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- PDB-9zll: Complex of N-terminal BrxC walker B, BrxB, and N-termianl PglZ fr... -

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Basic information

Entry
Database: PDB / ID: 9zll
TitleComplex of N-terminal BrxC walker B, BrxB, and N-termianl PglZ from the Acinetobacter BREX system
Components
  • BREX-1 system phosphatase PglZ type A
  • DUF1788 domain-containing protein
  • Putative conjugative transfer protein
KeywordsANTIMICROBIAL PROTEIN / Restriction / Bacteriophage / Defense / AlphaFold
Function / homology
Function and homology information


: / : / : / : / BREX ATP-binding protein BrxC winged helix-turn-helix domain / BREX ATP-binding protein BrxC alpha helical domain / BREX ATP-binding protein BrxC 4th domain with six-stranded beta sheet / Alkaline phosphatase-like protein PglZ / BREX protein BrxB / BREX protein BrxB / BREX system PglZ alkaline phosphatase-like domain
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Putative conjugative transfer protein / DUF1788 domain-containing protein / BREX-1 system phosphatase PglZ type A
Similarity search - Component
Biological speciesAcinetobacter sp. NEB 394 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsDoyle, L.A. / Stoddard, B.L. / Kaiser, B. / Kaiser, A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R35GM148166 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R15 GM140375 United States
Other privateNew England Biolabs
CitationJournal: bioRxiv / Year: 2026
Title: Competing forms of protein-protein association and DNA binding exhibited by BrxC from the BREX phage restriction system.
Authors: Alexander J Kaiser / Jennifer J Readshaw / Lindsey A Doyle / Maria Puiu / Abigail Kelly / Sydney F McGuire / Julieta Peralta Acosta / Duc Vu / Andrew Nelson / Darren L Smith / Lidia Araújo- ...Authors: Alexander J Kaiser / Jennifer J Readshaw / Lindsey A Doyle / Maria Puiu / Abigail Kelly / Sydney F McGuire / Julieta Peralta Acosta / Duc Vu / Andrew Nelson / Darren L Smith / Lidia Araújo-Bazán / Ernesto Arias-Palomo / Yvette A Luyten / Barry L Stoddard / Tim R Blower / Brett K Kaiser /
Abstract: Bacteriophage exclusion (BREX) defense systems restrict phage infection via inhibition of phage DNA replication, while also modifying and protecting the bacterial genome. Type I BREX systems encode ...Bacteriophage exclusion (BREX) defense systems restrict phage infection via inhibition of phage DNA replication, while also modifying and protecting the bacterial genome. Type I BREX systems encode six conserved proteins, including a site-specific DNA methyltransferase. Host methylation requires a subset of BREX proteins, whereas phage restriction generally requires them all, suggesting that distinct but overlapping complexes mediate these activities. Full details of the mechanism and regulation of BREX remains to be understood. Here, we characterize the behavior and structures of the conserved BrxC AAA+ ATPase protein. BrxC forms multiple competing assemblages - various self-associating multimers, as well as a complex with BrxB-PglZ - that can be uncoupled via distinct point mutations, leading to differing effects on host methylation versus phage restriction. BrxC's self-association, as well as its ability to bind DNA, is regulated by ATP binding and hydrolysis; BrxA and BrxB appear to also regulate those behaviors. These collective results suggest that BrxC may play a key role in controlling the two activities of BREX, with BrxB, BrxC and PglZ forming a core complex, and the equilibrium among competing assemblies containing those proteins modulating the balance between idling and activated restrictive states.
History
DepositionDec 8, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative conjugative transfer protein
B: Putative conjugative transfer protein
C: Putative conjugative transfer protein
D: Putative conjugative transfer protein
E: DUF1788 domain-containing protein
F: BREX-1 system phosphatase PglZ type A
G: DUF1788 domain-containing protein
H: BREX-1 system phosphatase PglZ type A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)326,68821
Polymers324,3358
Non-polymers2,35313
Water6,017334
1
A: Putative conjugative transfer protein
B: Putative conjugative transfer protein
G: DUF1788 domain-containing protein
H: BREX-1 system phosphatase PglZ type A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,37811
Polymers162,1684
Non-polymers1,2107
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Putative conjugative transfer protein
D: Putative conjugative transfer protein
E: DUF1788 domain-containing protein
F: BREX-1 system phosphatase PglZ type A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,31110
Polymers162,1684
Non-polymers1,1436
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.248, 114.986, 194.050
Angle α, β, γ (deg.)90.000, 108.034, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 5 through 8 or (resid 9...
d_2ens_1(chain "B" and (resid 5 through 56 or (resid 57...
d_3ens_1(chain "C" and (resid 5 through 8 or (resid 9...
d_4ens_1(chain "D" and (resid 5 through 8 or (resid 9...
d_1ens_2(chain "E" and ((resid 3 and (name N or name...
d_2ens_2(chain "G" and (resid 3 through 57 or (resid 58...
d_1ens_3(chain "F" and ((resid 3 through 6 and (name N...
d_2ens_3chain "H"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1GLUGLULYSLYSAA5 - 1126 - 113
d_12ens_1HISHISSERSERAA129 - 317130 - 318
d_13ens_1ALAALAARGARGAA328 - 416329 - 417
d_14ens_1LEULEUGLUGLUAA425 - 538426 - 539
d_15ens_1ILEILEPHEPHEAA541 - 550542 - 551
d_21ens_1GLUGLUSERSERBB5 - 3176 - 318
d_22ens_1ALAALAARGARGBB328 - 416329 - 417
d_23ens_1LEULEUPHEPHEBB425 - 550426 - 551
d_31ens_1GLUGLULYSLYSCC5 - 1126 - 113
d_32ens_1HISHISGLUGLUCC129 - 538130 - 539
d_33ens_1ILEILEPHEPHECC541 - 550542 - 551
d_41ens_1GLUGLULYSLYSDD5 - 1126 - 113
d_42ens_1HISHISSERSERDD129 - 317130 - 318
d_43ens_1ALAALAARGARGDD328 - 416329 - 417
d_44ens_1LEULEUGLUGLUDD425 - 538426 - 539
d_45ens_1ILEILEPHEPHEDD541 - 550542 - 551
d_11ens_2GLNGLNPROPROEE3 - 1914 - 192
d_21ens_2GLNGLNPROPROGG3 - 1914 - 192
d_11ens_3LEULEUALAALAFF3 - 374 - 38
d_12ens_3ILEILEPHEPHEFF45 - 9546 - 96
d_21ens_3LEULEUPHEPHEHH3 - 954 - 96

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(0.830334530642, -0.472383921323, 0.295631524198), (0.494085586524, 0.378708314804, -0.782597882369), (0.25772854016, 0.795885320366, 0.547852677654)21.21586231, -5.94884861945, -20.0132109765
2given(0.860994217619, 0.000726213557796, 0.50861422497), (0.0202995349026, -0.999251268564, -0.0329367751238), (0.508209490378, 0.0386830051403, -0.860364305979)-8.23693924825, 103.304499543, 18.5451665407
3given(0.877503559078, 0.0466432209592, 0.477296463159), (-0.400593216353, -0.475870344321, 0.782989457405), (0.263652382537, -0.878277760924, -0.398892962896)-4.48519304943, 115.461442232, 43.5384514706
4given(0.883227541134, 0.114799035846, 0.454676029665), (0.0545272945583, -0.988137059658, 0.143568539304), (0.46576376494, -0.102011434155, -0.879009546348)-7.6206565919, 101.64944213, 26.1323540158
5given(0.905837242851, 0.0665747923328, 0.418361908507), (0.019349163037, -0.993045468533, 0.116130561506), (0.423183765466, -0.0971004348692, -0.900825735753)-0.236370464411, 100.39078287, 23.0669267805

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Components

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Protein , 3 types, 8 molecules ABCDEGFH

#1: Protein
Putative conjugative transfer protein


Mass: 63922.598 Da / Num. of mol.: 4 / Mutation: E269Q
Source method: isolated from a genetically manipulated source
Details: BrxC containing the E269Q Walker B mutation and truncated to residues 1-551
Source: (gene. exp.) Acinetobacter sp. NEB 394 (bacteria) / Gene: ABAC_0086 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1J0HS39
#2: Protein DUF1788 domain-containing protein


Mass: 21901.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: BrxB / Source: (gene. exp.) Acinetobacter sp. NEB 394 (bacteria) / Gene: AhaeAN43_17405, J5N55_15600 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1L6KSM0
#3: Protein BREX-1 system phosphatase PglZ type A


Mass: 12420.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PglZ truncated to residues 1-98 / Source: (gene. exp.) Acinetobacter sp. NEB 394 (bacteria) / Gene: pglZ, FPV60_17765 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A558EY06

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Non-polymers , 5 types, 347 molecules

#4: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.44 Å3/Da / Density % sol: 49.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 250 mM NaCl, 100 mM HEPES pH 8.5, 21% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 15, 2025
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 77820 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 59.31 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.038 / Rrim(I) all: 0.101 / Χ2: 1 / Net I/σ(I): 14.3
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5362 / CC1/2: 0.78 / Rpim(I) all: 0.32 / Rrim(I) all: 0.84 / Χ2: 0.79 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286+SVNrefinement
BOSdata collection
XDSdata reduction
XDSdata scaling
PHASER2.8.3phasing
Coot0.9model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.74→49.68 Å / SU ML: 0.3588 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.4027
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2476 1889 2.43 %
Rwork0.2058 75931 -
obs0.2068 77820 94.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.69 Å2
Refinement stepCycle: LAST / Resolution: 2.74→49.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20646 0 133 334 21113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003121215
X-RAY DIFFRACTIONf_angle_d0.679428828
X-RAY DIFFRACTIONf_chiral_restr0.04723217
X-RAY DIFFRACTIONf_plane_restr0.00483760
X-RAY DIFFRACTIONf_dihedral_angle_d17.18617434
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS2.62213552769
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS1.17264402791
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS2.36675809049
ens_2d_2EEX-RAY DIFFRACTIONTorsion NCS1.05236456148
ens_3d_2FFX-RAY DIFFRACTIONTorsion NCS1.28056527387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.74-2.810.34641310.2855231X-RAY DIFFRACTION85.92
2.81-2.90.34851290.26775373X-RAY DIFFRACTION87.72
2.9-2.990.30951400.25265522X-RAY DIFFRACTION90.32
2.99-3.10.29031320.24065657X-RAY DIFFRACTION91.79
3.1-3.220.25151430.23785720X-RAY DIFFRACTION93.55
3.22-3.370.29321450.23035867X-RAY DIFFRACTION95.2
3.37-3.550.29021570.22375896X-RAY DIFFRACTION96.59
3.55-3.770.28311510.20666039X-RAY DIFFRACTION97.73
3.77-4.060.26871490.19376026X-RAY DIFFRACTION98.33
4.06-4.470.21921520.18116055X-RAY DIFFRACTION98.6
4.47-5.110.19171510.17796128X-RAY DIFFRACTION98.94
5.11-6.440.25421560.21636149X-RAY DIFFRACTION99.35
6.44-49.680.20191530.18496268X-RAY DIFFRACTION99.38

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