› 3h1c

X-ray diffraction
3.57Å resolution

Crystal structure of Polynucleotide Phosphorylase (PNPase) core bound to RNase E and Tungstate

Released:
DOI: 10.2210/pdb3h1c/pdb
PDB entry 3h1c coloured by chain, front view.
PDB entry 3h1c coloured by chain, side view.
PDB entry 3h1c coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structure of Escherichia coli polynucleotide phosphorylase core bound to RNase E, RNA and manganese: implications for catalytic mechanism and RNA degradosome assembly.
Nurmohamed S, Vaidialingam B, Callaghan AJ, Luisi BF
J Mol Biol 389 17-33 (2009)
PMID: 19327365

Function and Biology Details

Reactions catalysed: 
RNA(n+1) + phosphate = RNA(n) + a nucleoside diphosphate
Endonucleolytic cleavage of single-stranded RNA in A- and U-rich regions
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
homo trimer (preferred)
monomeric
Assembly name:
PDBe Complex ID:
PDB-CPX-138342 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Polyribonucleotide nucleotidyltransferase Chains: A, B, C, G, I, K, M, O, R, T, V, X
Molecule details ›
Chains: A, B, C, G, I, K, M, O, R, T, V, X
Length: 549 amino acids
Theoretical weight: 59.66 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P05055 (Residues: 1-549; Coverage: 77%)
Gene names: JW5851, b3164, pnp
Sequence domains:
Structure domains:
Ribonuclease E Chains: D, E, F, H, J, L, N, P, S, U, W, Y
Molecule details ›
Chains: D, E, F, H, J, L, N, P, S, U, W, Y
Length: 41 amino acids
Theoretical weight: 4.34 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided
UniProt:
  • Canonical: P21513 (Residues: 1021-1061; Coverage: 4%)
Gene names: JW1071, ams, b1084, hmp1, rne
Sequence domains: Polyribonucleotide phosphorylase C terminal

Ligands and Environments

1 bound ligand:
Ligand WO4 21 x WO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: P212121
Unit cell:
a: 167.742Å b: 262.887Å c: 264.125Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.301 0.27 0.304
Expression system: Not provided

Quick links

Citations

22 review citations

Classification of intrinsically disordered regions and proteins.
van der Lee et al. (2014)
21 more

1 mention without citation

Crystal structure of Escherichia coli polynucleotide phosphorylase core bound to RNase E, RNA and manganese: implications for catalytic mechanism and RNA degradosome assembly.
Nurmohamed et al. (2009)