Structure of PDB 3avy Chain A

Receptor sequence

>3avyA (length=1203) Species: 39803,83334

AEITASLVKELRERTGAGMMDCKKALTEANGDIELAIENMRKSGAIKAAK
KAGNVAADGVIKTKIDGNYGIILEVNCQTDFVAKDAGFQAFADKVLDAAV
AGKITDVEVLKAQFEEERVALVAKIGENINIRRVAALEGDVLGSYQHGAR
IGVLVAAKGADEELVKHIAMHVAASKPEFIKPEDVSAEVVEKEYQVQLDI
AMQSGKPKEIAEKMVEGRMKKFTGEVSLTGQPFVMEPSKTVGQLLKEHNA
EVTGFIRFEVGEGIEKVETDFAAEVAAMSKQSHMSFERTKPHVNVGTIGH
VDHGKTTLTAAITTVLAKTYGGNTSHVEYDTPTRHYAHVDCPGHADYVKN
MITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMV
DDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILE
LAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGE
EVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQ
VLAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGT
IELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAK
VLSGASSRNSLSAQLRRAANTRIEVEGNLALSIANDLLLAYGQSPFNSEA
ECISFSPRFDGTPDDFRINYLKAEIMSKYDDFSLGIDTEAVAWEKFLAAE
AECALTNARLYRPDYSEDFNFSLGESCIHMARRKIAKLIGDVPSVEGMLR
HCRFSGGATTTNNRSYGHPSFKFALPQACTPRALKYVLALRASTHFDIRI
SDISPFNKAVTVPKNSKTDRCIAIEPGWNMFFQLGIGGILRDRLRCWGID
LNDQTINQRRAHEGSVTNNLATVDLSAASDSISLALCELLLPPGWFEVLM
DLRSPKGRLPDGSVVTYEKISSMGNGYTFELESLIFASLARSVCEILDLD
SSEVTVYGDDIILPSCAVPALREVFKYVGFTTNTKKTFSEGPFRESCGKH
YYSGVDVTPFYIRHRIVSPADLILVLNNLYRWATIDGVWDPRAHSVYLKY
RKLLPKQLQRNTIPDGYGDGALVGSVLINPFAKNRGWIRYVPVITDHTRD
RERAELGSYLYDLFSRCLSESNAIDQLICRSNPTKISRSTGKFDIQYIAC
SSR

3D structure

• PDB: 3avy Molecular basis for RNA polymerization by Q beta replicase
• Chain: A
• Resolution: 2.616 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): D306 K309 T310 H369
• Catalytic site (residue number reindexed from 1): D302 K305 T306 H344
• Enzyme Commision number:
  2.7.7.48: RNA-directed RNA polymerase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	rna	A	S849 G850 R858 H862 D1053 D1054 G1092 L1118 D1190	S805 G806 R814 H818 D1009 D1010 G1048 L1074 D1146
BS02	rna	A	T620 D621 R662 G851 A852 T854 T855 N857 R858 H862 I916 I918 M924 R935 N946 G1018 Y1051 G1160 Y1161 N1243 P1244 T1245 K1246 Q1257	T595 D596 R637 G807 A808 T810 T811 N813 R814 H818 I872 I874 M880 R891 N902 G974 Y1007 G1116 Y1117 N1182 P1183 T1184 K1185 Q1196
BS03	CH1	A	K908 R914 S970 A972 S973 M1017 E1026 D1053	K864 R870 S926 A928 S929 M973 E982 D1009
BS04	CA	A	D968 L969 D1053	D924 L925 D1009
BS05	CA	A	D968 D1053 D1054	D924 D1009 D1010

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0003723 RNA binding
• GO:0003746 translation elongation factor activity
• GO:0003924 GTPase activity
• GO:0003968 RNA-dependent RNA polymerase activity
• GO:0005515 protein binding
• GO:0005525 GTP binding
• GO:0034062 5'-3' RNA polymerase activity
• GO:0046872 metal ion binding
• GO:0097216 guanosine tetraphosphate binding

Biological Process

• GO:0001172 RNA-templated transcription
• GO:0006412 translation
• GO:0006414 translational elongation
• GO:0019079 viral genome replication
• GO:0039694 viral RNA genome replication
• GO:0046677 response to antibiotic

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005886 plasma membrane

External links

• PDB: RCSB:3avy, PDBe:3avy, PDBj:3avy
• PDBsum: 3avy
• PubMed: 22245970
• UniProt: P0A6N3;
  P0A6P3;
  P14647|RDRP_BPQBE RNA-directed RNA polymerase subunit beta