Reviewed, UniProtKB/Swiss-Prot P03354 (POL_RSVP)

Names and origin

Protein names

Recommended name:
    Pol polyprotein
Cleaved into the following 2 chains:
    1- Recommended name:
            Reverse transcriptase/ribonuclease H alpha-subunit
                Short name=RT
              EC=2.7.7.49
              EC=2.7.7.7
              EC=3.1.26.4
    2- Recommended name:
            Integrase
                Short name=IN
        Alternative name(s):
            pp32

Gene names

Name:

pol

Organism

Rous sarcoma virus (strain Prague C) (RSV-PrC)

Taxonomic identifier

11888 [NCBI]

Taxonomic lineage

Viruses › Retro-transcribing viruses › Retroviridae › Orthoretrovirinae › Alpharetrovirus

Virus host

Gallus gallus (Chicken) [TaxID: 9031]

Protein attributes

Sequence length	895 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	During replicative cycle of retroviruses, the reverse-transcribed viral DNA is integrated into the host chromosome by the viral integrase enzyme. RNase H activity is associated with the reverse transcriptase.
Catalytic activity	Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Endonucleolytic cleavage to 5'-phosphomonoester.
Cofactor	Binds 8 manganese or magnesium ions per integrase homotetramer By similarity.
Subunit structure	The integrase forms a homotetramer. Reverse transcriptase is a heterodimer of alpha and beta subunits.
Domain	The integrase is composed of three domains. The N-terminal domain is a zinc binding domain. The central domain is the catalytic domain. The C-terminal domain is a non-specific DNA binding domain.
Post-translational modification	Specific enzymatic cleavages in vivo yield mature proteins. The pol-derived portion of gag-pol precursor is processed to yield the reverse transcriptase beta subunit, which in turn is processed to yield the reverse transcriptase alpha subunit and the integrase.
Miscellaneous	This protein is synthesized as a Gag-Pol polyprotein.
Sequence similarities	Contains 1 integrase catalytic domain. Contains 1 integrase-type DNA-binding domain. Contains 1 integrase-type zinc finger. Contains 1 reverse transcriptase domain. Contains 1 RNase H domain.

Ontologies

Keywords
Biological process	DNA integration DNA recombination
Domain	Zinc-finger
Ligand	DNA-binding Magnesium Manganese Metal-binding Zinc
Molecular function	Endonuclease Hydrolase Nuclease Nucleotidyltransferase RNA-directed DNA polymerase Transferase
Technical term	3D-structure Multifunctional enzyme
Gene Ontology (GO)
Biological process	DNA integration Inferred from electronic annotation. Source: InterPro DNA recombination Inferred from electronic annotation. Source: UniProtKB-KW RNA-dependent DNA replication Inferred from electronic annotation. Source: InterPro transposition Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW DNA-directed DNA polymerase activity Inferred from electronic annotation. Source: EC RNA binding Inferred from electronic annotation. Source: InterPro RNA-directed DNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW integrase activity Inferred from electronic annotation. Source: InterPro magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW manganese ion binding Inferred from electronic annotation. Source: UniProtKB-KW ribonuclease H activity Inferred from electronic annotation. Source: EC zinc ion binding 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 – 572

572

Reverse transcriptase/ribonuclease H alpha-subunit Potential

PRO_0000040986

Chain

573 – 895

323

Integrase Potential

PRO_0000040987

Regions

Domain

42 – 230

189

Reverse transcriptase

Domain

441 – 571

131

RNase H

Domain

625 – 788

164

Integrase catalytic

Zinc finger

573 – 613

41

Integrase-type

DNA binding

794 – 842

49

Integrase-type

Sites

Metal binding

636

1

Magnesium; catalytic; for integrase activity By similarity

Metal binding

693

1

Magnesium; catalytic; for integrase activity By similarity

Metal binding

729

1

Magnesium; catalytic; for integrase activity By similarity

Natural variations

Natural variant

14

1

P → S

Natural variant

16

1

H → R

Natural variant

176

1

C → R

Natural variant

199

1

E → K

Natural variant

247

1

A → T

Natural variant

304

1

R → Q

Natural variant

474

1

A → V

Natural variant

535

1

S → G

Natural variant

867

1

E → G

Natural variant

869

1

E → K

Experimental info

Sequence conflict

48

1

E → V in CAA48535. Ref.3

Sequence conflict

498

1

T → A in CAA48535. Ref.3

Sequence conflict

566

1

Q → K in CAA48535. Ref.3

Sequence conflict

673

1

V → A in CAA48535. Ref.3

Secondary structure

1

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895

Helix Strand Turn

Details...

Beta strand

631 – 639

9

Helix

641 – 643

3

Beta strand

648 – 654

7

Turn

655 – 657

3

Beta strand

660 – 667

8

Helix

670 – 684

15

Beta strand

688 – 692

5

Helix

696 – 699

4

Helix

701 – 710

10

Beta strand

713 – 716

4

Beta strand

719 – 722

4

Helix

726 – 745

20

Beta strand

749 – 751

3

Helix

754 – 756

3

Helix

757 – 769

13

Helix

780 – 785

6

Beta strand

795 – 799

5

Beta strand

805 – 814

10

Beta strand

816 – 823

8

Turn

824 – 826

3

Beta strand

829 – 833

5

Helix

834 – 836

3

Beta strand

837 – 839

3

Sequences

	Sequence		Length	Mass (Da)
	P03354-1 [UniParc]. Last modified July 21, 1986. Version 1. Checksum: 7C28319ED8985465	FASTA	895	98,662
	10 20 30 40 50 60 TVALHLAIPL KWKPDHTPVW IDQWPLPEGK LVALTQLVEK ELQLGHIEPS LSCWNTPVFV 70 80 90 100 110 120 IRKASGSYRL LHDLRAVNAK LVPFGAVQQG APVLSALPRG WPLMVLDLKD CFFSIPLAEQ 130 140 150 160 170 180 DREAFAFTLP SVNNQAPARR FQWKVLPQGM TCSPTICQLV VGQVLEPLRL KHPSLCMLHY 190 200 210 220 230 240 MDDLLLAASS HDGLEAAGEE VISTLERAGF TISPDKVQRE PGVQYLGYKL GSTYVAPVGL 250 260 270 280 290 300 VAEPRIATLW DVQKLVGSLQ WLRPALGIPP RLMGPFYEQL RGSDPNEARE WNLDMKMAWR 310 320 330 340 350 360 EIVRLSTTAA LERWDPALPL EGAVARCEQG AIGVLGQGLS THPRPCLWLF STQPTKAFTA 370 380 390 400 410 420 WLEVLTLLIT KLRASAVRTF GKEVDILLLP ACFREDLPLP EGILLALKGF AGKIRSSDTP 430 440 450 460 470 480 SIFDIARPLH VSLKVRVTDH PVPGPTVFTD ASSSTHKGVV VWREGPRWEI KEIADLGASV 490 500 510 520 530 540 QQLEARAVAM ALLLWPTTPT NVVTDSAFVA KMLLKMGQEG VPSTAAAFIL EDALSQRSAM 550 560 570 580 590 600 AAVLHVRSHS EVPGFFTEGN DVADSQATFQ AYPLREAKDL HTALHIGPRA LSKACNISMQ 610 620 630 640 650 660 QAREVVQTCP HCNSAPALEA GVNPRGLGPL QIWQTDFTLE PRMAPRSWLA VTVDTASSAI 670 680 690 700 710 720 VVTQHGRVTS VAVQHHWATA IAVLGRPKAI KTDNGSCFTS KSTREWLARW GIAHTTGIPG 730 740 750 760 770 780 NSQGQAMVER ANRLLKDRIR VLAEGDGFMK RIPTSKQGEL LAKAMYALNH FERGENTKTP 790 800 810 820 830 840 IQKHWRPTVL TEGPPVKIRI ETGEWEKGWN VLVWGRGYAA VKNRDTDKVI WVPSRKVKPD 850 860 870 880 890 ITQKDEVTKK DEASPLFAGI SDWIPWEDEQ EGLQGETASN KQERPGEDTL AANES

References

[1]	"Nucleotide sequence of Rous sarcoma virus." Schwartz D., Tizard R., Gilbert W. Cell 32:853-869(1983) [PubMed: 6299578] [Abstract] Cited for: NUCLEOTIDE SEQUENCE.
[2]	"Rous sarcoma virus encodes a transcriptional activator." Broome S., Gilbert W. Cell 40:537-546(1985) [PubMed: 2982497] [Abstract] Cited for: NUCLEOTIDE SEQUENCE, POST-TRANSLATIONAL MODIFICATIONS.
[3]	"Complete nucleotide sequence of Rous sarcoma virus variants adapted to duck cells." Kashuba V.I., Kavsan V.M., Ryndich A.V., Lazurkevich Z.V., Zubak S.V., Popov S.V., Dostalova V., Glozhanek I. Mol. Biol. (Mosk.) 27:436-450(1993) [PubMed: 8387633] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[4]	"Crystal structure of an active two-domain derivative of Rous sarcoma virus integrase." Yang Z.-N., Mueser T.C., Bushman F.D., Hyde C.C. J. Mol. Biol. 296:535-548(2000) [PubMed: 10669607] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.53 ANGSTROMS) OF 621-858. Strain: Clone pATV8.

Cross-references

Sequence databases

EMBLGenBankDDBJ

V01197 Genomic DNA. No translation available.
J02342 Genomic RNA. Translation: AAB59933.1. Different initiation.
X68524 Genomic DNA. Translation: CAA48535.1.

PIR

GNFV1R. A03955.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1C0M	X-ray	2.53	A/B/C/D	621-858	[»]
1C1A	X-ray	3.10	A/B	621-858	[»]

ModBase

Search...

Family and domain databases

InterPro

IPR000477. DNA_pol_RVTase.
IPR001037. Integrase_C_retrovir.
IPR001584. Integrase_cat-core.
IPR003308. Integrase_Zn-bd_dom_N.
IPR002156. RNase_H.
IPR010661. RVT_thumb.
[Graphical view]

Gene3D

G3DSA:2.30.30.10. Integrase_C. 1 hit.

Pfam

PF00552. Integrase. 1 hit.
PF02022. Integrase_Zn. 1 hit.
PF00075. RnaseH. 1 hit.
PF00665. rve. 1 hit.
PF00078. RVT_1. 1 hit.
PF06817. RVT_thumb. 1 hit.
[Graphical view]

PROSITE

PS50994. INTEGRASE. 1 hit.
PS51027. INTEGRASE_DBD. 1 hit.
PS50879. RNASE_H. 1 hit.
PS50878. RT_POL. 1 hit.
PS50876. ZF_INTEGRASE. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

POL_RSVP

Accession

Primary (citable) accession number: P03354
Secondary accession number(s): Q07462, Q64983

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	July 21, 1986
Last modified:	June 16, 2009
This is version 81 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

Virus (Virus annotation project)