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- PDB-3h1c: Crystal structure of Polynucleotide Phosphorylase (PNPase) core b... -

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Basic information

Entry
Database: PDB / ID: 3h1c
TitleCrystal structure of Polynucleotide Phosphorylase (PNPase) core bound to RNase E and Tungstate
Components
  • Polyribonucleotide nucleotidyltransferase
  • Ribonuclease E
KeywordsTRANSFERASE / polynucleotide phosphorylase / RNA turnover / Cytoplasm / Nucleotidyltransferase / RNA-binding / Stress response / Endonuclease / Hydrolase / Nuclease
Function / homology
Function and homology information


regulation of RNA helicase activity / rRNA 5'-end processing / bacterial degradosome / ribonuclease E / ribonuclease E activity / polyribonucleotide nucleotidyltransferase / polyribonucleotide nucleotidyltransferase activity / endoribonuclease complex / DEAD/H-box RNA helicase binding / 7S RNA binding ...regulation of RNA helicase activity / rRNA 5'-end processing / bacterial degradosome / ribonuclease E / ribonuclease E activity / polyribonucleotide nucleotidyltransferase / polyribonucleotide nucleotidyltransferase activity / endoribonuclease complex / DEAD/H-box RNA helicase binding / 7S RNA binding / cyclic-di-GMP binding / RNA catabolic process / tRNA processing / mRNA catabolic process / protein complex oligomerization / RNA nuclease activity / RNA processing / RNA endonuclease activity / cytoplasmic side of plasma membrane / rRNA processing / response to heat / 3'-5'-RNA exonuclease activity / protein homotetramerization / molecular adaptor activity / tRNA binding / rRNA binding / magnesium ion binding / RNA binding / zinc ion binding / identical protein binding / membrane / cytoplasm / cytosol
Similarity search - Function
Polyribonucleotide nucleotidyltransferase, RNA-binding domain / Polyribonucleotide phosphorylase C-terminal / Polyribonucleotide phosphorylase C terminal / : / RNase E/G, Thioredoxin-like domain / Ribonuclease E/G / Ribonuclease E / RNA-binding protein AU-1/Ribonuclease E/G / Ribonuclease E/G family / Polyribonucleotide nucleotidyltransferase, RNA-binding domain superfamily ...Polyribonucleotide nucleotidyltransferase, RNA-binding domain / Polyribonucleotide phosphorylase C-terminal / Polyribonucleotide phosphorylase C terminal / : / RNase E/G, Thioredoxin-like domain / Ribonuclease E/G / Ribonuclease E / RNA-binding protein AU-1/Ribonuclease E/G / Ribonuclease E/G family / Polyribonucleotide nucleotidyltransferase, RNA-binding domain superfamily / Polyribonucleotide nucleotidyltransferase / Polyribonucleotide nucleotidyltransferase, RNA-binding domain / Polyribonucleotide nucleotidyltransferase, RNA binding domain / GHMP Kinase, N-terminal domain / Exoribonuclease, phosphorolytic domain 2 / 3' exoribonuclease family, domain 2 / Exoribonuclease, phosphorolytic domain 1 / PNPase/RNase PH domain superfamily / Exoribonuclease, PH domain 2 superfamily / 3' exoribonuclease family, domain 1 / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / Ribosomal Protein S5; domain 2 / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / K Homology domain / K homology RNA-binding domain / Arc Repressor Mutant, subunit A / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TUNGSTATE(VI)ION / Polyribonucleotide nucleotidyltransferase / Ribonuclease E
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.57 Å
AuthorsNurmohamed, S.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structure of Escherichia coli polynucleotide phosphorylase core bound to RNase E, RNA and manganese: implications for catalytic mechanism and RNA degradosome assembly
Authors: Nurmohamed, S. / Vaidialingam, B. / Callaghan, A.J. / Luisi, B.F.
History
DepositionApr 11, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyribonucleotide nucleotidyltransferase
D: Ribonuclease E
B: Polyribonucleotide nucleotidyltransferase
E: Ribonuclease E
C: Polyribonucleotide nucleotidyltransferase
F: Ribonuclease E
G: Polyribonucleotide nucleotidyltransferase
H: Ribonuclease E
I: Polyribonucleotide nucleotidyltransferase
J: Ribonuclease E
K: Polyribonucleotide nucleotidyltransferase
L: Ribonuclease E
M: Polyribonucleotide nucleotidyltransferase
N: Ribonuclease E
O: Polyribonucleotide nucleotidyltransferase
P: Ribonuclease E
R: Polyribonucleotide nucleotidyltransferase
S: Ribonuclease E
T: Polyribonucleotide nucleotidyltransferase
U: Ribonuclease E
V: Polyribonucleotide nucleotidyltransferase
W: Ribonuclease E
X: Polyribonucleotide nucleotidyltransferase
Y: Ribonuclease E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)773,17545
Polymers767,97024
Non-polymers5,20521
Water00
1
A: Polyribonucleotide nucleotidyltransferase
B: Polyribonucleotide nucleotidyltransferase
C: Polyribonucleotide nucleotidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,2108
Polymers178,9703
Non-polymers1,2395
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12590 Å2
ΔGint-33 kcal/mol
Surface area64850 Å2
MethodPISA
2
D: Ribonuclease E


Theoretical massNumber of molelcules
Total (without water)4,3411
Polymers4,3411
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
E: Ribonuclease E


Theoretical massNumber of molelcules
Total (without water)4,3411
Polymers4,3411
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
F: Ribonuclease E


Theoretical massNumber of molelcules
Total (without water)4,3411
Polymers4,3411
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
G: Polyribonucleotide nucleotidyltransferase
I: Polyribonucleotide nucleotidyltransferase
K: Polyribonucleotide nucleotidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,9627
Polymers178,9703
Non-polymers9914
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12410 Å2
ΔGint-32 kcal/mol
Surface area65560 Å2
MethodPISA
6
H: Ribonuclease E


Theoretical massNumber of molelcules
Total (without water)4,3411
Polymers4,3411
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
J: Ribonuclease E


Theoretical massNumber of molelcules
Total (without water)4,3411
Polymers4,3411
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
L: Ribonuclease E


Theoretical massNumber of molelcules
Total (without water)4,3411
Polymers4,3411
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
M: Polyribonucleotide nucleotidyltransferase
O: Polyribonucleotide nucleotidyltransferase
R: Polyribonucleotide nucleotidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,4589
Polymers178,9703
Non-polymers1,4876
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13340 Å2
ΔGint-33 kcal/mol
Surface area65680 Å2
MethodPISA
10
N: Ribonuclease E


Theoretical massNumber of molelcules
Total (without water)4,3411
Polymers4,3411
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
11
P: Ribonuclease E


Theoretical massNumber of molelcules
Total (without water)4,3411
Polymers4,3411
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
12
S: Ribonuclease E


Theoretical massNumber of molelcules
Total (without water)4,3411
Polymers4,3411
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
13
T: Polyribonucleotide nucleotidyltransferase
V: Polyribonucleotide nucleotidyltransferase
X: Polyribonucleotide nucleotidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,4589
Polymers178,9703
Non-polymers1,4876
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13080 Å2
ΔGint-29 kcal/mol
Surface area66200 Å2
MethodPISA
14
U: Ribonuclease E


Theoretical massNumber of molelcules
Total (without water)4,3411
Polymers4,3411
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
15
W: Ribonuclease E


Theoretical massNumber of molelcules
Total (without water)4,3411
Polymers4,3411
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
16
Y: Ribonuclease E


Theoretical massNumber of molelcules
Total (without water)4,3411
Polymers4,3411
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)167.742, 262.887, 264.125
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Polyribonucleotide nucleotidyltransferase / Polynucleotide phosphorylase / PNPase


Mass: 59656.828 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: BL21 DE3
References: UniProt: P05055, polyribonucleotide nucleotidyltransferase
#2: Protein/peptide
Ribonuclease E / RNase E


Mass: 4340.687 Da / Num. of mol.: 12 / Fragment: UNP residues 1021-1061 / Source method: obtained synthetically / Details: This sequence occurs naturally in E. coli / References: UniProt: P21513, ribonuclease E
#3: Chemical...
ChemComp-WO4 / TUNGSTATE(VI)ION


Mass: 247.838 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: WO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.79 Å3/Da / Density % sol: 67.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.2M ammonium hydrogen citrate, 17% PEG 3350, 50mM disodium tungstate, pH4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 15, 2006 / Details: Monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 3.57→79.5 Å / Num. all: 129998 / Num. obs: 123425 / % possible obs: 94.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Biso Wilson estimate: 57.1 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 11.4
Reflection shellResolution: 3.57→3.73 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 2.3 / Num. unique all: 129998 / % possible all: 94.2

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Processing

Software
NameVersionClassification
HKL-3000data collection
X-PLORmodel building
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GCM

3gcm


Resolution: 3.57→25 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.304 123425 -random
Rwork0.2703 ---
obs0.301 123425 94.2 %-
all-129998 --
Refinement stepCycle: LAST / Resolution: 3.57→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms51004 0 105 0 51109

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