DNA mismatch repair protein MSH3 - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

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P25336 (MSH3_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 99. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
DNA mismatch repair protein MSH3

Alternative name(s):
Mismatch-binding protein
Short name=MBP
MutS protein homolog 3

Gene names

Name:	MSH3
Ordered Locus Names:	YCR092C
ORF Names:	YCR92C, YCR1152

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

Protein attributes

Sequence length	1018 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Component of the post-replicative DNA mismatch repair system (MMR). Heterodimerizes with MSH2 to form MutS beta, which binds to DNA mismatches thereby initiating DNA repair. MSH3 provides substrate-binding and substrate-specificity to the complex. When bound, the MutS beta heterodimer bends the DNA helix and shields approximately 20 base pairs. Acts mainly to repair insertion-deletion loops (IDLs) from 2 to 13 nucleotides in size, but can also repair base-base and single insertion-deletion mismatches that occur during replication. After mismatch binding, forms a ternary complex with either the MutL alpha or MutL beta heterodimer, which is thought to be responsible for directing the downstream MMR events, including strand discrimination, excision, and resynthesis. MutS beta also has a role in regulation of heteroduplex formation during mitotic and meiotic recombination. MutS beta binds to DNA flap structures predicted to form during recombination, and is required for 3' non-homologous tail removal (NHTR). MutS beta-binding alters the DNA conformation of its substrate at the ds/ssDNA junction and may facilitate its recognition and/or cleavage by the downstream nucleotide excision repair (NER) RAD1-RAD10 endonuclease. ATP binding and hydrolysis play a pivotal role in MMR and NHTR. Ref.6 Ref.8 Ref.9 Ref.10 Ref.11 Ref.17 Ref.18 Ref.19 Ref.20 Ref.21
Subunit structure	Heterodimer consisting of MSH2-MSH3 (MutS beta). Forms a ternary complex with either MutL alpha (MLH1-PMS1) or MutL beta (MLH1-MLH3). MutS beta interacts with proliferating cell nuclear antigen (PCNA/POL30). Interacts with SAW1. Ref.5 Ref.6 Ref.7 Ref.22
Subcellular location	Nucleus Ref.15.
Domain	The PIP box serves as a PCNA(POL30)-recognition and -binding motif.
Miscellaneous	Present with 736 molecules/cell in log phase SD medium. Ref.16
Sequence similarities	Belongs to the DNA mismatch repair mutS family. MSH3 subfamily.
Sequence caution	The sequence AAA34803.1 differs from that shown. Reason: Erroneous initiation. The sequence CAA42247.1 differs from that shown. Reason: Erroneous initiation. The sequence CAA46116.1 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
Biological process	DNA damage DNA repair
Cellular component	Nucleus
Ligand	ATP-binding DNA-binding Nucleotide-binding
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	maintenance of DNA repeat elements Inferred from Biological aspect of Ancestor. Source: RefGenome meiotic mismatch repair Inferred from mutant phenotype Ref.17. Source: SGD reciprocal meiotic recombination Inferred from Biological aspect of Ancestor. Source: RefGenome removal of nonhomologous ends Inferred from mutant phenotype Ref.10. Source: SGD
Cellular component	MutSbeta complex Inferred from physical interaction Ref.5. Source: SGD cytoplasm Inferred from direct assay Ref.15. Source: SGD nuclear chromosome Inferred from Biological aspect of Ancestor. Source: RefGenome
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW DNA insertion or deletion binding Inferred from direct assay Ref.5. Source: SGD DNA-dependent ATPase activity Inferred from Biological aspect of Ancestor. Source: RefGenome damaged DNA binding Inferred from Biological aspect of Ancestor. Source: RefGenome double-strand/single-strand DNA junction binding Inferred from direct assay Ref.18. Source: SGD protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
MSH2	P25847	3	EBI-11362,EBI-11352

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 1018

1018

DNA mismatch repair protein MSH3

PRO_0000115195

Regions

Nucleotide binding

791 – 798

ATP Potential

Region

126 – 256

131

Mispair-binding domain

Motif

4 – 11

PIP box

Experimental info

Mutagenesis

Q → A: Partially functional in a mismatch repair assay; when associated with 10-AA-11. Ref.13

Mutagenesis

10 – 11

FF → AA: Partially functional in a mismatch repair assay; when associated with A-4.

Mutagenesis

158

K → A: Alters DNA-binding activity and impairs MSH2-MSH3-mediated DNA mismatch repair; when associated with ALA-160. Ref.19

Mutagenesis

160

K → A: Alters DNA-binding activity and impairs MSH2-MSH3-mediated DNA mismatch repair; when associated with ALA-158. Ref.19

Mutagenesis

203

P → A: No effect. Ref.19

Mutagenesis

226

Q → A: No effect. Ref.19

Mutagenesis

247

R → A: Impairs MSH2-MSH3-mediated DNA mismatch repair. Ref.19

Mutagenesis

796

G → D: Defective in MMR and in NHTR. Ref.12

Sequences

Sequence

Length

Mass (Da)

Tools

P25336 [UniParc].

Last modified June 10, 2008. Version 2.
Checksum: 1AD91C2E2F2856EF
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FASTA

1,018

116,534

        10         20         30         40         50         60 
MAGQPTISRF FKKAVKSELT HKQEQEVAVG NGAGSESICL DTDEEDNLSS VASTTVTNDS 

        70         80         90        100        110        120 
FPLKGSVSSK NSKNSEKTSG TSTTFNDIDF AKKLDRIMKR RSDENVEAED DEEEGEEDFV 

       130        140        150        160        170        180 
KKKARKSPTA KLTPLDKQVK DLKMHHRDKV LVIRVGYKYK CFAEDAVTVS RILHIKLVPG 

       190        200        210        220        230        240 
KLTIDESNPQ DCNHRQFAYC SFPDVRLNVH LERLVHHNLK VAVVEQAETS AIKKHDPGAS 

       250        260        270        280        290        300 
KSSVFERKIS NVFTKATFGV NSTFVLRGKR ILGDTNSIWA LSRDVHQGKV AKYSLISVNL 

       310        320        330        340        350        360 
NNGEVVYDEF EEPNLADEKL QIRIKYLQPI EVLVNTDDLP LHVAKFFKDI SCPLIHKQEY 

       370        380        390        400        410        420 
DLEDHVVQAI KVMNEKIQLS PSLIRLVSKL YSHMVEYNNE QVMLIPSIYS PFASKIHMLL 

       430        440        450        460        470        480 
DPNSLQSLDI FTHDGGKGSL FWLLDHTRTS FGLRMLREWI LKPLVDVHQI EERLDAIECI 

       490        500        510        520        530        540 
TSEINNSIFF ESLNQMLNHT PDLLRTLNRI MYGTTSRKEV YFYLKQITSF VDHFKMHQSY 

       550        560        570        580        590        600 
LSEHFKSSDG RIGKQSPLLF RLFSELNELL STTQLPHFLT MINVSAVMEK NSDKQVMDFF 

       610        620        630        640        650        660 
NLNNYDCSEG IIKIQRESES VRSQLKEELA EIRKYLKRPY LNFRDEVDYL IEVKNSQIKD 

       670        680        690        700        710        720 
LPDDWIKVNN TKMVSRFTTP RTQKLTQKLE YYKDLLIRES ELQYKEFLNK ITAEYTELRK 

       730        740        750        760        770        780 
ITLNLAQYDC ILSLAATSCN VNYVRPTFVN GQQAIIAKNA RNPIIESLDV HYVPNDIMMS 

       790        800        810        820        830        840 
PENGKINIIT GPNMGGKSSY IRQVALLTIM AQIGSFVPAE EIRLSIFENV LTRIGAHDDI 

       850        860        870        880        890        900 
INGDSTFKVE MLDILHILKN CNKRSLLLLD EVGRGTGTHD GIAISYALIK YFSELSDCPL 

       910        920        930        940        950        960 
ILFTTHFPML GEIKSPLIRN YHMDYVEEQK TGEDWMSVIF LYKLKKGLTY NSYGMNVAKL 

       970        980        990       1000       1010 
ARLDKDIINR AFSISEELRK ESINEDALKL FSSLKRILKS DNITATDKLA KLLSLDIH

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The yeast gene MSH3 defines a new class of eukaryotic MutS homologues." New L., Liu K., Crouse G.F. Mol. Gen. Genet. 239:97-108(1993) [PubMed: 8510668] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"The sequence of a 6.3 kb segment of yeast chromosome III reveals an open reading frame coding for a putative mismatch binding protein." Valle G., Bergantino E., Lanfranchi G., Carignani G. Yeast 7:981-988(1991) [PubMed: 1803822] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	"The complete DNA sequence of yeast chromosome III." Oliver S.G., van der Aart Q.J.M., Agostoni-Carbone M.L., Aigle M., Alberghina L., Alexandraki D., Antoine G., Anwar R., Ballesta J.P.G., Benit P., Berben G., Bergantino E., Biteau N., Bolle P.-A., Bolotin-Fukuhara M., Brown A., Brown A.J.P., Buhler J.-M. Sgouros J.G. Nature 357:38-46(1992) [PubMed: 1574125] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[4]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[5]	"Binding of insertion/deletion DNA mismatches by the heterodimer of yeast mismatch repair proteins MSH2 and MSH3." Habraken Y., Sung P., Prakash L., Prakash S. Curr. Biol. 6:1185-1187(1996) [PubMed: 8805366] [Abstract] Cited for: DNA-BINDING SPECIFICITY, INTERACTION WITH MSH2.
[6]	"Redundancy of Saccharomyces cerevisiae MSH3 and MSH6 in MSH2-dependent mismatch repair." Marsischky G.T., Filosi N., Kane M.F., Kolodner R.D. Genes Dev. 10:407-420(1996) [PubMed: 8600025] [Abstract] Cited for: FUNCTION, INTERACTION WITH MSH2.
[7]	"Evidence for involvement of yeast proliferating cell nuclear antigen in DNA mismatch repair." Johnson R.E., Kovvali G.K., Guzder S.N., Amin N.S., Holm C., Habraken Y., Sung P., Prakash L., Prakash S. J. Biol. Chem. 271:27987-27990(1996) [PubMed: 8910404] [Abstract] Cited for: INTERACTION WITH POL30.
[8]	"Enhancement of MSH2-MSH3-mediated mismatch recognition by the yeast MLH1-PMS1 complex." Habraken Y., Sung P., Prakash L., Prakash S. Curr. Biol. 7:790-793(1997) [PubMed: 9368761] [Abstract] Cited for: FUNCTION, DNA-BINDING SPECIFICITY, COMPLEX FORMATION WITH MLH1-PMS1.
[9]	"Microsatellite instability in yeast: dependence on repeat unit size and DNA mismatch repair genes." Sia E.A., Kokoska R.J., Dominska M., Greenwell P., Petes T.D. Mol. Cell. Biol. 17:2851-2858(1997) [PubMed: 9111357] [Abstract] Cited for: FUNCTION IN MMR.
[10]	"Role of Saccharomyces cerevisiae Msh2 and Msh3 repair proteins in double-strand break-induced recombination." Sugawara N., Paques F., Colaiacovo M., Haber J.E. Proc. Natl. Acad. Sci. U.S.A. 94:9214-9219(1997) [PubMed: 9256462] [Abstract] Cited for: FUNCTION IN NHTR.
[11]	"The Saccharomyces cerevisiae MLH3 gene functions in MSH3-dependent suppression of frameshift mutations." Flores-Rozas H., Kolodner R.D. Proc. Natl. Acad. Sci. U.S.A. 95:12404-12409(1998) [PubMed: 9770499] [Abstract] Cited for: FUNCTION.
[12]	"Separation-of-function mutations in Saccharomyces cerevisiae MSH2 that confer mismatch repair defects but do not affect nonhomologous-tail removal during recombination." Studamire B., Price G., Sugawara N., Haber J.E., Alani E. Mol. Cell. Biol. 19:7558-7567(1999) [PubMed: 10523644] [Abstract] Cited for: MUTAGENESIS OF GLY-796.
[13]	"Functional interaction of proliferating cell nuclear antigen with MSH2-MSH6 and MSH2-MSH3 complexes." Clark A.B., Valle F., Drotschmann K., Gary R.K., Kunkel T.A. J. Biol. Chem. 275:36498-36501(2000) [PubMed: 11005803] [Abstract] Cited for: MUTAGENESIS OF GLN-4 AND 10-PHE-PHE-11.
[14]	"Sequencing and comparison of yeast species to identify genes and regulatory elements." Kellis M., Patterson N., Endrizzi M., Birren B.W., Lander E.S. Nature 423:241-254(2003) [PubMed: 12748633] [Abstract] Cited for: IDENTIFICATION OF PROBABLE INITIATION SITE.
[15]	"Global analysis of protein localization in budding yeast." Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K. Nature 425:686-691(2003) [PubMed: 14562095] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[16]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[17]	"Analysis of the proteins involved in the in vivo repair of base-base mismatches and four-base loops formed during meiotic recombination in the yeast Saccharomyces cerevisiae." Stone J.E., Petes T.D. Genetics 173:1223-1239(2006) [PubMed: 16702432] [Abstract] Cited for: FUNCTION.
[18]	"Mismatch repair factor MSH2-MSH3 binds and alters the conformation of branched DNA structures predicted to form during genetic recombination." Surtees J.A., Alani E. J. Mol. Biol. 360:523-536(2006) [PubMed: 16781730] [Abstract] Cited for: FUNCTION IN NHTR, DNA-BINDING.
[19]	"Saccharomyces cerevisiae MSH2-MSH3 and MSH2-MSH6 complexes display distinct requirements for DNA binding domain I in mismatch recognition." Lee S.D., Surtees J.A., Alani E. J. Mol. Biol. 366:53-66(2007) [PubMed: 17157869] [Abstract] Cited for: FUNCTION, DNA-BINDING, MUTAGENESIS OF LYS-158; LYS-160; PRO-203; GLN-226 AND ARG-247.
[20]	"Saccharomyces cerevisiae Msh2-Msh3 acts in repair of base-base mispairs." Harrington J.M., Kolodner R.D. Mol. Cell. Biol. 27:6546-6554(2007) [PubMed: 17636021] [Abstract] Cited for: FUNCTION, IDENTIFICATION OF INITIATION SITE.
[21]	"Chimeric Saccharomyces cerevisiae Msh6 protein with an Msh3 mispair-binding domain combines properties of both proteins." Shell S.S., Putnam C.D., Kolodner R.D. Proc. Natl. Acad. Sci. U.S.A. 104:10956-10961(2007) [PubMed: 17573527] [Abstract] Cited for: FUNCTION.
[22]	"Microarray-based genetic screen defines SAW1, a gene required for Rad1/Rad10-dependent processing of recombination intermediates." Li F., Dong J., Pan X., Oum J.-H., Boeke J.D., Lee S.E. Mol. Cell 30:325-335(2008) [PubMed: 18471978] [Abstract] Cited for: INTERACTION WITH SAW1.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	X64954 Genomic DNA. Translation: CAA46116.1. Different initiation. M96250 Genomic DNA. Translation: AAA34803.1. Different initiation. X59720 Genomic DNA. Translation: CAA42247.1. Different initiation. BK006937 Genomic DNA. Translation: DAA07561.1.
PIR	S19508.
RefSeq	NP_010016.2. NM_001178798.1.
3D structure databases
ProteinModelPortal	P25336.
SMR	P25336. Positions 124-980.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-2422N.
IntAct	P25336. 27 interactions.
MINT	MINT-633647.
STRING	P25336.
Proteomic databases
PeptideAtlas	P25336.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YCR092C; YCR092C; YCR092C.
GeneID	850454.
KEGG	sce:YCR092C.
NMPDR	fig\|4932.3.peg.745.
Organism-specific databases
CYGD	YCR092c.
SGD	S000000688. MSH3.
Phylogenomic databases
eggNOG	fuNOG07126.
GeneTree	EFGT00050000003033.
HOGENOM	HBG735169.
OMA	CDSAPPQ.
OrthoDB	EOG42NN7M.
Gene expression databases
ArrayExpress	P25336.
Genevestigator	P25336.
GermOnline	YCR092C. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR007695. DNA_mismatch_repair_MutS-lik_N. IPR000432. DNA_mismatch_repair_MutS_C. IPR007861. DNA_mismatch_repair_MutS_clamp. IPR007860. DNA_mismatch_repair_MutS_connt. IPR007696. DNA_mismatch_repair_MutS_core. IPR016151. DNA_mismatch_repair_MutS_N. [Graphical view]
Gene3D	G3DSA:3.40.1170.10. DNA_mismatch_repair_MutS_N. 1 hit.
KO	K08736.
Pfam	PF01624. MutS_I. 1 hit. PF05188. MutS_II. 1 hit. PF05192. MutS_III. 1 hit. PF05190. MutS_IV. 1 hit. PF00488. MutS_V. 1 hit. [Graphical view]
SMART	SM00534. MUTSac. 1 hit. SM00533. MUTSd. 1 hit. [Graphical view]
SUPFAM	SSF55271. DNA_mismatch_repair_MutS_N. 1 hit. SSF48334. DNA_repair_MutS_domIII. 1 hit.
PROSITE	PS00486. DNA_MISMATCH_REPAIR_2. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	966078.

Entry information

Entry name

MSH3_YEAST

Accession

Primary (citable) accession number: P25336
Secondary accession number(s): D6VR92

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 1, 1992
Last sequence update:	June 10, 2008
Last modified:	January 25, 2012
This is version 99 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program

Relevant documents

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

Yeast chromosome III

Yeast (Saccharomyces cerevisiae) chromosome III: entries and gene names

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Experimental info

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents