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- PDB-9bhc: Salmonella undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose... -

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Basic information

Entry
Database: PDB / ID: 9bhc
TitleSalmonella undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase (ArnC)
ComponentsUndecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase
KeywordsMEMBRANE PROTEIN / transferase / glycolipid biosynthesis / Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID
Function / homology
Function and homology information


undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase / undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase activity / 4-amino-4-deoxy-alpha-L-arabinopyranosyl undecaprenyl phosphate biosynthetic process / phosphotransferase activity, for other substituted phosphate groups / lipopolysaccharide biosynthetic process / lipid A biosynthetic process / response to antibiotic / plasma membrane
Similarity search - Function
Undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase / : / Glycosyltransferase 2-like / Glycosyl transferase family 2 / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsGuo, Y. / Borek, D. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Protein Sci / Year: 2025
Title: Cryo-EM SPR structures of Salmonella typhimurium ArnC; the key enzyme in lipid-A modification conferring polymyxin resistance.
Authors: Dhruvin H Patel / Elina Karimullina / Yirui Guo / Cameron Semper / Deepak T Patel / Tabitha Emde / Dominika Borek / Alexei Savchenko /
Abstract: Polymyxins are last-resort antimicrobial peptides administered clinically against multi-drug resistant bacteria, specifically in the case of Gram-negative species. However, an increasing number of ...Polymyxins are last-resort antimicrobial peptides administered clinically against multi-drug resistant bacteria, specifically in the case of Gram-negative species. However, an increasing number of these pathogens employ a defense strategy that involves a relay of enzymes encoded by the pmrE (ugd) loci and the arnBCDTEF operon. The pathway modifies the lipid-A component of the outer membrane (OM) lipopolysaccharide (LPS) by adding a 4-amino-4-deoxy-l-arabinose (L-Ara4N) headgroup, which renders polymyxins ineffective. Here, we report the cryo-EM SPR structures of glycosyltransferase ArnC from Salmonella typhimurium determined in apo and UDP-bound forms at resolutions 2.75 Å and 3.8 Å, respectively. The structure of the ArnC protomer comprises three distinct regions: an N-terminal glycosyltransferase domain, transmembrane region, and the interface helices (IHs). ArnC forms a tetramer with C2 symmetry, where the C-terminal strand inserts into the adjacent protomer. This tetrameric state is further stabilized by two distinct interfaces formed by ArnC that form a network of hydrogen bonds and salt bridges. The binding of UDP induces conformational changes that stabilize the loop between residues H201 to S213, and part of the putative catalytic pocket formed by IH1 and IH2. The surface property analysis revealed a hydrophobic cavity formed by TM1 and TM2 in the apo state, which is disrupted upon UDP binding. The comparison of ArnC structures to their homologs GtrB and DPMS suggests the key residues involved in ArnC catalytic activity.
History
DepositionApr 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release
Revision 1.0Feb 12, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 12, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 12, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 12, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 12, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 12, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2025Group: Data collection / Source and taxonomy
Category: em_admin / em_entity_assembly_naturalsource / entity_src_gen
Item: _em_admin.last_update / _em_entity_assembly_naturalsource.ncbi_tax_id ..._em_admin.last_update / _em_entity_assembly_naturalsource.ncbi_tax_id / _em_entity_assembly_naturalsource.organism / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.1Feb 26, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Experimental summary / Source and taxonomy / Data content type: EM metadata / EM metadata / EM metadata
Category: em_admin / em_entity_assembly_naturalsource / entity_src_gen
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _em_admin.last_update / _em_entity_assembly_naturalsource.ncbi_tax_id ..._em_admin.last_update / _em_entity_assembly_naturalsource.ncbi_tax_id / _em_entity_assembly_naturalsource.organism / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase
D: Undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase
A: Undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase
B: Undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase


Theoretical massNumber of molelcules
Total (without water)146,2214
Polymers146,2214
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase / Undecaprenyl-phosphate Ara4FN transferase / Ara4FN transferase


Mass: 36555.238 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: arnC, pmrF, A7D45_16095, AL463_15935, ASQ14_23645, ATP91_09815, ATQ15_08305, ATR96_07550, AZF90_19445, BH006_03370, CIC26_13560, CQW68_14900, D3346_04750, D3Q81_13430, DT651_10455, EAW95_08415, ...Gene: arnC, pmrF, A7D45_16095, AL463_15935, ASQ14_23645, ATP91_09815, ATQ15_08305, ATR96_07550, AZF90_19445, BH006_03370, CIC26_13560, CQW68_14900, D3346_04750, D3Q81_13430, DT651_10455, EAW95_08415, EBH50_05830, EKD96_13640, F2D26_03380, FJR52_16380, GCH85_08890, NCTC6385_01766, ND68_10730, VH79_14330
Production host: Escherichia coli (E. coli)
References: UniProt: A0A663DHR7, undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: ArnC homo tetramer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 311189 / Symmetry type: POINT
RefinementResolution: 2.75→113.424 Å / Cor.coef. Fo:Fc: 0.907 / WRfactor Rwork: 0.359 / SU B: 9.641 / SU ML: 0.175 / Average fsc overall: 0.7351 / Average fsc work: 0.7351 / ESU R: 0.309
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rwork0.359 136308 -
all0.359 --
Rfree--0 %
obs--100 %
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso mean: 109.868 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.010.0139782
ELECTRON MICROSCOPYr_bond_other_d0.0320.0159668
ELECTRON MICROSCOPYr_angle_refined_deg1.311.63213252
ELECTRON MICROSCOPYr_angle_other_deg1.5341.5722140
ELECTRON MICROSCOPYr_dihedral_angle_1_deg4.86651222
ELECTRON MICROSCOPYr_dihedral_angle_2_deg29.11620.52500
ELECTRON MICROSCOPYr_dihedral_angle_3_deg14.014151712
ELECTRON MICROSCOPYr_dihedral_angle_4_deg16.2981588
ELECTRON MICROSCOPYr_chiral_restr0.0780.21330
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.0210904
ELECTRON MICROSCOPYr_gen_planes_other0.0030.022280
ELECTRON MICROSCOPYr_nbd_refined0.1940.24606
ELECTRON MICROSCOPYr_symmetry_nbd_other0.1830.219092
ELECTRON MICROSCOPYr_nbtor_refined0.1730.29968
ELECTRON MICROSCOPYr_symmetry_nbtor_other0.0780.211996
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.2040.2432
ELECTRON MICROSCOPYr_symmetry_xyhbond_nbd_other0.0860.28
ELECTRON MICROSCOPYr_mcbond_it10.20110.6894912
ELECTRON MICROSCOPYr_mcbond_other10.20110.6874911
ELECTRON MICROSCOPYr_mcangle_it15.24616.0816126
ELECTRON MICROSCOPYr_mcangle_other15.24616.0836127
ELECTRON MICROSCOPYr_scbond_it12.69712.4624870
ELECTRON MICROSCOPYr_scbond_other12.69512.4564868
ELECTRON MICROSCOPYr_scangle_it20.22418.0387126
ELECTRON MICROSCOPYr_scangle_other20.22518.0387126
ELECTRON MICROSCOPYr_lrange_it29.011207.24838769
ELECTRON MICROSCOPYr_lrange_other29.007207.20438762
ELECTRON MICROSCOPYr_ncsr_local_group_10.1930.0516774
ELECTRON MICROSCOPYr_ncsr_local_group_20.0420.0519320
ELECTRON MICROSCOPYr_ncsr_local_group_30.1910.0516812
ELECTRON MICROSCOPYr_ncsr_local_group_40.1940.0516776
ELECTRON MICROSCOPYr_ncsr_local_group_50.0570.0519270
ELECTRON MICROSCOPYr_ncsr_local_group_60.1930.0516818
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: _ / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc workWRfactor Rwork
2.75-2.8211.557100971.557100970.1911.557
2.821-2.8991.54398061.54398060.3081.543
2.899-2.9831.38196011.38196010.4151.381
2.983-3.0741.15692721.15692720.5461.156
3.074-3.1750.84589010.84589010.6670.845
3.175-3.2870.60687800.60687800.7750.606
3.287-3.410.42583810.42583810.8370.425
3.41-3.550.3181340.3181340.8810.31
3.55-3.7070.26376940.26376940.9150.263
3.707-3.8880.2773920.2773920.9270.27
3.888-4.0980.30270210.30270210.9340.302
4.098-4.3460.33467380.33467380.9510.334
4.346-4.6460.34462190.34462190.9590.344
4.646-5.0170.31158160.31158160.9530.311
5.017-5.4950.2753870.2753870.9410.27
5.495-6.1420.24748550.24748550.9230.247
6.142-7.0890.2742700.2742700.9080.27
7.089-8.6740.25936150.25936150.9190.259
8.674-12.2310.20627870.20627870.9560.206
12.231-113.4240.57315420.57315420.9790.573

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