDESVWRP Y
	Isoform 2 [UniParc]. Checksum: 7228C267328DE1DC		507	55,054
	10 20 30 40 50 60 MRIPVDPSTS RRFSPPSSSL QPGKMSDVSP VVAAQQQQQQ QQQQQQQQQQ QQQQQQQEAA 70 80 90 100 110 120 AAAAAAAAAA AAAAAVPRLR PPHDNRTMVE IIADHPAELV RTDSPNFLCS VLPSHWRCNK 130 140 150 160 170 180 TLPVAFKVVA LGEVPDGTVV TVMAGNDENY SAELRNASAV MKNQVARFND LRFVGRSGRG 190 200 210 220 230 240 KSFTLTITVF TNPPQVATYH RAIKVTVDGP REPRRHRQKL DDSKPSLFSD RLSDLGRIPH 250 260 270 280 290 300 PSMRVGVPPQ NPRPSLNSAP SPFNPQGQSQ ITDPRQAQSS PPWSYDQSYP SYLSQMTSPS 310 320 330 340 350 360 IHSTTPLSST RGTGLPAITD VPRRISDDDT ATSDFCLWPS TLSKKSQAGA SELGPFSDPR 370 380 390 400 410 420 QFPSISSLTE SRFSNPRMHY PATFTYTPPV TSGMSLGMSA TTHYHTYLPP PYPGSSQSQS 430 440 450 460 470 480 GPFQTSSTPY LYYGTSSGSY QFPMVPGGDR SPSRMLPPCT TTSNGSTLLN PNLPNQNDGV 490 500 DADGSHSSSP TVLNSSGRMD ESVWRPY
	Isoform 3 (Cbfa1b) [UniParc]. Checksum: 4BA956230C96EB2E		499	54,249
	10 20 30 40 50 60 MASNSLFSTV TPCQQNFFWD PSTSRRFSPP SSSLQPGKMS DVSPVVAAQQ QQQQQQQQQQ 70 80 90 100 110 120 QQQQQQQQQQ QEAAAAAAAA AAAAAAAAAV PRLRPPHDNR TMVEIIADHP AELVRTDSPN 130 140 150 160 170 180 FLCSVLPSHW RCNKTLPVAF KVVALGEVPD GTVVTVMAGN DENYSAELRN ASAVMKNQVA 190 200 210 220 230 240 RFNDLRFVGR SGRGKSFTLT ITVFTNPPQV ATYHRAIKVT VDGPREPRRH RQKLDDSKPS 250 260 270 280 290 300 LFSDRLSDLG RIPHPSMRVG VPPQNPRPSL NSAPSPFNPQ GQSQITDPRQ AQSSPPWSYD 310 320 330 340 350 360 QSYPSYLSQM TSPSIHSTTP LSSTRGTGLP AITDVPRRIS GASELGPFSD PRQFPSISSL 370 380 390 400 410 420 TESRFSNPRM HYPATFTYTP PVTSGMSLGM SATTHYHTYL PPPYPGSSQS QSGPFQTSST 430 440 450 460 470 480 PYLYYGTSSG SYQFPMVPGG DRSPSRMLPP CTTTSNGSTL LNPNLPNQND GVDADGSHSS 490 SPTVLNSSGR MDESVWRPY

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Mutations involving the transcription factor CBFA1 cause cleidocranial dysplasia." Mundlos S., Otto F., Mundlos C., Mulliken J.B., Aylsworth A.S., Albright S., Lindhout D., Cole W.G., Henn W., Knoll J.H.M., Owen M.J., Mertelsmann R., Zabel B.U., Olsen B.R. Cell 89:773-779(1997) [PubMed: 9182765] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORMS 1 AND 2), VARIANT CCD ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-84 INS, VARIANT 78-ALA--ALA-83 DEL.
[2]	"Genomic organization, expression of the human CBFA1 gene, and evidence for an alternative splicing event affecting protein function." Geoffroy V., Corral D.A., Zhou L., Lee B., Karsenty G. Mamm. Genome 9:54-57(1998) [PubMed: 9434946] [Abstract] Cited for: NUCLEOTIDE SEQUENCE (ISOFORMS 1 AND 3), ALTERNATIVE SPLICING.
[3]	"The DNA sequence and analysis of human chromosome 6." Mungall A.J., Palmer S.A., Sims S.K., Edwards C.A., Ashurst J.L., Wilming L., Jones M.C., Horton R., Hunt S.E., Scott C.E., Gilbert J.G.R., Clamp M.E., Bethel G., Milne S., Ainscough R., Almeida J.P., Ambrose K.D., Andrews T.D. , Ashwell R.I.S., Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beare D.M., Beasley H., Beasley O., Bird C.P., Blakey S.E., Bray-Allen S., Brook J., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Clark S.Y., Clark G., Clee C.M., Clegg S., Cobley V., Collier R.E., Collins J.E., Colman L.K., Corby N.R., Coville G.J., Culley K.M., Dhami P., Davies J., Dunn M., Earthrowl M.E., Ellington A.E., Evans K.A., Faulkner L., Francis M.D., Frankish A., Frankland J., French L., Garner P., Garnett J., Ghori M.J., Gilby L.M., Gillson C.J., Glithero R.J., Grafham D.V., Grant M., Gribble S., Griffiths C., Griffiths M.N.D., Hall R., Halls K.S., Hammond S., Harley J.L., Hart E.A., Heath P.D., Heathcott R., Holmes S.J., Howden P.J., Howe K.L., Howell G.R., Huckle E., Humphray S.J., Humphries M.D., Hunt A.R., Johnson C.M., Joy A.A., Kay M., Keenan S.J., Kimberley A.M., King A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C.R., Lloyd D.M., Loveland J.E., Lovell J., Martin S., Mashreghi-Mohammadi M., Maslen G.L., Matthews L., McCann O.T., McLaren S.J., McLay K., McMurray A., Moore M.J.F., Mullikin J.C., Niblett D., Nickerson T., Novik K.L., Oliver K., Overton-Larty E.K., Parker A., Patel R., Pearce A.V., Peck A.I., Phillimore B.J.C.T., Phillips S., Plumb R.W., Porter K.M., Ramsey Y., Ranby S.A., Rice C.M., Ross M.T., Searle S.M., Sehra H.K., Sheridan E., Skuce C.D., Smith S., Smith M., Spraggon L., Squares S.L., Steward C.A., Sycamore N., Tamlyn-Hall G., Tester J., Theaker A.J., Thomas D.W., Thorpe A., Tracey A., Tromans A., Tubby B., Wall M., Wallis J.M., West A.P., White S.S., Whitehead S.L., Whittaker H., Wild A., Willey D.J., Wilmer T.E., Wood J.M., Wray P.W., Wyatt J.C., Young L., Younger R.M., Bentley D.R., Coulson A., Durbin R.M., Hubbard T., Sulston J.E., Dunham I., Rogers J., Beck S. Nature 425:805-811(2003) [PubMed: 14574404] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]	"Genomic structure and isoform expression of the mouse, rat and human Cbfa1/Osf2 transcription factor." Xiao Z.S., Thomas R., Hinson T.K., Quarles L.D. Gene 214:187-197(1998) [PubMed: 9651525] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA] OF 1-19 (ISOFORM 1).
[5]	"The cDNA cloning of the transcripts of human PEBP2alphaA/CBFA1 mapped to 6p12.3-p21.1, the locus for cleidocranial dysplasia." Zhang Y.-W., Bae S.-C., Takahashi E., Ito Y. Oncogene 15:367-371(1997) [PubMed: 9233771] [Abstract] Cited for: NUCLEOTIDE SEQUENCE OF 60-521 (ISOFORM 3).
[6]	"Regulation of osteocalcin gene expression by a novel Ku antigen transcription factor complex." Willis D.M., Loewy A.P., Charlton-Kachigian N., Shao J.-S., Ornitz D.M., Towler D.A. J. Biol. Chem. 277:37280-37291(2002) [PubMed: 12145306] [Abstract] Cited for: INTERACTION WITH G22P1 AND XRCC5. Tissue: Osteoblast.
[7]	"MOZ and MORF histone acetyltransferases interact with the Runt-domain transcription factor Runx2." Pelletier N., Champagne N., Stifani S., Yang X.-J. Oncogene 21:2729-2740(2002) [PubMed: 11965546] [Abstract] Cited for: INTERACTION WITH MYST3 AND MYST4, FUNCTION.
[8]	"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-340 (ISOFORM 3), MASS SPECTROMETRY.
[9]	"Missense mutations abolishing DNA binding of the osteoblast-specific transcription factor OSF2/CBFA1 in cleidocranial dysplasia." Lee B., Thirunavukkarasu K., Zhou L., Pastore L., Baldini A., Hecht J., Geoffroy V., Ducy P., Karsenty G. Nat. Genet. 16:307-310(1997) [PubMed: 9207800] [Abstract] Cited for: VARIANTS CCD ARG-175 AND ASN-191.
[10]	"Mutation analysis of core binding factor A1 in patients with cleidocranial dysplasia." Quack I., Vonderstrass B., Stock M., Aylsworth A.S., Becker A., Brueton L., Lee P.J., Majewski F., Mulliken J.B., Suri M., Zenker M., Mundlos S., Otto F. Am. J. Hum. Genet. 65:1268-1278(1999) [PubMed: 10521292] [Abstract] Cited for: VARIANTS CCD ARG-113; ARG-118; CYS-121; ARG-123; ARG-205; GLN-225; TRP-225 AND SER-511.
[11]	"CBFA1 mutation analysis and functional correlation with phenotypic variability in cleidocranial dysplasia." Zhou G., Chen Y., Zhou L., Thirunavukkarasu K., Hecht J., Chitayat D., Gelb B.D., Pirinen S., Berry S.A., Greenberg C.R., Karsenty G., Lee B. Hum. Mol. Genet. 8:2311-2316(1999) [PubMed: 10545612] [Abstract] Cited for: VARIANTS CCD ASN-133 DEL; GLN-169; ARG-175; GLN-190; ASN-191; CYS-193; PHE-199; ALA-200; ARG-209 AND GLN-225.
[12]	"PEBP2alphaA/CBFA1 mutations in Japanese cleidocranial dysplasia patients." Zhang Y.-W., Yasui N., Kakazu N., Abe T., Takada K., Imai S., Sato M., Nomura S., Ochi T., Okuzumi S., Nogami H., Nagai T., Ohashi H., Ito Y. Gene 244:21-28(2000) [PubMed: 10689183] [Abstract] Cited for: VARIANT CCD SER-197.
[13]	"A novel CBFA1 mutation (R190W) in an Italian family with cleidocranial dysplasia." Giannotti A., Tessa A., Patrono C., De Florio L., Velardo M., Dionisi-Vici C., Bertini E., Santorelli F.M. Hum. Mutat. 16:277-277(2000) [PubMed: 10980549] [Abstract] Cited for: VARIANT CCD TRP-190.
+	Additional computationally mapped references.

Web resources

GeneReviews

Atlas of Genetics and Cytogenetics in Oncology and Haematology

Cross-references

Sequence databases
EMBLGenBankDDBJ	AF001450 , AF001443, AF001444, AF001445, AF001446, AF001447, AF001448, AF001449 Genomic DNA. Translation: AAB65159.2. AF001450 , AF001444, AF001445, AF001446, AF001447, AF001448, AF001449 Genomic DNA. Translation: AAB65158.1. AL161907, AL096865, AL358135 Genomic DNA. Translation: CAI19638.1. AL161907, AL096865, AL358135 Genomic DNA. Translation: CAI19639.1. AL358135, AL096865, AL161907 Genomic DNA. Translation: CAI13528.1. AL358135, AL096865, AL161907 Genomic DNA. Translation: CAI13531.1. AL096865, AL161907, AL358135 Genomic DNA. Translation: CAI19925.1. AL096865, AL161907, AL358135 Genomic DNA. Translation: CAI19931.1. AF053952 mRNA. Translation: AAC78624.1. AF053949 Genomic DNA. Translation: AAC77441.1. L40992 mRNA. Translation: AAA89072.1.
RefSeq	NP_001015051.2. NP_001019801.2. NP_004339.3.
UniGene	Hs.535845
3D structure databases
HSSP	HSSP built from PDB template 1HJB based on UniProtKB Q03347.
SMR	Q13950. Positions 105-229.
ModBase