P15436 (DPOD_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
DNA polymerase delta catalytic subunit
EC=2.7.7.7

Alternative name(s):
DNA polymerase III

Gene names

Name:	POL3
Synonyms:	CDC2, TEX1
Ordered Locus Names:	YDL102W
ORF Names:	D2366

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	1097 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	DNA polymerase delta (DNA polymerase III) participates in chromosomal DNA replication. It is required during synthesis of the leading and lagging DNA strands at the replication fork and binds at/or near replication origins and moves along DNA with the replication fork. It has 3'-5' proofreading exonuclease activity that correct errors arising during DNA replication. It is also involved in DNA synthesis during DNA repair. POL3 contains the polymerase active site and most likely the active site for the 3'-5' exonuclease activity. Ref.6
Catalytic activity	Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
Cofactor	Binds 1 4Fe-4S cluster. Ref.13
Subunit structure	DNA polymerase delta is a heterotrimer of POL3, POL32 and HYS2. Interacts with PCNA. Ref.13
Subcellular location	Nucleus Ref.8.
Domain	The CysA-type zinc finger is required for PCNA-binding (Ref.13). The CysB motif binds 1 4Fe-4S cluster and is required for the formation of polymerase complexes (Ref.13).
Miscellaneous	In eukaryotes there are five DNA polymerases: alpha, beta, gamma, delta, and epsilon which are responsible for different reactions of DNA synthesis.
Sequence similarities	Belongs to the DNA polymerase type-B family. Contains 1 CysA-type zinc finger.

Ontologies

Keywords
Biological process	DNA replication
Cellular component	Nucleus
Domain	Zinc-finger
Ligand	4Fe-4S DNA-binding Iron Iron-sulfur Metal-binding Zinc
Molecular function	DNA-directed DNA polymerase Exonuclease Hydrolase Nuclease Nucleotidyltransferase Transferase
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA replication proofreading Inferred from Biological aspect of Ancestor. Source: RefGenome DNA replication, removal of RNA primer Inferred from direct assay PubMed 16837458. Source: SGD RNA-dependent DNA replication Inferred from direct assay PubMed 17429354. Source: SGD S phase of mitotic cell cycle Inferred from Biological aspect of Ancestor. Source: RefGenome base-excision repair, gap-filling Inferred from Biological aspect of Ancestor. Source: RefGenome leading strand elongation Traceable author statement PubMed 9745046. Source: SGD mismatch repair Non-traceable author statement PubMed 10072354PubMed 9745046. Source: SGD nucleotide-excision repair, DNA gap filling Inferred from Biological aspect of Ancestor. Source: RefGenome postreplication repair Traceable author statement PubMed 9745046. Source: SGD regulation of mitotic cell cycle Inferred from Biological aspect of Ancestor. Source: RefGenome
Cellular_component	delta DNA polymerase complex Inferred from Biological aspect of Ancestor. Source: RefGenome
Molecular_function	4 iron, 4 sulfur cluster binding Inferred from electronic annotation. Source: UniProtKB-KW DNA binding Inferred from electronic annotation. Source: UniProtKB-KW DNA-directed DNA polymerase activity Inferred from direct assay PubMed 1678279PubMed 18635534. Source: SGD metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW nucleotide binding Inferred from electronic annotation. Source: InterPro single-stranded DNA specific 3'-5' exodeoxyribonuclease activity Traceable author statement PubMed 9745046. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
POL31	P46957	3	EBI-6134,EBI-6080

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 1097

1097

DNA polymerase delta catalytic subunit

PRO_0000046454

Regions

Zinc finger

1009 – 1027

19

CysA-type

Motif

1056 – 1074

19

CysB motif

Sites

Metal binding

1009

1

Zinc

Metal binding

1012

1

Zinc

Metal binding

1024

1

Zinc

Metal binding

1027

1

Zinc

Metal binding

1056

1

Iron-sulfur (4Fe-4S)

Metal binding

1059

1

Iron-sulfur (4Fe-4S)

Metal binding

1069

1

Iron-sulfur (4Fe-4S)

Metal binding

1074

1

Iron-sulfur (4Fe-4S)

Amino acid modifications

Modified residue

30

1

Phosphoserine Ref.9 Ref.10 Ref.11 Ref.12

Modified residue

37

1

Phosphoserine Ref.12

Modified residue

50

1

Phosphoserine Ref.12

Modified residue

56

1

Phosphoserine; by ATM or ATR Ref.11

Experimental info

Mutagenesis

1009

1

C → A: Impairs iron-sulfur-binding. Ref.13

Mutagenesis

1012

1

C → A: Impairs iron-sulfur-binding. Ref.13

Mutagenesis

1024

1

C → A: Impairs iron-sulfur-binding. Ref.13

Mutagenesis

1027

1

C → A: Impairs iron-sulfur-binding. Ref.13

Mutagenesis

1056

1

C → A: Abolishes iron-sulfur-binding. Ref.13

Mutagenesis

1059

1

C → A: Abolishes iron-sulfur-binding.

Mutagenesis

1069

1

C → A: Abolishes iron-sulfur-binding. Ref.13

Mutagenesis

1074

1

C → A: Abolishes iron-sulfur-binding. Ref.13

Mutagenesis

1074

1

C → S in pol3-13; synthetically lethal with mutations of NBP35, DRE2 and TAH18. Ref.13

Sequence conflict

78 – 79

2

EL → DV in CAA33504. Ref.1

Sequence conflict

78 – 79

2

EL → DV in CAA64911. Ref.3

Sequence conflict

78 – 79

2

EL → DV in CAA98669. Ref.4

Sequence conflict

189

1

H → R in CAA33504. Ref.1

Sequence conflict

204

1

G → D in CAA33504. Ref.1

Sequence conflict

347 – 363

17

SIAGA…VFTLN → YLALRNHSFVMCYSD in CAA33504. Ref.1

Sequence conflict

647 – 649

3

TPN → HY in CAA33504. Ref.1

Sequence conflict

870

1

V → D in CAA33504. Ref.1

Sequence conflict

974

1

Missing in CAA33504. Ref.1

Secondary structure

1

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1097

Helix Strand Turn

Details...

Turn

108 – 110

3

Beta strand

113 – 124

12

Beta strand

126 – 128

3

Beta strand

135 – 143

9

Beta strand

148 – 155

8

Beta strand

159 – 163

5

Helix

168 – 171

4

Helix

173 – 184

12

Turn

185 – 189

5

Beta strand

191 – 203

13

Beta strand

211 – 220

10

Helix

223 – 233

11

Helix

238 – 240

3

Helix

254 – 262

9

Beta strand

269 – 272

4

Helix

282 – 284

3

Beta strand

290 – 296

7

Turn

297 – 299

3

Beta strand

301 – 303

3

Helix

307 – 309

3

Beta strand

316 – 324

9

Turn

334 – 336

3

Beta strand

339 – 348

10

Beta strand

355 – 363

9

Beta strand

371 – 378

8

Helix

379 – 393

15

Beta strand

396 – 402

7

Turn

403 – 406

4

Helix

407 – 417

11

Beta strand

427 – 429

3

Beta strand

439 – 443

5

Turn

444 – 446

3

Beta strand

447 – 451

5

Beta strand

460 – 463

4

Helix

464 – 471

8

Helix

479 – 487

9

Helix

499 – 503

5

Helix

507 – 530

24

Helix

533 – 544

12

Helix

550 – 553

4

Helix

556 – 570

15

Beta strand

598 – 600

3

Beta strand

604 – 609

6

Helix

612 – 619

8

Helix

624 – 626

3

Helix

630 – 635

6

Turn

641 – 643

3

Beta strand

644 – 646

3

Beta strand

652 – 654

3

Turn

656 – 658

3

Helix

662 – 682

21

Helix

687 – 711

25

Beta strand

714 – 717

4

Helix

721 – 745

25

Helix

748 – 750

3

Beta strand

757 – 760

4

Beta strand

762 – 769

8

Helix

775 – 790

16

Beta strand

799 – 812

14

Beta strand

815 – 826

12

Beta strand

829 – 835

7

Helix

836 – 838

3

Helix

844 – 858

15

Helix

863 – 878

16

Helix

884 – 887

4

Beta strand

889 – 892

4

Helix

902 – 914

13

Beta strand

922 – 929

8

Beta strand

931 – 933

3

Helix

935 – 937

3

Helix

942 – 947

6

Helix

954 – 960

7

Helix

963 – 974

12

Helix

976 – 982

7

Sequences

	Sequence		Length	Mass (Da)
	P15436 [UniParc]. Last modified July 27, 2011. Version 4. Checksum: 16E4245C5DCC66DB	FASTA	1,097	124,619
	10 20 30 40 50 60 MSEKRSLPMV DVKIDDEDTP QLEKKIKRQS IDHGVGSEPV STIEIIPSDS FRKYNSQGFK 70 80 90 100 110 120 AKDTDLMGTQ LESTFEQELS QMEHDMADQE EHDLSSFERK KLPTDFDPSL YDISFQQIDA 130 140 150 160 170 180 EQSVLNGIKD ENTSTVVRFF GVTSEGHSVL CNVTGFKNYL YVPAPNSSDA NDQEQINKFV 190 200 210 220 230 240 HYLNETFDHA IDSIEVVSKQ SIWGYSGDTK LPFWKIYVTY PHMVNKLRTA FERGHLSFNS 250 260 270 280 290 300 WFSNGTTTYD NIAYTLRLMV DCGIVGMSWI TLPKGKYSMI EPNNRVSSCQ LEVSINYRNL 310 320 330 340 350 360 IAHPAEGDWS HTAPLRIMSF DIECAGRIGV FPEPEYDPVI QIANVVSIAG AKKPFIRNVF 370 380 390 400 410 420 TLNTCSPITG SMIFSHATEE EMLSNWRNFI IKVDPDVIIG YNTTNFDIPY LLNRAKALKV 430 440 450 460 470 480 NDFPYFGRLK TVKQEIKESV FSSKAYGTRE TKNVNIDGRL QLDLLQFIQR EYKLRSYTLN 490 500 510 520 530 540 AVSAHFLGEQ KEDVHYSIIS DLQNGDSETR RRLAVYCLKD AYLPLRLMEK LMALVNYTEM 550 560 570 580 590 600 ARVTGVPFSY LLARGQQIKV VSQLFRKCLE IDTVIPNMQS QASDDQYEGA TVIEPIRGYY 610 620 630 640 650 660 DVPIATLDFN SLYPSIMMAH NLCYTTLCNK ATVERLNLKI DEDYVITPNG DYFVTTKRRR 670 680 690 700 710 720 GILPIILDEL ISARKRAKKD LRDEKDPFKR DVLNGRQLAL KISANSVYGF TGATVGKLPC 730 740 750 760 770 780 LAISSSVTAY GRTMILKTKT AVQEKYCIKN GYKHDAVVVY GDTDSVMVKF GTTDLKEAMD 790 800 810 820 830 840 LGTEAAKYVS TLFKHPINLE FEKAYFPYLL INKKRYAGLF WTNPDKFDKL DQKGLASVRR 850 860 870 880 890 900 DSCSLVSIVM NKVLKKILIE RNVDGALAFV RETINDILHN RVDISKLIIS KTLAPNYTNP 910 920 930 940 950 960 QPHAVLAERM KRREGVGPNV GDRVDYVIIG GNDKLYNRAE DPLFVLENNI QVDSRYYLTN 970 980 990 1000 1010 1020 QLQNPIISIV APIIGDKQAN GMFVVKSIKI NTGSQKGGLM SFIKKVEACK SCKGPLRKGE 1030 1040 1050 1060 1070 1080 GPLCSNCLAR SGELYIKALY DVRDLEEKYS RLWTQCQRCA GNLHSEVLCS NKNCDIFYMR 1090 VKVKKELQEK VEQLSKW

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Structure and function of the Saccharomyces cerevisiae CDC2 gene encoding the large subunit of DNA polymerase III." Boulet A., Simon M., Faye G., Bauer G.A., Burgers M.J. EMBO J. 8:1849-1854(1989) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: YAB2.
[2]	"Nucleotide sequence of the POL3 gene encoding DNA polymerase III (delta) of Saccharomyces cerevisiae." Morrison A., Sugino A. Nucleic Acids Res. 20:375-375(1992) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], SEQUENCE REVISION.
[3]	"The sequence of a 20.3 kb DNA fragment from the left arm of Saccharomyces cerevisiae chromosome IV contains the KIN28, MSS2, PHO2, POL3 and DUN1 genes, and six new open reading frames." Saiz J.E., Buitrago M.J., Garcia R., Revuelta J.L., del Rey F. Yeast 12:1077-1084(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[4]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome IV." Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T. , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P. Nature 387:75-78(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[5]	Saccharomyces Genome Database Submitted (MAR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION, SEQUENCE REVISION TO 78-79. Strain: ATCC 204508 / S288c.
[6]	"The 3' to 5' exonuclease activity located in the DNA polymerase delta subunit of Saccharomyces cerevisiae is required for accurate replication." Simon M., Giot L., Faye G. EMBO J. 10:2165-2170(1991) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION AS AN EXONUCLEASE.
[7]	"Structure of DNA polymerase delta from Saccharomyces cerevisiae." Johansson E., Majka J., Burgers P.M. J. Biol. Chem. 276:43824-43828(2001) [PubMed] [Europe PMC] [Abstract] Cited for: COMPOSITION OF THE DNA POLYMERASE DELTA COMPLEX.
[8]	"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] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[9]	"Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae." Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P. J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-30, MASS SPECTROMETRY. Strain: ADR376.
[10]	"Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry." Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L., Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F. Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-30, MASS SPECTROMETRY.
[11]	"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H. Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-30 AND SER-56, MASS SPECTROMETRY.
[12]	"A multidimensional chromatography technology for in-depth phosphoproteome analysis." Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H. Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-30; SER-37 AND SER-50, MASS SPECTROMETRY.
[13]	"Eukaryotic DNA polymerases require an iron-sulfur cluster for the formation of active complexes." Netz D.J., Stith C.M., Stumpfig M., Kopf G., Vogel D., Genau H.M., Stodola J.L., Lill R., Burgers P.M., Pierik A.J. Nat. Chem. Biol. 8:125-132(2012) [PubMed] [Europe PMC] [Abstract] Cited for: COFACTOR, IRON-SULFUR-BINDING, ZINC-BINDING, INTERACTION WITH PCNA, MUTAGENESIS OF CYS-1009; CYS-1012; CYS-1024; CYS-1027; CYS-1056; CYS-1069; CYS-1069 AND CYS-1074.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X15477 Genomic DNA. Translation: CAA33504.1.
X61920 Genomic DNA. Translation: CAA43922.1.
X95644 Genomic DNA. Translation: CAA64911.1.
Z74150 Genomic DNA. Translation: CAA98669.1.
BK006938 Genomic DNA. Translation: DAA11758.2.

PIR

RNBYL3. S67644.

RefSeq

NP_010181.2. NM_001180161.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3IAY	X-ray	2.00	A	67-985	[»]

ProteinModelPortal

P15436.

SMR

P15436. Positions 95-985.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-2524N.

IntAct

P15436. 3 interactions.

MINT

MINT-2781941.

STRING

4932.YDL102W.

Proteomic databases

PaxDb

P15436.

PeptideAtlas

P15436.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YDL102W; YDL102W; YDL102W.

GeneID

851456.

KEGG

sce:YDL102W.

Organism-specific databases

CYGD

YDL102w.

SGD

S000002260. POL3.

Phylogenomic databases

eggNOG

COG0417.

GeneTree

ENSGT00560000077365.

HOGENOM

HOG000036616.

KO

K02327.

OMA

MIEQTKQ.

OrthoDB

EOG4B01XB.

Gene expression databases

Genevestigator

P15436.

GermOnline

YDL102W. Saccharomyces cerevisiae.

Family and domain databases

Gene3D

3.90.1600.10. 2 hits.

InterPro

IPR006172. DNA-dir_DNA_pol_B.
IPR017964. DNA-dir_DNA_pol_B_CS.
IPR006133. DNA-dir_DNA_pol_B_exonuc.
IPR006134. DNA-dir_DNA_pol_B_multi_dom.
IPR004578. DNA-dir_DNA_pol_B_pol2.
IPR023211. DNA_pol_palm_dom.
IPR012337. RNaseH-like_dom.
IPR025687. Znf-C4pol.
[Graphical view]

Pfam

PF00136. DNA_pol_B. 1 hit.
PF03104. DNA_pol_B_exo1. 1 hit.
PF14260. zf-C4pol. 1 hit.
[Graphical view]

PRINTS

PR00106. DNAPOLB.

SMART

SM00486. POLBc. 1 hit.
[Graphical view]

SUPFAM

SSF53098. RNaseH_fold. 1 hit.

TIGRFAMs

TIGR00592. pol2. 1 hit.

PROSITE

PS00116. DNA_POLYMERASE_B. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

NextBio

968726.

Entry information

Entry name

DPOD_YEAST

Accession

Primary (citable) accession number: P15436
Secondary accession number(s): D6VRP8

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1990
Last sequence update:	July 27, 2011
Last modified:	April 3, 2013
This is version 138 of the entry and version 4 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program