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- PDB-7or2: Crystal structure of UDP-N-acetylenolpyruvoylglucosamine reductas... -

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Basic information

Entry
Database: PDB / ID: 7or2
TitleCrystal structure of UDP-N-acetylenolpyruvoylglucosamine reductase (MurB) from Pseudomonas aeruginosa in complex with FAD and a pyrazole derivative (fragment 4)
ComponentsUDP-N-acetylenolpyruvoylglucosamine reductase
KeywordsOXIDOREDUCTASE / Peptidoglycan-biosynthesis Fragment based drug discovery
Function / homology
Function and homology information


UDP-N-acetylmuramate dehydrogenase / UDP-N-acetylmuramate dehydrogenase activity / peptidoglycan biosynthetic process / FAD binding / cell wall organization / flavin adenine dinucleotide binding / regulation of cell shape / cell division / cytosol
Similarity search - Function
UDP-N-acetylenolpyruvoylglucosamine reductase / UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal / UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain superfamily / UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily
Similarity search - Domain/homology
5-methyl-1-phenyl-pyrazole-4-carboxylic acid / FLAVIN-ADENINE DINUCLEOTIDE / UDP-N-acetylenolpyruvoylglucosamine reductase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsAcebron-Garcia de Eulate, M. / Blundell, T.L. / Kim, S.Y. / Mendes, V. / Abell, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other privateCystic Fibrosis Trust United Kingdom
Citation
Journal: J.Med.Chem. / Year: 2022
Title: Discovery of Novel Inhibitors of Uridine Diphosphate- N -Acetylenolpyruvylglucosamine Reductase (MurB) from Pseudomonas aeruginosa , an Opportunistic Infectious Agent Causing Death in Cystic Fibrosis Patients.
Authors: Acebron-Garcia-de-Eulate, M. / Mayol-Llinas, J. / Holland, M.T.O. / Kim, S.Y. / Brown, K.P. / Marchetti, C. / Hess, J. / Di Pietro, O. / Mendes, V. / Abell, C. / Floto, R.A. / Coyne, A.G. / Blundell, T.L.
History
DepositionJun 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Feb 23, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-N-acetylenolpyruvoylglucosamine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7543
Polymers37,7661
Non-polymers9882
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-9 kcal/mol
Surface area14710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.220, 87.220, 101.390
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#1: Protein UDP-N-acetylenolpyruvoylglucosamine reductase / UDP-N-acetylmuramate dehydrogenase


Mass: 37765.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: murB, PA2977 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9HZM7, UDP-N-acetylmuramate dehydrogenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-9FH / 5-methyl-1-phenyl-pyrazole-4-carboxylic acid


Mass: 202.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H10N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.95 Å3/Da / Density % sol: 58.33 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 30% glycerol and 22% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.915 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 8, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.915 Å / Relative weight: 1
ReflectionResolution: 2.35→43.61 Å / Num. obs: 18162 / % possible obs: 99.33 % / Redundancy: 9.1 % / Biso Wilson estimate: 54.52 Å2 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.034 / Rrim(I) all: 0.103 / Net I/σ(I): 12.9
Reflection shellResolution: 2.35→2.62 Å / Redundancy: 8.59 % / Rmerge(I) obs: 1.497 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1829 / CC1/2: 0.773 / Rpim(I) all: 0.541 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JB1

4jb1


Resolution: 2.35→43.61 Å / SU ML: 0.3147 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 38.5009
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2831 1829 10.1 %
Rwork0.2349 16285 -
obs0.2399 18114 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 81.47 Å2
Refinement stepCycle: LAST / Resolution: 2.35→43.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2399 0 68 8 2475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00822515
X-RAY DIFFRACTIONf_angle_d1.23243443
X-RAY DIFFRACTIONf_chiral_restr0.0567395
X-RAY DIFFRACTIONf_plane_restr0.0078452
X-RAY DIFFRACTIONf_dihedral_angle_d26.0775367
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.410.3991380.36381246X-RAY DIFFRACTION99.14
2.41-2.480.40531420.34791246X-RAY DIFFRACTION98.23
2.48-2.560.39361400.32811243X-RAY DIFFRACTION98.09
2.57-2.660.37621330.30361238X-RAY DIFFRACTION98.63
2.66-2.760.33981380.30111229X-RAY DIFFRACTION99.06
2.76-2.890.33221420.29461256X-RAY DIFFRACTION99.01
2.89-3.040.29671400.27111248X-RAY DIFFRACTION98.65
3.04-3.230.27721380.27591240X-RAY DIFFRACTION98.43
3.23-3.480.29631460.24131251X-RAY DIFFRACTION99.36
3.48-3.830.2781420.23071256X-RAY DIFFRACTION99.79
3.83-4.380.2511410.20591274X-RAY DIFFRACTION99.79
4.38-5.520.2491400.20191271X-RAY DIFFRACTION100
5.53-43.610.26611490.2011287X-RAY DIFFRACTION99.86
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)
13.49711797585-0.393973654156-1.61331925234.454422542450.7773765463576.8335767175-0.1898166070890.0570770184790.0665323467658-0.3133958576260.412298313535-0.6036243145180.02430482277271.66621818393-0.2113482999320.629490664319-0.05417277947610.02965204074170.805763040775-0.08258475972560.375883601271-31.417028108715.9523670136-4.02817705442
23.942253210821.854116073971.256570012925.66521503229-1.139045273278.246299374280.284634658025-0.9205748634-0.233122096371.34902967448-0.1348395687190.3036974634840.6678329316690.0352536406819-0.1547605367640.9340896607040.1397185749640.04616562723890.699664347722-0.02638652583240.450422979309-39.458611637410.488153962314.3445127402
38.8542156357-1.53803882302-1.135659639957.011877641111.321837985.04293834995-0.5530273781120.256584333626-0.939222582460.1395143236450.1874476048331.07200502951.55451884623-0.7506654913780.3107187657291.02723897017-0.1331909324270.006896239343830.5409975035880.04064175696850.523090976621-52.45482256492.71578130087-6.3278386518
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 176 )3 - 1761 - 174
22chain 'A' and (resid 177 through 227 )177 - 227175 - 225
33chain 'A' and (resid 228 through 339 )228 - 339226 - 337

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