DNA polymerase II large subunit - Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)

Preferred order of sections

Names and origin

Protein names

Recommended name:
DNA polymerase II large subunit
Short name=Pol II
EC=2.7.7.7

Cleaved into the following chain:

Pho polC intein
Alternative name(s):
Pho pol II intein

Gene names

Name:	polC
Ordered Locus Names:	PH0121

Organism

Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) [Complete proteome] [HAMAP]

Taxonomic identifier

70601 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Thermococci › Thermococcales › Thermococcaceae › Pyrococcus

Protein attributes

Sequence length	1431 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Possesses two activities: a DNA synthesis (polymerase) and an exonucleolytic activity that degrades single stranded DNA in the 3'- to 5'-direction. Has a template-primer preference which is characteristic of a replicative DNA polymerase By similarity. HAMAP MF_00324
Catalytic activity	Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). HAMAP MF_00324 Degradation of single-stranded DNA. It acts progressively in a 3'- to 5'-direction, releasing nucleoside 5'-phosphates. HAMAP MF_00324
Subunit structure	Heterodimer of a large subunit and a small subunit By similarity.
Post-translational modification	This protein undergoes a protein self splicing that involves a post-translational excision of the intervening region (intein) followed by peptide ligation Potential. HAMAP MF_00324
Sequence similarities	Belongs to the archaeal DNA polymerase II family.
Sequence caution	The sequence BAA29190.1 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
Biological process	DNA replication
Ligand	DNA-binding
Molecular function	DNA-directed DNA polymerase Exonuclease Hydrolase Nuclease Nucleotidyltransferase Transferase
PTM	Autocatalytic cleavage Protein splicing
Technical term	3D-structure Complete proteome Multifunctional enzyme
Gene Ontology (GO)
Biological process	DNA catabolic process Inferred from electronic annotation. Source: InterPro DNA replication Inferred from electronic annotation. Source: UniProtKB-KW intein-mediated protein splicing Inferred from electronic annotation. Source: InterPro
Molecular function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW DNA-directed DNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW exonuclease activity Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 951

951

DNA polymerase II large subunit, 1st part Potential

PRO_0000007307

Chain

952 – 1117

166

Pho polC intein Potential

PRO_0000007308

Chain

1118 – 1431

314

DNA polymerase II large subunit, 2nd part Potential

PRO_0000007309

Secondary structure

1

.

1431

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

O57861 [UniParc].

Last modified April 27, 2001. Version 2.
Checksum: 59B73A48868B6298
Show »

FASTA

1,431

162,928

        10         20         30         40         50         60 
MELPKEMEEY FSMLQREIDK AYEIAKKARA QGKDPSLDVE IPQASDMAGR VESLVGPPGV 

        70         80         90        100        110        120 
AERIRELVKE YGKEIAALKI VDEIIDGKFG DLGSKEKYAE QAVRTALAIL TEGVVSAPIE 

       130        140        150        160        170        180 
GIASVKIKRN TWSDNSEYLA LYYAGPIRSS GGTAQALSVL VGDYVRRKLG LDRFKPSEKH 

       190        200        210        220        230        240 
IERMVEEVDL YHRTVSRLQY HPSPEEVRLA MRNIPIEITG EATDEVEVSH RDIPGVETNQ 

       250        260        270        280        290        300 
LRGGAILVLA EGVLQKAKKL VKYIDKMGIE GWEWLKEFVE AKEKGEEIEE EGSAESTVEE 

       310        320        330        340        350        360 
TKVEVDMGFY YSLYQKFKSE IAPNDKYAKE IIGGRPLFSD PSRNGGFRLR YGRSRVSGFA 

       370        380        390        400        410        420 
TWGINPATMI LVDEFLAIGT QLKTERPGKG AVVTPVTTIE GPIVKLKDGS VVKVDDYKLA 

       430        440        450        460        470        480 
LKIRDEVEEI LYLGDAVIAF GDFVENNQTL LPANYCEEWW ILEFTKALNE IYEVELKPFE 

       490        500        510        520        530        540 
VNSSEDLEEA ADYLEVDIEF LKELLKDPLR TKPPVELAIH FSEILGIPLH PYYTLYWNSV 

       550        560        570        580        590        600 
KPEQVEKLWR VLKEHAHIDW DNFRGIKFAR RIVIPLEKLR DSKRALELLG LPHKVEGKNV 

       610        620        630        640        650        660 
IVDYPWAAAL LTPLGNLEWE FRAKPLHTTI DIINENNEIK LRDRGISWIG ARMGRPEKAK 

       670        680        690        700        710        720 
ERKMKPPVQV LFPIGLAGGS SRDIKKAAEE GKVAEVEIAL FKCPKCGHVG PEHICPNCGT 

       730        740        750        760        770        780 
RKELIWVCPR CNAEYPESQA SGYNYTCPKC NVKLKPYAKR KIKPSELLKR AMDNVKVYGI 

       790        800        810        820        830        840 
DKLKGVMGMT SGWKMPEPLE KGLLRAKNDV YVFKDGTIRF DATDAPITHF RPREIGVSVE 

       850        860        870        880        890        900 
KLRELGYTHD FEGNPLVSED QIVELKPQDI ILSKEAGKYL LKVAKFVDDL LEKFYGLPRF 

       910        920        930        940        950        960 
YNAEKMEDLI GHLVIGLAPH TSAGIVGRII GFVDALVGYA HPYFHAAKRR NCFPGDTRIL 

       970        980        990       1000       1010       1020 
VQINGTPQRV TLKELYELFD EEHYESMVYV RKKPKVDIKV YSFNPEEGKV VLTDIEEVIK 

      1030       1040       1050       1060       1070       1080 
APATDHLIRF ELELGSSFET TVDHPVLVYE NGKFVEKRAF EVREGNIIII IDESTLEPLK 

      1090       1100       1110       1120       1130       1140 
VAVKKIEFIE PPEDFVFSLN AKKYHTVIIN ENIVTHQCDG DEDAVMLLLD ALLNFSRYYL 

      1150       1160       1170       1180       1190       1200 
PEKRGGKMDA PLVITTRLDP REVDSEVHNM DIVRYYPLEF YEATYELKSP KELVGVIERV 

      1210       1220       1230       1240       1250       1260 
EDRLGKPEMY YGLKFTHDTD DIALGPKMSL YKQLGDMEEK VKRQLDVARR IRAVDEHKVA 

      1270       1280       1290       1300       1310       1320 
ETILNSHLIP DLRGNLRSFT RQEFRCVKCN TKFRRPPLDG KCPICGGKIV LTVSKGAIEK 

      1330       1340       1350       1360       1370       1380 
YLGTAKMLVT EYKVKNYTRQ RICLTERDID SLFETVFPET QLTLLVNPND ICQRIIMERT 

      1390       1400       1410       1420       1430 
GGSKKSGLLE NFANGYNKGK KEEMPKKQRK KEQEKSKKRK VISLDDFFSR K

« Hide

References

[1]

"Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3."
Kawarabayasi Y., Sawada M., Horikawa H., Haikawa Y., Hino Y., Yamamoto S., Sekine M., Baba S., Kosugi H., Hosoyama A., Nagai Y., Sakai M., Ogura K., Otsuka R., Nakazawa H., Takamiya M., Ohfuku Y., Funahashi T.

Kikuchi H.
DNA Res. 5:55-76(1998) [PubMed: 9679194] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3.

+

Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

BA000001 Genomic DNA. Translation: BAA29190.1. Different initiation.

PIR

G71232.

RefSeq

NP_142130.1. NC_000961.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3O59	X-ray	2.20	X	1-297	[»]

ProteinModelPortal

O57861.

ModBase

Search...

Protein family/group databases

MEROPS

N10.005.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBPYRT00000001181; EBPYRP00000001181; EBPYRG00000001181.

GeneID

1444018.

GenomeReviews

Gene locus PH0121 in contig BA000001_GR.

KEGG

pho:PH0121.

NMPDR

fig|70601.1.peg.118.

Organism-specific databases

CMR

Search...

Phylogenomic databases

GeneTree

EBGT00050000022161.

HOGENOM

HBG497074.

OMA

NCDGDED.

ProtClustDB

PRK14714.

Enzyme and pathway databases

BioCyc

PHOR70601:PH0121-MONOMER.

Family and domain databases

HAMAP

MF_00324. DNApol_II_L_arch.
[Tree]

InterPro

IPR003586. Hedgehog_hint_C.
IPR003587. Hedgehog_hint_N.
IPR006141. Intein_splice_site.
IPR004475. PolC_DP2.
IPR016033. PolC_DP2_N.
[Graphical view]

KO

K02322.

Pfam

PF03833. PolC_DP2. 1 hit.
[Graphical view]

SMART

SM00305. HintC. 1 hit.
SM00306. HintN. 1 hit.
[Graphical view]

TIGRFAMs

TIGR01445. Intein_Nterm. 1 hit.
TIGR00354. PolC. 1 hit.

PROSITE

PS50818. INTEIN_C_TER. 1 hit.
PS50817. INTEIN_N_TER. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

DP2L_PYRHO

Accession

Primary (citable) accession number: O57861

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 27, 2001
Last sequence update:	April 27, 2001
Last modified:	November 16, 2011
This is version 78 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Intein-containing proteins

List of intein-containing protein entries

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families