DNA polymerase II large subunit - Pyrococcus abyssi (strain GE5 / Orsay)

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:

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

Gene names

Name:	polC
Ordered Locus Names:	PYRAB01200
ORF Names:	PAB2404

Organism

Pyrococcus abyssi (strain GE5 / Orsay) [Complete proteome] [HAMAP]

Taxonomic identifier

272844 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Thermococci › Thermococcales › Thermococcaceae › Pyrococcus ›

Protein attributes

Sequence length	1455 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-Rule MF_00324
Catalytic activity	Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). HAMAP-Rule MF_00324 Degradation of single-stranded DNA. It acts progressively in a 3'- to 5'-direction, releasing nucleoside 5'-phosphates. HAMAP-Rule 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-Rule MF_00324
Sequence similarities	Belongs to the archaeal DNA polymerase II family.

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, exonucleolytic Inferred from electronic annotation. Source: HAMAP DNA-dependent DNA replication Inferred from electronic annotation. Source: HAMAP intein-mediated protein splicing Inferred from electronic annotation. Source: InterPro
Molecular_function	3'-5' exonuclease activity Inferred from electronic annotation. Source: HAMAP DNA binding Inferred from electronic annotation. Source: HAMAP DNA-directed DNA polymerase activity Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 954

954

DNA polymerase II large subunit, 1st part Potential

PRO_0000007304

Chain

955 – 1139

185

Pab polC intein Potential

PRO_0000007305

Chain

1140 – 1455

316

DNA polymerase II large subunit, 2nd part Potential

PRO_0000007306

Secondary structure

1

.

1455

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

Q9V2F4 [UniParc].

Last modified May 1, 2000. Version 1.
Checksum: BB092E7BB2FE0D21
Show »

FASTA

1,455

165,711

        10         20         30         40         50         60 
MELPKEMEEY FEMLQREIDK AYEIAKKARA QGKDPSLDVE IPQATDMAGR VESLVGPPGV 

        70         80         90        100        110        120 
AKRIRELVKE YGKEIAALKI VDEIIEGKFG DLGSREKYAE QAVRTALAIL TEGIVSAPIE 

       130        140        150        160        170        180 
GIANVKIKRN TWADNSEYLA LYYAGPIRSS GGTAQALSVL VGDYVRRKLG LDRFKPSEKH 

       190        200        210        220        230        240 
IERMVEEVDL YHRAVTRLQY HPSPEEVRLA MRNIPIEITG EATDDVEVSH RDVPGVETNQ 

       250        260        270        280        290        300 
LRGGAILVLA EGVLQKAKKL VKYIDKMGIE GWEWLKEFVE AKEKGEPKEE GKEESLAEST 

       310        320        330        340        350        360 
LEETKVEVDM GFYYSLYQKF KEEIAPSDKY AKEVIGGRPL FSDPSKPGGF RLRYGRSRAS 

       370        380        390        400        410        420 
GFATWGINPA TMILVDEFLA IGTQLKTERP GKGAVVTPVT TIEGPIVKLK DGSVLRVDDY 

       430        440        450        460        470        480 
NLALKVREDV EEILYLGDAV IAFGDFVENN QTLLPANYCE EWWILEFVKA LKEIYEVHLE 

       490        500        510        520        530        540 
PFTENEEESI EEASDYLEID PEFLKEMLRD PLRVKPPVEL AIHFSEVLGI PLHPYYTLYW 

       550        560        570        580        590        600 
NSVEPKDVEK LWRLLKNYAE IEWSNFRGIK FAKKIVISQE KLGDSKRTLE LLGLPHTVRD 

       610        620        630        640        650        660 
GNVIVDYPWA AALLTPLGNL NWEFMAKPLY ATIDIINENN EIKLRDRGIS WIGARMGRPE 

       670        680        690        700        710        720 
KAKERKMKPP VQVLFPIGLA GGSSRDIKKA AEEGKVAEVE IAFFKCPKCG HVGPEHLCPN 

       730        740        750        760        770        780 
CGTRKELLWV CPRCNAEYPE SQAEGYNYTC PKCNVKLRPY AKRKIRPSEL LNRAMENVKV 

       790        800        810        820        830        840 
YGVDKLKGVM GMTSGWKMPE PLEKGLLRAK NDVYVFKDGT IRFDATDAPI THFRPREIGV 

       850        860        870        880        890        900 
SVEKLRELGY THDFEGKPLV SEDQIVELKP QDIILSKEAG RYLLKVAKFV DDLLEKFYGL 

       910        920        930        940        950        960 
PRFYNAEKME DLIGHLVIGL APHTSAGIVG RIIGFVDALV GYAHPYFHAA KRRNCFPGDT 

       970        980        990       1000       1010       1020 
RILVQIDGVP QKITLRELYE LFEDERYENM VYVRKKPKRE IKVYSIDLET GKVVLTDIED 

      1030       1040       1050       1060       1070       1080 
VIKAPATDHL IRFELEDGRS FETTVDHPVL VYENGRFIEK RAFEVKEGDK VLVSELELVE 

      1090       1100       1110       1120       1130       1140 
QSSSSQDNPK NENLGSPEHD QLLEIKNIKY VRANDDFVFS LNAKKYHNVI INENIVTHQC 

      1150       1160       1170       1180       1190       1200 
DGDEDAVMLL LDALLNFSRY YLPEKRGGKM DAPLVITTRL DPREVDSEVH NMDIVRYYPL 

      1210       1220       1230       1240       1250       1260 
EFYEATYELK SPKELVGVIE RVEDRLGKPE MYYGLKFTHD TDDIALGPKM SLYKQLGDME 

      1270       1280       1290       1300       1310       1320 
EKVRRQLEVA KRIRAVDEHG VAEKILNSHL IPDLRGNLRS FTRQEFRCVK CNTKFRRPPL 

      1330       1340       1350       1360       1370       1380 
NGKCPVCGGK IVLTVSKGAI EKYLGTAKML VTEYNVKNYT RQRICLTERD IDSLFENVFP 

      1390       1400       1410       1420       1430       1440 
ETQLTLIVNP NDICQRLVMA RTGEVNKSGL LENLSNGSKK TEKAEKAEKP RKKSDEKPKK 

      1450 
KRVISLEEFF SRKSK

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"An integrated analysis of the genome of the hyperthermophilic archaeon Pyrococcus abyssi." Cohen G.N., Barbe V., Flament D., Galperin M., Heilig R., Lecompte O., Poch O., Prieur D., Querellou J., Ripp R., Thierry J.-C., Van der Oost J., Weissenbach J., Zivanovic Y., Forterre P. Mol. Microbiol. 47:1495-1512(2003) [PubMed] [Europe PMC] [Abstract] 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.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AJ248283 Genomic DNA. Translation: CAB49044.1.
HE613800 Genomic DNA. Translation: CCE69496.1.

PIR

E75199.

RefSeq

NP_125813.1. NC_000868.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2LCJ	NMR	-	A	955-1139	[»]

ProteinModelPortal

Q9V2F4.

ModBase

Search...

Protein-protein interaction databases

STRING

272844.PAB2404.

Protein family/group databases

MEROPS

N10.005.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

CAB49044; CAB49044; PAB2404.

GeneID

1495007.

KEGG

pab:PAB2404.

Organism-specific databases

CMR

Search...

Phylogenomic databases

eggNOG

COG1933.

HOGENOM

HOG000286435.

KO

K02322.

OMA

RNCDGDE.

ProtClustDB

PRK14714.

Family and domain databases

HAMAP

MF_00324. DNApol_II_L_arch.

InterPro

IPR003587. Hint_dom_N.
IPR006141. Intein_splice_site.
IPR004475. PolC_DP2.
IPR016033. PolC_DP2_N.
[Graphical view]

Pfam

PF03833. PolC_DP2. 1 hit.
[Graphical view]

SMART

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_PYRAB

Accession

Primary (citable) accession number: Q9V2F4
Secondary accession number(s): G8ZFV5

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 27, 2001
Last sequence update:	May 1, 2000
Last modified:	May 1, 2013
This is version 83 of the entry and version 1 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