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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

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. 5242.

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
Proteomesi
  • UP000000810 Componenti: Chromosome
  • UP000009139 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000073041 – 954DNA polymerase II large subunit, 1st partSequence analysisAdd BLAST954
ChainiPRO_0000007305955 – 1139Pab polC inteinSequence analysisAdd BLAST185
ChainiPRO_00000073061140 – 1455DNA polymerase II large subunit, 2nd partSequence analysisAdd BLAST316

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

11455
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi5 – 29Combined sources25
Beta strandi43 – 46Combined sources4
Helixi47 – 55Combined sources9
Helixi60 – 71Combined sources12
Helixi73 – 85Combined sources13
Turni86 – 89Combined sources4
Helixi95 – 110Combined sources16
Turni111 – 113Combined sources3
Turni117 – 121Combined sources5
Beta strandi122 – 129Combined sources8
Turni131 – 134Combined sources4
Beta strandi137 – 143Combined sources7
Helixi145 – 150Combined sources6
Helixi151 – 168Combined sources18
Helixi178 – 194Combined sources17
Helixi204 – 213Combined sources10
Beta strandi215 – 219Combined sources5
Beta strandi224 – 227Combined sources4
Beta strandi239 – 241Combined sources3
Helixi243 – 251Combined sources9
Turni252 – 256Combined sources5
Helixi257 – 267Combined sources11
Helixi273 – 283Combined sources11
Helixi312 – 322Combined sources11
Beta strandi344 – 346Combined sources3
Beta strandi349 – 355Combined sources7
Helixi369 – 374Combined sources6
Beta strandi400 – 402Combined sources3
Beta strandi406 – 409Combined sources4
Beta strandi414 – 416Combined sources3
Helixi420 – 426Combined sources7
Helixi427 – 429Combined sources3
Beta strandi430 – 435Combined sources6
Beta strandi438 – 443Combined sources6
Helixi460 – 475Combined sources16
Helixi487 – 497Combined sources11
Helixi501 – 509Combined sources9
Turni511 – 513Combined sources3
Helixi518 – 528Combined sources11
Helixi534 – 536Combined sources3
Helixi540 – 542Combined sources3
Helixi545 – 558Combined sources14
Beta strandi560 – 566Combined sources7
Beta strandi569 – 578Combined sources10
Helixi579 – 582Combined sources4
Helixi585 – 591Combined sources7
Beta strandi596 – 599Combined sources4
Beta strandi602 – 606Combined sources5
Helixi609 – 614Combined sources6
Turni615 – 617Combined sources3
Helixi618 – 620Combined sources3
Helixi632 – 639Combined sources8
Turni678 – 681Combined sources4
Helixi682 – 684Combined sources3
Helixi687 – 692Combined sources6
Beta strandi697 – 701Combined sources5
Beta strandi707 – 709Combined sources3
Beta strandi712 – 714Combined sources3
Turni719 – 721Combined sources3
Beta strandi726 – 730Combined sources5
Turni732 – 734Combined sources3
Beta strandi737 – 739Combined sources3
Helixi740 – 745Combined sources6
Turni746 – 748Combined sources3
Beta strandi753 – 756Combined sources4
Beta strandi761 – 765Combined sources5
Helixi767 – 778Combined sources12
Beta strandi789 – 791Combined sources3
Beta strandi794 – 796Combined sources3
Helixi802 – 811Combined sources10
Beta strandi823 – 829Combined sources7
Beta strandi831 – 833Combined sources3
Helixi835 – 838Combined sources4
Helixi842 – 847Combined sources6
Beta strandi872 – 876Combined sources5
Helixi877 – 896Combined sources20
Helixi909 – 912Combined sources4
Beta strandi916 – 920Combined sources5
Beta strandi926 – 943Combined sources18
Turni945 – 948Combined sources4
Turni950 – 955Combined sources6
Beta strandi960 – 966Combined sources7
Beta strandi969 – 974Combined sources6
Helixi975 – 978Combined sources4
Helixi979 – 981Combined sources3
Beta strandi985 – 988Combined sources4
Beta strandi991 – 994Combined sources4
Beta strandi996 – 999Combined sources4
Beta strandi1001 – 1007Combined sources7
Turni1008 – 1011Combined sources4
Beta strandi1012 – 1025Combined sources14
Beta strandi1030 – 1035Combined sources6
Beta strandi1040 – 1043Combined sources4
Beta strandi1045 – 1053Combined sources9
Beta strandi1056 – 1061Combined sources6
Helixi1062 – 1064Combined sources3
Beta strandi1070 – 1073Combined sources4
Beta strandi1083 – 1086Combined sources4
Beta strandi1103 – 1111Combined sources9
Beta strandi1114 – 1119Combined sources6
Beta strandi1126 – 1131Combined sources6
Turni1132 – 1134Combined sources3
Beta strandi1135 – 1138Combined sources4
Beta strandi1144 – 1149Combined sources6
Helixi1150 – 1156Combined sources7
Helixi1159 – 1161Combined sources3
Beta strandi1162 – 1165Combined sources4
Beta strandi1174 – 1177Combined sources4
Helixi1200 – 1205Combined sources6
Helixi1206 – 1208Combined sources3
Helixi1212 – 1222Combined sources11

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2LCJNMR-A955-1139[»]
5IJLX-ray2.19A2-1246[»]
ProteinModelPortaliQ9V2F4.
SMRiQ9V2F4.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the archaeal DNA polymerase II family.Curated

Phylogenomic databases

eggNOGiarCOG04447. Archaea.
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.
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]
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.
RefSeqiWP_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.
RefSeqiWP_010867244.1. NC_000868.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2LCJNMR-A955-1139[»]
5IJLX-ray2.19A2-1246[»]
ProteinModelPortaliQ9V2F4.
SMRiQ9V2F4.
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

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

Enzyme and pathway databases

BRENDAi2.7.7.7. 5242.

Family and domain databases

Gene3Di2.170.16.10. 1 hit.
HAMAPiMF_00324. DNApol_II_L_arch. 1 hit.
InterProiIPR028992. Hedgehog/Intein_dom.
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]
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...

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: November 30, 2016
This is version 101 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

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.