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Protein

DNA polymerase II large subunit

Gene

polC

Organism
Pyrococcus abyssi (strain GE5 / Orsay)
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

  1. 3'-5' exonuclease activity Source: UniProtKB-HAMAP
  2. DNA binding Source: UniProtKB-HAMAP
  3. DNA-directed DNA polymerase activity Source: UniProtKB-HAMAP

GO - Biological processi

  1. DNA catabolic process, exonucleolytic Source: UniProtKB-HAMAP
  2. DNA-dependent DNA replication Source: UniProtKB-HAMAP
  3. intein-mediated protein splicing Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

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

Keywords - Biological processi

DNA replication

Keywords - Ligandi

DNA-binding

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):
Pab pol II intein
Gene namesi
Name:polC
Ordered Locus Names:PYRAB01200
ORF Names:PAB2404
OrganismiPyrococcus abyssi (strain GE5 / Orsay)
Taxonomic identifieri272844 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
ProteomesiUP000000810: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 954954DNA polymerase II large subunit, 1st partSequence AnalysisPRO_0000007304Add
BLAST
Chaini955 – 1139185Pab polC inteinSequence AnalysisPRO_0000007305Add
BLAST
Chaini1140 – 1455316DNA polymerase II large subunit, 2nd partSequence AnalysisPRO_0000007306Add
BLAST

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

Protein-protein interaction databases

STRINGi272844.PAB2404.

Structurei

Secondary structure

1
1455
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi960 – 9667Combined sources
Beta strandi969 – 9746Combined sources
Helixi975 – 9784Combined sources
Helixi979 – 9813Combined sources
Beta strandi985 – 9884Combined sources
Beta strandi991 – 9944Combined sources
Beta strandi996 – 9994Combined sources
Beta strandi1001 – 10077Combined sources
Turni1008 – 10114Combined sources
Beta strandi1012 – 102514Combined sources
Beta strandi1030 – 10356Combined sources
Beta strandi1040 – 10434Combined sources
Beta strandi1045 – 10539Combined sources
Beta strandi1056 – 10616Combined sources
Helixi1062 – 10643Combined sources
Beta strandi1070 – 10734Combined sources
Beta strandi1083 – 10864Combined sources
Beta strandi1103 – 11119Combined sources
Beta strandi1114 – 11196Combined sources
Beta strandi1126 – 11316Combined sources
Turni1132 – 11343Combined sources
Beta strandi1135 – 11384Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2LCJNMR-A955-1139[»]
ProteinModelPortaliQ9V2F4.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the archaeal DNA polymerase II family.Curated

Phylogenomic databases

eggNOGiCOG1933.
HOGENOMiHOG000286435.
KOiK02322.
OMAiRNCDGDE.

Family and domain databases

Gene3Di2.170.16.10. 1 hit.
HAMAPiMF_00324. DNApol_II_L_arch.
InterProiIPR028992. Hedgehog/Intein_dom.
IPR003587. Hint_dom_N.
IPR006141. Intein_splice_site.
IPR004475. PolC_DP2.
IPR016033. PolC_DP2_N.
[Graphical view]
PfamiPF03833. PolC_DP2. 1 hit.
[Graphical view]
SMARTiSM00306. 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.

Q9V2F4-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MELPKEMEEY FEMLQREIDK AYEIAKKARA QGKDPSLDVE IPQATDMAGR
60 70 80 90 100
VESLVGPPGV AKRIRELVKE YGKEIAALKI VDEIIEGKFG DLGSREKYAE
110 120 130 140 150
QAVRTALAIL TEGIVSAPIE GIANVKIKRN TWADNSEYLA LYYAGPIRSS
160 170 180 190 200
GGTAQALSVL VGDYVRRKLG LDRFKPSEKH IERMVEEVDL YHRAVTRLQY
210 220 230 240 250
HPSPEEVRLA MRNIPIEITG EATDDVEVSH RDVPGVETNQ LRGGAILVLA
260 270 280 290 300
EGVLQKAKKL VKYIDKMGIE GWEWLKEFVE AKEKGEPKEE GKEESLAEST
310 320 330 340 350
LEETKVEVDM GFYYSLYQKF KEEIAPSDKY AKEVIGGRPL FSDPSKPGGF
360 370 380 390 400
RLRYGRSRAS GFATWGINPA TMILVDEFLA IGTQLKTERP GKGAVVTPVT
410 420 430 440 450
TIEGPIVKLK DGSVLRVDDY NLALKVREDV EEILYLGDAV IAFGDFVENN
460 470 480 490 500
QTLLPANYCE EWWILEFVKA LKEIYEVHLE PFTENEEESI EEASDYLEID
510 520 530 540 550
PEFLKEMLRD PLRVKPPVEL AIHFSEVLGI PLHPYYTLYW NSVEPKDVEK
560 570 580 590 600
LWRLLKNYAE IEWSNFRGIK FAKKIVISQE KLGDSKRTLE LLGLPHTVRD
610 620 630 640 650
GNVIVDYPWA AALLTPLGNL NWEFMAKPLY ATIDIINENN EIKLRDRGIS
660 670 680 690 700
WIGARMGRPE KAKERKMKPP VQVLFPIGLA GGSSRDIKKA AEEGKVAEVE
710 720 730 740 750
IAFFKCPKCG HVGPEHLCPN CGTRKELLWV CPRCNAEYPE SQAEGYNYTC
760 770 780 790 800
PKCNVKLRPY AKRKIRPSEL LNRAMENVKV YGVDKLKGVM GMTSGWKMPE
810 820 830 840 850
PLEKGLLRAK NDVYVFKDGT IRFDATDAPI THFRPREIGV SVEKLRELGY
860 870 880 890 900
THDFEGKPLV SEDQIVELKP QDIILSKEAG RYLLKVAKFV DDLLEKFYGL
910 920 930 940 950
PRFYNAEKME DLIGHLVIGL APHTSAGIVG RIIGFVDALV GYAHPYFHAA
960 970 980 990 1000
KRRNCFPGDT RILVQIDGVP QKITLRELYE LFEDERYENM VYVRKKPKRE
1010 1020 1030 1040 1050
IKVYSIDLET GKVVLTDIED VIKAPATDHL IRFELEDGRS FETTVDHPVL
1060 1070 1080 1090 1100
VYENGRFIEK RAFEVKEGDK VLVSELELVE QSSSSQDNPK NENLGSPEHD
1110 1120 1130 1140 1150
QLLEIKNIKY VRANDDFVFS LNAKKYHNVI INENIVTHQC DGDEDAVMLL
1160 1170 1180 1190 1200
LDALLNFSRY YLPEKRGGKM DAPLVITTRL DPREVDSEVH NMDIVRYYPL
1210 1220 1230 1240 1250
EFYEATYELK SPKELVGVIE RVEDRLGKPE MYYGLKFTHD TDDIALGPKM
1260 1270 1280 1290 1300
SLYKQLGDME EKVRRQLEVA KRIRAVDEHG VAEKILNSHL IPDLRGNLRS
1310 1320 1330 1340 1350
FTRQEFRCVK CNTKFRRPPL NGKCPVCGGK IVLTVSKGAI EKYLGTAKML
1360 1370 1380 1390 1400
VTEYNVKNYT RQRICLTERD IDSLFENVFP ETQLTLIVNP NDICQRLVMA
1410 1420 1430 1440 1450
RTGEVNKSGL LENLSNGSKK TEKAEKAEKP RKKSDEKPKK KRVISLEEFF

SRKSK
Length:1,455
Mass (Da):165,711
Last modified:May 1, 2000 - v1
Checksum:iBB092E7BB2FE0D21
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ248283 Genomic DNA. Translation: CAB49044.1.
HE613800 Genomic DNA. Translation: CCE69496.1.
PIRiE75199.
RefSeqiNP_125813.1. NC_000868.1.
WP_010867244.1. NC_000868.1.

Genome annotation databases

EnsemblBacteriaiCAB49044; CAB49044; PAB2404.
GeneIDi1495007.
KEGGipab:PAB2404.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ248283 Genomic DNA. Translation: CAB49044.1.
HE613800 Genomic DNA. Translation: CCE69496.1.
PIRiE75199.
RefSeqiNP_125813.1. NC_000868.1.
WP_010867244.1. NC_000868.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2LCJNMR-A955-1139[»]
ProteinModelPortaliQ9V2F4.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi272844.PAB2404.

Protein family/group databases

MEROPSiN10.005.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB49044; CAB49044; PAB2404.
GeneIDi1495007.
KEGGipab:PAB2404.

Phylogenomic databases

eggNOGiCOG1933.
HOGENOMiHOG000286435.
KOiK02322.
OMAiRNCDGDE.

Family and domain databases

Gene3Di2.170.16.10. 1 hit.
HAMAPiMF_00324. DNApol_II_L_arch.
InterProiIPR028992. Hedgehog/Intein_dom.
IPR003587. Hint_dom_N.
IPR006141. Intein_splice_site.
IPR004475. PolC_DP2.
IPR016033. PolC_DP2_N.
[Graphical view]
PfamiPF03833. PolC_DP2. 1 hit.
[Graphical view]
SMARTiSM00306. 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...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: GE5 / Orsay.
  2. "Re-annotation of two hyperthermophilic archaea Pyrococcus abyssi GE5 and Pyrococcus furiosus DSM 3638."
    Gao J., Wang J.
    Curr. Microbiol. 64:118-129(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENOME REANNOTATION.
    Strain: GE5 / Orsay.

Entry informationi

Entry nameiDP2L_PYRAB
AccessioniPrimary (citable) accession number: Q9V2F4
Secondary accession number(s): G8ZFV5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 27, 2001
Last sequence update: May 1, 2000
Last modified: February 4, 2015
This is version 93 of the entry and version 1 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

External Data

Dasty 3

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 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.