EzCatDB: M00220
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DB codeM00220
CATH domainDomain 13.-.-.-
Domain 22.-.-.-
Domain 31.10.10.- : Arc Repressor Mutant, subunit A
Domain 43.-.-.-
Domain 52.-.-.-
Domain 63.30.1370.- : Ribosomal Protein S8; Chain
Domain 72.40.50.140 : OB fold (Dihydrolipoamide Acetyltransferase, E2P)
E.C.2.7.7.8

CATH domainRelated DB codes (homologues)
2.40.50.140 : OB fold (Dihydrolipoamide Acetyltransferase, E2P)M00186,T00050,D00291,D00294,T00254

Enzyme Name
UniProtKBKEGG

P05055
Protein namePolyribonucleotide nucleotidyltransferasepolyribonucleotide nucleotidyltransferase
polynucleotide phosphorylase
PNPase
nucleoside diphosphate:polynucleotidyl transferase
polyribonucleotide nucleotidyltransferase
polynucleotide phosphorylase
polyribonucleotide phosphorylase
SynonymsEC 2.7.7.8
Polynucleotide phosphorylase
PNPase
RefSeqNP_417633.4 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_491351.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PfamPF00013 (KH_1)
PF03726 (PNPase)
PF01138 (RNase_PH)
PF03725 (RNase_PH_C)
PF00575 (S1)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00230Purine metabolism
MAP00240Pyrimidine metabolism

UniProtKB:Accession NumberP05055
Entry namePNP_ECOLI
ActivityRNA(n+1) + phosphate = RNA(n) + a nucleoside diphosphate.
SubunitHomotrimer. Organized into a structure (processome or RNA degradosome) containing a number of RNA-processing enzymes.
Subcellular locationCytoplasm. Note=Has also been isolated in association with the inner membrane.
Cofactor

Compound table: links to PDB-related databases & PoSSuM

SubstratesProducts
KEGG-idC00046C00009C00046C00454
CompoundRNA(n+1)OrthophosphateRNA(n)Nucleoside diphosphate
Typenucleic acidsphosphate group/phosphate ionnucleic acidsnucleotide
ChEBI
26078


PubChem
22486802
1004


            
1sroAUnboundUnboundUnboundUnbound

Active-site residues
pdb
        
1sroA


references
[1]
PubMed ID4589553
JournalEur J Biochem
Year1973
Volume40
Pages77-87
AuthorsPortier C, van Rapenbusch R, Minh-Nguy-Thang, Grunberg-Manago M
TitleQuaternary structure of polynucleotide phosphorylase from Escherichia coli.
[2]
PubMed ID794831
JournalNucleic Acids Res
Year1976
Volume3
Pages3015-24
AuthorsGuissani A, Portier C
TitleStudy on the structure-function relationship of polynucleotide phosphorylase: model of a proteolytic degraded polynucleotide phosphorylase.
[3]
PubMed ID351564
JournalNucleic Acids Res
Year1978
Volume5
Pages1539-49
AuthorsTrip EM, Smith M
TitleEnzymatic synthesis of oligodeoxyribonucleotides of defined sequence. Polynucleotide phosphorylase catalysed synthesis using pyrimidine analog-containing deoxyribonucleoside 5'-diphosphates.
[4]
PubMed ID8612276
JournalCell
Year1996
Volume85
Pages237-45
AuthorsMusco G, Stier G, Joseph C, Castiglione Morelli MA, Nilges M, Gibson TJ, Pastore A
TitleThree-dimensional structure and stability of the KH domain: molecular insights into the fragile X syndrome.
[5]
CommentsSTRUCTURE BY NMR OF 617-692
Medline ID97160844
PubMed ID9008164
JournalCell
Year1997
Volume88
Pages235-42
AuthorsBycroft M, Hubbard TJ, Proctor M, Freund SM, Murzin AG
TitleThe solution structure of the S1 RNA binding domain: a member of an ancient nucleic acid-binding fold.
Related PDB1sro
Related UniProtKBP05055
[6]
PubMed ID10411741
JournalMol Microbiol
Year1999
Volume33
Pages235-48
AuthorsGarcia-Mena J, Das A, Sanchez-Trujillo A, Portier C, Montanez C
TitleA novel mutation in the KH domain of polynucleotide phosphorylase affects autoregulation and mRNA decay in Escherichia coli.
[7]
PubMed ID11080643
JournalStructure Fold Des
Year2000
Volume8
Pages1215-26
AuthorsSymmons MF, Jones GH, Luisi BF
TitleA duplicated fold is the structural basis for polynucleotide phosphorylase catalytic activity, processivity, and regulation.
[8]
PubMed ID11222749
JournalNucleic Acids Res
Year2001
Volume29
Pages1017-26
AuthorsZuo Y, Deutscher MP
TitleExoribonuclease superfamilies: structural analysis and phylogenetic distribution.
[9]
PubMed ID12162954
JournalJ Mol Biol
Year2002
Volume321
Pages397-409
AuthorsJarrige A, Brechemier-Baey D, Mathy N, Duche O, Portier C
TitleMutational analysis of polynucleotide phosphorylase from Escherichia coli.

comments
This structure corresponds to S1 motif (PNP_ECOLI;P05055, residues 617-692), which is originally found in ribosomal protein S1. According to the paper [5], this domain is derived from an ancient nucleic acid-binding protein. Thus, this domain is not involved in catalysis.

createdupdated
2003-07-222009-03-23


Copyright: Nozomi Nagano, JST & CBRC-AIST
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Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
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