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- PDB-9qlr: Nonamer crystal structure of the transcription factor MraZ from M... -

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Basic information

Entry
Database: PDB / ID: 9qlr
TitleNonamer crystal structure of the transcription factor MraZ from Mycoplasma genitalium
ComponentsTranscriptional regulator MraZ
KeywordsTRANSCRIPTION / Transcription factor / nonamer
Function / homology
Function and homology information


negative regulation of DNA-templated transcription initiation / nucleoid / transcription cis-regulatory region binding / DNA-binding transcription factor activity / cytoplasm
Similarity search - Function
Transcriptional regulator MraZ / MraZ domain / MraZ, C-terminal / MraZ superfamily / MraZ protein, putative antitoxin-like / SpoVT-AbrB domain profile. / SpoVT-AbrB domain / SpoVT-AbrB domain superfamily
Similarity search - Domain/homology
Transcriptional regulator MraZ
Similarity search - Component
Biological speciesMycoplasmoides genitalium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.85 Å
AuthorsReverter, D. / Sanchez-Alba, L.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2021-124602OB-I00 Spain
CitationJournal: Nat Commun / Year: 2026
Title: Structural basis for transcriptional regulation by the cell division regulator MraZ in Mycoplasma genitalium.
Authors: Lucía Sánchez-Alba / Nathalia Varejão / Alexandre Durand / Javier García-Pardo / Maria Carreras-Caballé / Virginia Amador / Jaume Pinyol / David Reverter /
Abstract: Cell division is a central process in all living organisms and requires the coordinated action of many proteins and regulatory elements. In most bacteria, the division and cell wall (dcw) gene ...Cell division is a central process in all living organisms and requires the coordinated action of many proteins and regulatory elements. In most bacteria, the division and cell wall (dcw) gene cluster is regulated by the first gene of the dcw operon, mraZ, a highly conserved DNA-binding transcriptional regulator. Here we report the structural basis of MraZ transcriptional regulation by the resolution of three different cryo-EM structures of MraZ in complex with the upstream promoter region of the dcw cluster from Mycoplasma genitalium at 3.36, 3.57 and 3.87 Å resolution. The structures reveal the specific interactions between MraZ DNA-binding motif and nucleobases of the binding boxes, which induces distortion in the MraZ octamer to enable the interaction with the four repetitive binding boxes of the promoter DNA. The "cradle-like" DNA-binding motif of MraZ exposes three highly conserved basic residues, Lys13, Arg15 and Arg86, which are essential for binding to the consensus sequence of its cognate promoter. Ultimately, the mechanism behind MraZ's DNA binding and regulation of the dcw operon could be translated to other species, working as a general mechanism for the regulation of dcw gene cluster in bacteria.
History
DepositionMar 21, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2026Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 18, 2026Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
J: Transcriptional regulator MraZ
K: Transcriptional regulator MraZ
L: Transcriptional regulator MraZ
M: Transcriptional regulator MraZ
N: Transcriptional regulator MraZ
O: Transcriptional regulator MraZ
P: Transcriptional regulator MraZ
Q: Transcriptional regulator MraZ
R: Transcriptional regulator MraZ
A: Transcriptional regulator MraZ
B: Transcriptional regulator MraZ
C: Transcriptional regulator MraZ
D: Transcriptional regulator MraZ
E: Transcriptional regulator MraZ
F: Transcriptional regulator MraZ
G: Transcriptional regulator MraZ
H: Transcriptional regulator MraZ
I: Transcriptional regulator MraZ
S: Transcriptional regulator MraZ
T: Transcriptional regulator MraZ
U: Transcriptional regulator MraZ
V: Transcriptional regulator MraZ
W: Transcriptional regulator MraZ
X: Transcriptional regulator MraZ
Y: Transcriptional regulator MraZ
Z: Transcriptional regulator MraZ
a: Transcriptional regulator MraZ
b: Transcriptional regulator MraZ
c: Transcriptional regulator MraZ
d: Transcriptional regulator MraZ
e: Transcriptional regulator MraZ
f: Transcriptional regulator MraZ
g: Transcriptional regulator MraZ
h: Transcriptional regulator MraZ
i: Transcriptional regulator MraZ
j: Transcriptional regulator MraZ


Theoretical massNumber of molelcules
Total (without water)626,28136
Polymers626,28136
Non-polymers00
Water00
1
J: Transcriptional regulator MraZ
K: Transcriptional regulator MraZ
L: Transcriptional regulator MraZ
M: Transcriptional regulator MraZ
N: Transcriptional regulator MraZ
O: Transcriptional regulator MraZ
P: Transcriptional regulator MraZ
Q: Transcriptional regulator MraZ
R: Transcriptional regulator MraZ


Theoretical massNumber of molelcules
Total (without water)156,5709
Polymers156,5709
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24670 Å2
ΔGint-155 kcal/mol
Surface area55150 Å2
MethodPISA
2
A: Transcriptional regulator MraZ
B: Transcriptional regulator MraZ
C: Transcriptional regulator MraZ
D: Transcriptional regulator MraZ
E: Transcriptional regulator MraZ
F: Transcriptional regulator MraZ
G: Transcriptional regulator MraZ
H: Transcriptional regulator MraZ
I: Transcriptional regulator MraZ


Theoretical massNumber of molelcules
Total (without water)156,5709
Polymers156,5709
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24530 Å2
ΔGint-154 kcal/mol
Surface area55290 Å2
MethodPISA
3
S: Transcriptional regulator MraZ
T: Transcriptional regulator MraZ
U: Transcriptional regulator MraZ
V: Transcriptional regulator MraZ
W: Transcriptional regulator MraZ
X: Transcriptional regulator MraZ
Y: Transcriptional regulator MraZ
Z: Transcriptional regulator MraZ
a: Transcriptional regulator MraZ


Theoretical massNumber of molelcules
Total (without water)156,5709
Polymers156,5709
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24670 Å2
ΔGint-154 kcal/mol
Surface area55060 Å2
MethodPISA
4
b: Transcriptional regulator MraZ
c: Transcriptional regulator MraZ
d: Transcriptional regulator MraZ
e: Transcriptional regulator MraZ
f: Transcriptional regulator MraZ
g: Transcriptional regulator MraZ
h: Transcriptional regulator MraZ
i: Transcriptional regulator MraZ
j: Transcriptional regulator MraZ


Theoretical massNumber of molelcules
Total (without water)156,5709
Polymers156,5709
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24700 Å2
ΔGint-152 kcal/mol
Surface area54920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.621, 203.821, 149.301
Angle α, β, γ (deg.)90.00, 111.76, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein ...
Transcriptional regulator MraZ


Mass: 17396.691 Da / Num. of mol.: 36
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasmoides genitalium (bacteria) / Gene: mraZ, MG221 / Production host: Escherichia coli (E. coli) / References: UniProt: P47463
Has protein modificationN

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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: 2.83 Å3/Da / Density % sol: 56.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 12.00 % w/v Polyethylene glycol 6,000, 2.00 M Sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.7749 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Oct 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 3.85→82.12 Å / Num. obs: 31414 / % possible obs: 83 % / Redundancy: 3.3 % / Biso Wilson estimate: 86.03 Å2 / CC1/2: 0.994 / Net I/σ(I): 3.4
Reflection shellResolution: 3.85→4.29 Å / Num. unique obs: 1572 / CC1/2: 0.663

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.85→82.12 Å / SU ML: 0.68 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 38.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3077 1540 4.92 %
Rwork0.2484 --
obs0.2513 31294 47.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.85→82.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms40248 0 0 0 40248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00440932
X-RAY DIFFRACTIONf_angle_d0.7855296
X-RAY DIFFRACTIONf_dihedral_angle_d8.1835292
X-RAY DIFFRACTIONf_chiral_restr0.0516300
X-RAY DIFFRACTIONf_plane_restr0.0057200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.85-3.980.573260.4503104X-RAY DIFFRACTION2
3.98-4.120.3444200.3575430X-RAY DIFFRACTION8
4.12-4.290.3961630.3232860X-RAY DIFFRACTION16
4.29-4.480.4027740.2861542X-RAY DIFFRACTION27
4.48-4.720.3311230.24762317X-RAY DIFFRACTION41
4.72-5.010.32611490.24882914X-RAY DIFFRACTION51
5.01-5.40.35691820.27373214X-RAY DIFFRACTION57
5.4-5.940.35441920.29983500X-RAY DIFFRACTION62
5.94-6.80.33511910.28974126X-RAY DIFFRACTION72
6.8-8.570.29892630.26485310X-RAY DIFFRACTION93
8.57-82.120.24372770.19655437X-RAY DIFFRACTION94

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