Structure of PDB 3avu Chain A

Receptor sequence

>3avuA (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: 3avu Molecular basis for RNA polymerization by Q beta replicase
• Chain: A
• Resolution: 2.907 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	R914 Q948 D968 A972 M1017 E1026 D1053 D1054 C1091 G1092 R1107 D1190	R870 Q904 D924 A928 M973 E982 D1009 D1010 C1047 G1048 R1063 D1146
BS02	rna	A	R847 S849 G850 G851 A852 N857 R858 V906 P907 I916 M924 R935 N946 Q948 G1018 F1023 Y1051 G1160 Q1257	R803 S805 G806 G807 A808 N813 R814 V862 P863 I872 M880 R891 N902 Q904 G974 F979 Y1007 G1116 Q1196
BS03	CA	A	D968 L969 S970	D924 L925 S926
BS04	CA	A	D968 D1054 E1089	D924 D1010 E1045

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