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: - .



- - (RdRs) -- , . RdRs - . RdRs 3 : N-, - (. 1) [1]. 3 : fingers, palm thumb (. 1,2).

1. - - Infectious Bursal DiseaseVirus (IBDV), PDB ID 2PGG, , [3]: N- - , - -- , fingers - , palm -- thumb -- .

2002 Gorbalenya et al. [2] palm. palm 3 , A-> B->C N- -. Mg2+ Mn2+, , , . . , , . , Birnaviridae Tetraviridae, A-> B->C C->A-> B (. 3). , ~ 22 100 N-, upstream , . ,


. , , . . , . 4 b.

2. RdRs IBDV, PDB ID 2PGG, , [3]: fingers - , palm -- thumb -- . , , -- -ADN- ( , , -GDD- ), .

, , , .


3. palm () , ( Thosea asigna virus (TaV), Euprosterna elaeasa virus (EeV), infectious bursal disease virus (IBDV), infectious pancreatic necrosis virus strain Jasper (IPNVJ) ). [2].

--, N- - (. 5). , , , , .

4.

4b.
4. C () () . . , [2]. RdRp 1RDR PDB. 4b. palm (, ) IBDV (, ) [3].

, , , , Tetraviridae Birnaviridae. Tetraviridae ss+ - (. . +), Birnaviridae -- ds, . . (. 6). , : (1) . - RdRp, ds ss+ . .


(2) - , . 2002 , , Gorbalenya et al. , 2009 Sabanadzovich et al. [5] RdRp Grapevine virus Q (GVQ) Grapevine Syrah virus 1 (GSV1).

5. [2].

6. , .3 neighbourjoining [2]. , Tav/EeV IBDV/IPNVJ .


, , : · RdRp Tymoviridae, GVQ GSV1. PSI-BLAST , palm GVO, , . 7. TaV EeV, TaV, EeV, Tetravirida Drosophila melanogaster tetravirus SW-2009a (DtV) , Tetraviridae - Drosophila A virus (DAV) .

7. Citrus sudden death-associated virus, (64% identity) GVQ BLAST. RdRp , . , , identity score.

· · ·

GVQ GVS1 -- ss+ - , - Timoviridae , , - Timoviridae, -

, , . . Gorbalenya et al. [2]:


1). 58 RdRp 13 ss+ - . 2). HMM-. 3). . . 3 i, j L, : 1 <= i < j < L <= N+1, i -- j -- L-- N-- 4). Eo/Es i L, Eo -- E-value , Es - -- E-value .

8. , TaV/EeV IBDV/IPNVJ. Eo/Es(i), - Eo/Es(L).


TaV, EeV, IBDV IPNVJ. i L (. 8). 1000 .. ~10 8 , , 9 .., . , Permutotetraviridae [4], TaV, EeV DtV. Tetraviridae RdRp, [2].

RdRp
RdRp. , , . . 9 1 ~1000, ~10 5. , . ( BLAST , . . . , IBDV RdRs , GVQ. , , , . ) 2 Tymoviridae (GVQ GSV1), 3 -- Permutotetraviridae ( TaV, Eev DtV). , RdRp Birnaviridae ( BLAST , Human poliovirus 1 (PDB ID 3OL7) Birnaviridae ). , palm TaV, EeV, DtV, DAV, IBDV, IPNV, BshV ( Blotched snakehead virus, Birnaviridae) GVQ COBALT (http://www.ncbi.nlm.nih.gov/tools/cobalt/cobalt.cgi) (. 9).


9. , palm TaV, EeV, DtV, DAV, IBDV, IPNV, BshV ( Blotched snakehead virus, Birnaviridae) GVQ COBALT.

pftools . (-DX4-5[DE]-), (-GX2-3TX3[DN]-) (-[GA]D[DN]-) c . , , , RNA Virus Database (http://tree.bio.ed.ac.uk/rnavirusdb/index.php) , (.. ). 1.
Sc re o . ,. 231T 0 26V .1 3 a 221E 55D 06V .6 3 e t 221D 0 55V .4 3 A 2 1 1 IP 92B 00V .3 3 N 6D 2 0 1 M e u rn 4 3 0 rin irn iv v .6 3 a b s a lvcs P a a iu l o s ty hb ce 201B 98h .2 2 s V 1 0 1 G p ru 3 2 4 0 Q ila .9 8 V h s s ro v Dx 0 9 .2 7 ro e iru 13Bbv dn aas ilt w 0 5 2 m ta u .2 7 u ro 3 in 1 3 H n G te tv C o o s lp R iu tra avc 0 .5 5 o tm s 1 3 C fo o s s k c ild a ru v ic .. ...... . ... i v tra e ea Td i v tra e ea Td i s la c nd U fie v ae irn a Bd v ae irn a Bd v ae irn a Bd v ae irn a Bd ir v o ce ea Sd ird v o ee Ra v m e b os S iru . ... . ...

1. . , .

, SwissProt/Uniprot trEMBL 2. 2.

RdRp



palm

1). (3OL7:A, Picornaviridae; Human enterovirus C) (2PGG, Birnaviridae; Infectious bursal disease virus) Pymol c align super. 10. , , RMSD 15.84 е. - RMSD 3.88 е. , , ,


2. SwissProt/Uniprot trEMBL 2. , . , .

align , . super , .

10. (3OL7:A, Picornaviridae; Human enterovirus C) (2PGG, Birnaviridae; Infectious bursal disease virus ) align () super ().


2). PDB , 2PGG SSM, PDBeFold (http://www.ebi.ac.uk/msd-srv/ssm/cgi-bin/ssmserver). : PDB Chains Lowest acceptable match (%) Source match individual chains match connectivity* best matches only unique matches only if no matches within limits of acceptability are found, show close ones Precision Sort by
* - , 3. PDBeFold.

2PGG A 30 Whole PDB archive yes yes yes yes normal RMSD

348 , IBDV, IPNV . 4 2 2 ( 4).

11. , palm. , -- , . 2uut:A -GDD- -GGD-, . . .


PDB ID 2PGG:A 2YI8:E 2UUT:A 3OL7:E IBDV IPNV





RMSD 0.0 0.798 3.013 3.392

Q-score 0.177 0.148 0.139

Sapporo virus Human enterovirus C

4. 4 PDBeFold.

palm 11. 12 - 14 , PDBeFold.

12. () () . 2PGG:A -- , 2YI8:E -- , 2UUT:A -- , 3OL7:E -- .

. RMSD 2PGG:A/2YI8:E 0.798 е, 2UUT/3OL7 -- , 3.194 е. , , -- RMSD 3.392 е (. 13). Gorbalenya et al., GDD ADN , , 100 .. (. 14). , [4] RdRp Permutotetraviridae PDB .


13. (2PGG:A, ) (3OL7:E, ) .

14. palm 2PGG () 3OL7 (). cartoons, GDD ADN -- .



[1] Koonin EV// The phylogeny of RNA-dependent RNA polymerases of positive-strand RNA viruses. // J Gen Virol. 1991 Sep;72 ( Pt 9):2197-206. [2] Gorbalenya AE, Pringle FM, Zeddam JL, Luke BT, Cameron CE, Kalmakoff J, Hanzlik TN, Gordon KH, Ward VK // The palm subdomain-based active site is internally permuted in viral RNA-dependent RNA polymerases of an ancient lineage. // J Mol Biol. 2002 Nov 15;324(1):47-62. [3] Pan J, Vakharia VN, Tao YJ // The structure of a birnavirus polymerase reveals a distinct active site topology // Proc Natl Acad Sci U S A. 2007 May 1;104(18):7385-90. Epub 2007 Apr 24. [4] Ferrero D, Buxaderas M, Rodriguez JF, Verdaguer N // Purification, crystallization and preliminary X-ray diffraction analysis of the RNA-dependent RNA polymerase from Thosea asigna virus // Acta Crystallogr Sect F Struct Biol Cryst Commun, 2012 Oct 1;68(Pt 10):1263-6. doi: 10.1107/S1744309112037529 [5] Sabanadzovic S, Ghanem-Sabanadzovic NA, Gorbalenya AE // Permutation of the active site of putative RNA-dependent RNA polymerase in a newly identified species of plant alpha-like virus. // Virology. 2009 Nov 10;394(1):1-7. doi: 10.1016/j.virol.2009.08.006. Epub 2009 Sep 29. [6] Garriga D, Navarro A, Querol-AudМ J, Abaitua F, RodrМguez JF, Verdaguer N // Activation mechanism of a noncanonical RNA-dependent RNA polymerase. // Proc Natl Acad Sci U S A. 2007 Dec 18;104(51):20540-5. Epub 2007 Dec 11.