Structure of PDB 3vnu Chain A

Receptor sequence

>3vnuA (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: 3vnu Mechanism for template-independent terminal adenylation activity of Q beta replicase
• Chain: A
• Resolution: 3.2 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	Y1051 D1054 G1092 R1107 D1190 S1248 S1250	Y1007 D1010 G1048 R1063 D1146 S1187 S1189
BS02	rna	A	R847 L928 R935 L945 N946 Q948 G1018 F1023	R803 L884 R891 L901 N902 Q904 G974 F979
BS03	ATP	A	R914 I916 D968 S970 A972 M1017 E1026 D1053	R870 I872 D924 S926 A928 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:3vnu, PDBe:3vnu, PDBj:3vnu
• PDBsum: 3vnu
• PubMed: 22884418
• UniProt: P0A6N3;
  P0A6P3;
  P14647|RDRP_BPQBE RNA-directed RNA polymerase subunit beta