DB code: M00220

CATH domain 3.-.-.- :
2.-.-.- :
1.10.10.- : Arc Repressor Mutant, subunit A
3.-.-.- :
2.-.-.- :
3.30.1370.- : Ribosomal Protein S8; Chain
2.40.50.140 : OB fold (Dihydrolipoamide Acetyltransferase, E2P)
E.C. 2.7.7.8
CSA
M-CSA
MACiE

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

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P05055 Polyribonucleotide nucleotidyltransferase
EC 2.7.7.8
Polynucleotide phosphorylase
PNPase
NP_417633.4 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_491351.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF00013 (KH_1)
PF03726 (PNPase)
PF01138 (RNase_PH)
PF03725 (RNase_PH_C)
PF00575 (S1)
[Graphical View]

KEGG enzyme name
polyribonucleotide nucleotidyltransferase
polynucleotide phosphorylase
PNPase
nucleoside diphosphate:polynucleotidyl transferase
polyribonucleotide nucleotidyltransferase
polynucleotide phosphorylase
polyribonucleotide phosphorylase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P05055 PNP_ECOLI RNA(n+1) + phosphate = RNA(n) + a nucleoside diphosphate. Homotrimer. Organized into a structure (processome or RNA degradosome) containing a number of RNA-processing enzymes. Cytoplasm. Note=Has also been isolated in association with the inner membrane.

KEGG Pathways
Map code Pathways E.C.
MAP00230 Purine metabolism
MAP00240 Pyrimidine metabolism

Compound table
Substrates Products Intermediates
KEGG-id C00046 C00009 C00046 C00454
E.C.
Compound RNA(n+1) Orthophosphate RNA(n) Nucleoside diphosphate
Type nucleic acids phosphate group/phosphate ion nucleic acids nucleotide
ChEBI 26078
PubChem 1004
22486802
1sroA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1sroA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis

References
[1]
Resource
Comments
Medline ID
PubMed ID 4589553
Journal Eur J Biochem
Year 1973
Volume 40
Pages 77-87
Authors Portier C, van Rapenbusch R, Minh-Nguy-Thang, Grunberg-Manago M
Title Quaternary structure of polynucleotide phosphorylase from Escherichia coli.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 794831
Journal Nucleic Acids Res
Year 1976
Volume 3
Pages 3015-24
Authors Guissani A, Portier C
Title Study on the structure-function relationship of polynucleotide phosphorylase: model of a proteolytic degraded polynucleotide phosphorylase.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 351564
Journal Nucleic Acids Res
Year 1978
Volume 5
Pages 1539-49
Authors Trip EM, Smith M
Title Enzymatic synthesis of oligodeoxyribonucleotides of defined sequence. Polynucleotide phosphorylase catalysed synthesis using pyrimidine analog-containing deoxyribonucleoside 5'-diphosphates.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 8612276
Journal Cell
Year 1996
Volume 85
Pages 237-45
Authors Musco G, Stier G, Joseph C, Castiglione Morelli MA, Nilges M, Gibson TJ, Pastore A
Title Three-dimensional structure and stability of the KH domain: molecular insights into the fragile X syndrome.
Related PDB
Related UniProtKB
[5]
Resource
Comments STRUCTURE BY NMR OF 617-692
Medline ID 97160844
PubMed ID 9008164
Journal Cell
Year 1997
Volume 88
Pages 235-42
Authors Bycroft M, Hubbard TJ, Proctor M, Freund SM, Murzin AG
Title The solution structure of the S1 RNA binding domain: a member of an ancient nucleic acid-binding fold.
Related PDB 1sro
Related UniProtKB P05055
[6]
Resource
Comments
Medline ID
PubMed ID 10411741
Journal Mol Microbiol
Year 1999
Volume 33
Pages 235-48
Authors Garcia-Mena J, Das A, Sanchez-Trujillo A, Portier C, Montanez C
Title A novel mutation in the KH domain of polynucleotide phosphorylase affects autoregulation and mRNA decay in Escherichia coli.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 11080643
Journal Structure Fold Des
Year 2000
Volume 8
Pages 1215-26
Authors Symmons MF, Jones GH, Luisi BF
Title A duplicated fold is the structural basis for polynucleotide phosphorylase catalytic activity, processivity, and regulation.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 11222749
Journal Nucleic Acids Res
Year 2001
Volume 29
Pages 1017-26
Authors Zuo Y, Deutscher MP
Title Exoribonuclease superfamilies: structural analysis and phylogenetic distribution.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 12162954
Journal J Mol Biol
Year 2002
Volume 321
Pages 397-409
Authors Jarrige A, Brechemier-Baey D, Mathy N, Duche O, Portier C
Title Mutational analysis of polynucleotide phosphorylase from Escherichia coli.
Related PDB
Related UniProtKB

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.

Created Updated
2003-07-22 2009-03-23