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Protein

DNA polymerase II large subunit

Gene

polC

Organism
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

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).By similarity

Catalytic activityi

Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
Degradation of single-stranded DNA. It acts progressively in a 3'- to 5'-direction, releasing nucleoside 5'-phosphates.

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

DNA-directed DNA polymerase, Exonuclease, Hydrolase, Nuclease, Nucleotidyltransferase, Transferase

Keywords - Biological processi

DNA replication

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

BRENDAi2.7.7.7. 5244.

Protein family/group databases

MEROPSiN10.005.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA polymerase II large subunit (EC:2.7.7.7)
Short name:
Pol II
Cleaved into the following chain:
Alternative name(s):
Pho pol II intein
Gene namesi
Name:polC
Ordered Locus Names:PH0121
OrganismiPyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Taxonomic identifieri70601 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
Proteomesi
  • UP000000752 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000073071 – 951DNA polymerase II large subunit, 1st partSequence analysisAdd BLAST951
ChainiPRO_0000007308952 – 1117Pho polC inteinSequence analysisAdd BLAST166
ChainiPRO_00000073091118 – 1431DNA polymerase II large subunit, 2nd partSequence analysisAdd BLAST314

Post-translational modificationi

This protein undergoes a protein self splicing that involves a post-translational excision of the intervening region (intein) followed by peptide ligation.Curated

Keywords - PTMi

Autocatalytic cleavage, Protein splicing

Interactioni

Subunit structurei

Heterodimer of a large subunit and a small subunit.By similarity

Binary interactionsi

WithEntry#Exp.IntActNotes
itself3EBI-8553242,EBI-8553242

GO - Molecular functioni

  • identical protein binding Source: IntAct

Protein-protein interaction databases

MINTiMINT-8081973.
STRINGi70601.PH0121.

Structurei

Secondary structure

11431
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi47 – 55Combined sources9
Helixi60 – 71Combined sources12
Helixi73 – 86Combined sources14
Turni87 – 89Combined sources3
Helixi95 – 110Combined sources16
Turni111 – 113Combined sources3
Helixi117 – 121Combined sources5
Beta strandi122 – 129Combined sources8
Turni131 – 134Combined sources4
Beta strandi137 – 143Combined sources7
Helixi145 – 149Combined sources5
Helixi152 – 168Combined sources17
Helixi178 – 194Combined sources17
Helixi204 – 213Combined sources10
Beta strandi215 – 220Combined sources6
Helixi243 – 250Combined sources8
Turni251 – 256Combined sources6
Helixi257 – 267Combined sources11
Helixi273 – 284Combined sources12

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3O59X-ray2.20X1-297[»]
ProteinModelPortaliO57861.
SMRiO57861.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the archaeal DNA polymerase II family.Curated

Phylogenomic databases

eggNOGiarCOG04447. Archaea.
COG1372. LUCA.
COG1933. LUCA.
HOGENOMiHOG000286435.
KOiK02322.
OMAiRNCDGDE.

Family and domain databases

Gene3Di2.170.16.10. 1 hit.
HAMAPiMF_00324. DNApol_II_L_arch. 1 hit.
InterProiIPR028992. Hedgehog/Intein_dom.
IPR003586. Hint_dom_C.
IPR003587. Hint_dom_N.
IPR030934. Intein_C.
IPR006141. Intein_N.
IPR004475. PolC_DP2.
IPR016033. PolC_DP2_N.
[Graphical view]
PfamiPF03833. PolC_DP2. 1 hit.
[Graphical view]
SMARTiSM00305. HintC. 1 hit.
SM00306. HintN. 1 hit.
[Graphical view]
SUPFAMiSSF51294. SSF51294. 1 hit.
TIGRFAMsiTIGR01445. intein_Nterm. 1 hit.
TIGR00354. polC. 1 hit.
PROSITEiPS50818. INTEIN_C_TER. 1 hit.
PS50817. INTEIN_N_TER. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

O57861-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MELPKEMEEY FSMLQREIDK AYEIAKKARA QGKDPSLDVE IPQASDMAGR
60 70 80 90 100
VESLVGPPGV AERIRELVKE YGKEIAALKI VDEIIDGKFG DLGSKEKYAE
110 120 130 140 150
QAVRTALAIL TEGVVSAPIE GIASVKIKRN TWSDNSEYLA LYYAGPIRSS
160 170 180 190 200
GGTAQALSVL VGDYVRRKLG LDRFKPSEKH IERMVEEVDL YHRTVSRLQY
210 220 230 240 250
HPSPEEVRLA MRNIPIEITG EATDEVEVSH RDIPGVETNQ LRGGAILVLA
260 270 280 290 300
EGVLQKAKKL VKYIDKMGIE GWEWLKEFVE AKEKGEEIEE EGSAESTVEE
310 320 330 340 350
TKVEVDMGFY YSLYQKFKSE IAPNDKYAKE IIGGRPLFSD PSRNGGFRLR
360 370 380 390 400
YGRSRVSGFA TWGINPATMI LVDEFLAIGT QLKTERPGKG AVVTPVTTIE
410 420 430 440 450
GPIVKLKDGS VVKVDDYKLA LKIRDEVEEI LYLGDAVIAF GDFVENNQTL
460 470 480 490 500
LPANYCEEWW ILEFTKALNE IYEVELKPFE VNSSEDLEEA ADYLEVDIEF
510 520 530 540 550
LKELLKDPLR TKPPVELAIH FSEILGIPLH PYYTLYWNSV KPEQVEKLWR
560 570 580 590 600
VLKEHAHIDW DNFRGIKFAR RIVIPLEKLR DSKRALELLG LPHKVEGKNV
610 620 630 640 650
IVDYPWAAAL LTPLGNLEWE FRAKPLHTTI DIINENNEIK LRDRGISWIG
660 670 680 690 700
ARMGRPEKAK ERKMKPPVQV LFPIGLAGGS SRDIKKAAEE GKVAEVEIAL
710 720 730 740 750
FKCPKCGHVG PEHICPNCGT RKELIWVCPR CNAEYPESQA SGYNYTCPKC
760 770 780 790 800
NVKLKPYAKR KIKPSELLKR AMDNVKVYGI DKLKGVMGMT SGWKMPEPLE
810 820 830 840 850
KGLLRAKNDV YVFKDGTIRF DATDAPITHF RPREIGVSVE KLRELGYTHD
860 870 880 890 900
FEGNPLVSED QIVELKPQDI ILSKEAGKYL LKVAKFVDDL LEKFYGLPRF
910 920 930 940 950
YNAEKMEDLI GHLVIGLAPH TSAGIVGRII GFVDALVGYA HPYFHAAKRR
960 970 980 990 1000
NCFPGDTRIL VQINGTPQRV TLKELYELFD EEHYESMVYV RKKPKVDIKV
1010 1020 1030 1040 1050
YSFNPEEGKV VLTDIEEVIK APATDHLIRF ELELGSSFET TVDHPVLVYE
1060 1070 1080 1090 1100
NGKFVEKRAF EVREGNIIII IDESTLEPLK VAVKKIEFIE PPEDFVFSLN
1110 1120 1130 1140 1150
AKKYHTVIIN ENIVTHQCDG DEDAVMLLLD ALLNFSRYYL PEKRGGKMDA
1160 1170 1180 1190 1200
PLVITTRLDP REVDSEVHNM DIVRYYPLEF YEATYELKSP KELVGVIERV
1210 1220 1230 1240 1250
EDRLGKPEMY YGLKFTHDTD DIALGPKMSL YKQLGDMEEK VKRQLDVARR
1260 1270 1280 1290 1300
IRAVDEHKVA ETILNSHLIP DLRGNLRSFT RQEFRCVKCN TKFRRPPLDG
1310 1320 1330 1340 1350
KCPICGGKIV LTVSKGAIEK YLGTAKMLVT EYKVKNYTRQ RICLTERDID
1360 1370 1380 1390 1400
SLFETVFPET QLTLLVNPND ICQRIIMERT GGSKKSGLLE NFANGYNKGK
1410 1420 1430
KEEMPKKQRK KEQEKSKKRK VISLDDFFSR K
Length:1,431
Mass (Da):162,928
Last modified:April 27, 2001 - v2
Checksum:i59B73A48868B6298
GO

Sequence cautioni

The sequence BAA29190 differs from that shown. Reason: Erroneous initiation.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000001 Genomic DNA. Translation: BAA29190.1. Different initiation.
PIRiG71232.
RefSeqiWP_048053037.1. NC_000961.1.

Genome annotation databases

EnsemblBacteriaiBAA29190; BAA29190; BAA29190.
GeneIDi1444018.
KEGGipho:PH0121.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000001 Genomic DNA. Translation: BAA29190.1. Different initiation.
PIRiG71232.
RefSeqiWP_048053037.1. NC_000961.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3O59X-ray2.20X1-297[»]
ProteinModelPortaliO57861.
SMRiO57861.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

MINTiMINT-8081973.
STRINGi70601.PH0121.

Protein family/group databases

MEROPSiN10.005.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAA29190; BAA29190; BAA29190.
GeneIDi1444018.
KEGGipho:PH0121.

Phylogenomic databases

eggNOGiarCOG04447. Archaea.
COG1372. LUCA.
COG1933. LUCA.
HOGENOMiHOG000286435.
KOiK02322.
OMAiRNCDGDE.

Enzyme and pathway databases

BRENDAi2.7.7.7. 5244.

Family and domain databases

Gene3Di2.170.16.10. 1 hit.
HAMAPiMF_00324. DNApol_II_L_arch. 1 hit.
InterProiIPR028992. Hedgehog/Intein_dom.
IPR003586. Hint_dom_C.
IPR003587. Hint_dom_N.
IPR030934. Intein_C.
IPR006141. Intein_N.
IPR004475. PolC_DP2.
IPR016033. PolC_DP2_N.
[Graphical view]
PfamiPF03833. PolC_DP2. 1 hit.
[Graphical view]
SMARTiSM00305. HintC. 1 hit.
SM00306. HintN. 1 hit.
[Graphical view]
SUPFAMiSSF51294. SSF51294. 1 hit.
TIGRFAMsiTIGR01445. intein_Nterm. 1 hit.
TIGR00354. polC. 1 hit.
PROSITEiPS50818. INTEIN_C_TER. 1 hit.
PS50817. INTEIN_N_TER. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDP2L_PYRHO
AccessioniPrimary (citable) accession number: O57861
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 27, 2001
Last sequence update: April 27, 2001
Last modified: November 2, 2016
This is version 106 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Multifunctional enzyme

Documents

  1. Intein-containing proteins
    List of intein-containing protein entries
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.