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- PDB-4njc: RNA Polymerase interacting protein YkzG from Geobacillus stearoth... -

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Basic information

Entry
Database: PDB / ID: 4njc
TitleRNA Polymerase interacting protein YkzG from Geobacillus stearothermophilus
ComponentsGeobacillus stearothermophilus YkzG
KeywordsTRANSCRIPTION / DNA Dependant RNA Polymerase
Function / homology
Function and homology information


DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / DNA-templated transcription / DNA binding
Similarity search - Function
RNAP, epsilon subunit-like / RNA polymerase epsilon subunit / RNA polymerase epsilon subunit / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit epsilon
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / MAD / Resolution: 2.3 Å
AuthorsKeller, A.N. / Lewis, P.J.
CitationJournal: J Bacteriol / Year: 2014
Title: ε, a new subunit of RNA polymerase found in gram-positive bacteria.
Authors: Andrew N Keller / Xiao Yang / Jana Wiedermannová / Olivier Delumeau / Libor Krásný / Peter J Lewis /
Abstract: RNA polymerase in bacteria is a multisubunit protein complex that is essential for gene expression. We have identified a new subunit of RNA polymerase present in the high-A+T Firmicutes phylum of ...RNA polymerase in bacteria is a multisubunit protein complex that is essential for gene expression. We have identified a new subunit of RNA polymerase present in the high-A+T Firmicutes phylum of Gram-positive bacteria and have named it ε. Previously ε had been identified as a small protein (ω1) that copurified with RNA polymerase. We have solved the structure of ε by X-ray crystallography and show that it is not an ω subunit. Rather, ε bears remarkable similarity to the Gp2 family of phage proteins involved in the inhibition of host cell transcription following infection. Deletion of ε shows no phenotype and has no effect on the transcriptional profile of the cell. Determination of the location of ε within the assembly of RNA polymerase core by single-particle analysis suggests that it binds toward the downstream side of the DNA binding cleft. Due to the structural similarity of ε with Gp2 and the fact they bind similar regions of RNA polymerase, we hypothesize that ε may serve a role in protection from phage infection.
History
DepositionNov 9, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Geobacillus stearothermophilus YkzG
B: Geobacillus stearothermophilus YkzG
C: Geobacillus stearothermophilus YkzG
D: Geobacillus stearothermophilus YkzG
E: Geobacillus stearothermophilus YkzG
F: Geobacillus stearothermophilus YkzG
G: Geobacillus stearothermophilus YkzG
H: Geobacillus stearothermophilus YkzG


Theoretical massNumber of molelcules
Total (without water)64,6938
Polymers64,6938
Non-polymers00
Water66737
1
A: Geobacillus stearothermophilus YkzG


Theoretical massNumber of molelcules
Total (without water)8,0871
Polymers8,0871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Geobacillus stearothermophilus YkzG


Theoretical massNumber of molelcules
Total (without water)8,0871
Polymers8,0871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Geobacillus stearothermophilus YkzG


Theoretical massNumber of molelcules
Total (without water)8,0871
Polymers8,0871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Geobacillus stearothermophilus YkzG


Theoretical massNumber of molelcules
Total (without water)8,0871
Polymers8,0871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Geobacillus stearothermophilus YkzG


Theoretical massNumber of molelcules
Total (without water)8,0871
Polymers8,0871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Geobacillus stearothermophilus YkzG


Theoretical massNumber of molelcules
Total (without water)8,0871
Polymers8,0871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Geobacillus stearothermophilus YkzG


Theoretical massNumber of molelcules
Total (without water)8,0871
Polymers8,0871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Geobacillus stearothermophilus YkzG


Theoretical massNumber of molelcules
Total (without water)8,0871
Polymers8,0871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.650, 82.780, 83.430
Angle α, β, γ (deg.)90.00, 92.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Geobacillus stearothermophilus YkzG


Mass: 8086.619 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0K2H5X8*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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: 1.9 Å3/Da / Density % sol: 35.29 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54179, 0.97941, 0.95369
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 5, 2011
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.541791
20.979411
30.953691
ReflectionResolution: 2.3→41.33 Å / Num. obs: 21483 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
BUCCANEERmodel building
PHENIX(phenix.refine: dev_1439)refinement
MOSFLMdata reduction
SCALAdata scaling
BUCCANEERphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→23.065 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 32.28 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2561 1125 5.22 %RANDOM
Rwork0.2135 ---
obs0.2158 19734 99.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→23.065 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3505 0 0 37 3542
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043572
X-RAY DIFFRACTIONf_angle_d0.7154779
X-RAY DIFFRACTIONf_dihedral_angle_d13.1591414
X-RAY DIFFRACTIONf_chiral_restr0.027489
X-RAY DIFFRACTIONf_plane_restr0.003621
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.350.33951410.2653251399
2.35-2.40460.281260.26552507100
2.4046-2.46470.31641400.2541242799
2.4647-2.53120.34951330.26612552100
2.5312-2.60560.30541560.25272486100
2.6056-2.68960.39351210.2794246898
2.6896-2.78560.3651410.2589248399
2.7856-2.89690.38961170.2592538100
2.8969-3.02850.27111360.26072506100
3.0285-3.18770.29281070.25292550100
3.1877-3.38690.25371340.24092457100
3.3869-3.64740.2861540.2267247898
3.6474-4.01280.26971450.2124245898
4.0128-4.58940.17331410.1572478100
4.5894-5.76720.18821490.15522490100
5.7672-23.06610.23581550.19592491100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.87951.51711.0536.06161.9328.19340.1461-0.0083-0.18830.6132-0.292-0.05070.08140.41420.12250.45670.01520.00060.32110.0270.282821.236243.93924.6401
24.8530.9302-2.65386.56280.05364.4638-0.29020.0650.1856-0.18080.3646-0.090.22560.1186-0.10530.6257-0.06360.00190.46840.00410.311713.384955.137940.5973
33.48480.0087-0.32969.2895-1.02597.6657-0.0658-0.0863-0.08960.02810.0378-0.40910.15590.28990.04220.49830.03550.02440.35140.00650.355121.233821.347523.1695
44.6174-1.638-0.74625.81710.28987.92340.23830.9198-0.3494-0.5382-0.1811-0.25210.32350.3934-0.04760.4753-0.00480.06680.561-0.03080.362122.649939.13756.9132
55.2078-0.6425-1.12585.90790.50586.70540.07540.643-0.3014-1.1767-0.19030.21430.3921-0.0120.15670.99960.02560.00970.5544-0.0580.412517.88544.992716.0713
65.55560.06782.39735.7253-1.66394.8216-0.0578-0.1558-0.6587-0.71910.14890.03940.768-0.1606-0.06660.8589-0.02210.12120.4049-0.02370.420613.661638.455247.0025
73.5913-1.97760.55525.99130.64164.1229-0.04220.43980.2799-0.044-0.1336-0.153-0.37850.16490.13480.663-0.11330.00250.64090.08370.418.880559.81340.9249
87.0652-2.44160.14826.3755-0.83288.0986-0.2678-0.03860.44980.09290.193-0.4412-0.99480.65450.03410.5862-0.1038-0.01570.35530.01630.35219.864764.227118.2863
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F
7X-RAY DIFFRACTION7CHAIN H
8X-RAY DIFFRACTION8CHAIN G

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