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- PDB-8dp2: Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate lig... -

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Basic information

Entry
Database: PDB / ID: 8dp2
TitleCrystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from Pseudomonas aeruginosa PAO1 in complex with UMA (Uridine-5'-diphosphate-N-acetylmuramoyl-L-Alanine)
ComponentsUDP-N-acetylmuramoylalanine--D-glutamate ligase
KeywordsLIGASE / SSGCID / UDP-N-acetylmuramoylalanine--D-glutamate ligase / D-glutamic acid-adding enzyme / UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase / MurD / UMA / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase / UDP-N-acetylmuramoylalanine-D-glutamate ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / ATP binding / cytoplasm
Similarity search - Function
Mur ligase MurD-like, N-terminal domain / UDP-N-acetylmuramoylalanine-D-glutamate ligase MurD / Mur ligase, C-terminal / Mur ligase, glutamate ligase domain / Mur ligase, C-terminal domain superfamily / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain
Similarity search - Domain/homology
ACETATE ION / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / PHOSPHATE ION / SUCCINIC ACID / URIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE / UDP-N-acetylmuramoylalanine--D-glutamate ligase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
CitationJournal: to be published
Title: Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from Pseudomonas aeruginosa PAO1 in complex with UMA (Uridine-5'-diphosphate-N-acetylmuramoyl-L-Alanine)
Authors: Abendroth, J. / DeBouver, N.D. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionJul 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-N-acetylmuramoylalanine--D-glutamate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9509
Polymers48,3481
Non-polymers1,6028
Water9,296516
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.460, 95.460, 99.550
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

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Protein , 1 types, 1 molecules A

#1: Protein UDP-N-acetylmuramoylalanine--D-glutamate ligase / D-glutamic acid-adding enzyme / UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase


Mass: 48348.320 Da / Num. of mol.: 1 / Fragment: PsaeA.17938.a.B2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: murD, PA4414 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9HVZ9, UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase

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Non-polymers , 8 types, 524 molecules

#2: Chemical ChemComp-UMA / URIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE


Type: L-peptide linking / Mass: 750.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H36N4O20P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O9
#7: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#8: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 516 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.72 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: RigakuReagents JCSG Top96 screen, condition b1: 100mM HEPES free acid / sodium hydroxide pH 7.5, 30% (V/V) PEG 400, 5% (w/V) PEG 3000, 10% (V/V) Glycerol: PsaeA.17938.a.B2.PS38065 at 40mg/ml ...Details: RigakuReagents JCSG Top96 screen, condition b1: 100mM HEPES free acid / sodium hydroxide pH 7.5, 30% (V/V) PEG 400, 5% (w/V) PEG 3000, 10% (V/V) Glycerol: PsaeA.17938.a.B2.PS38065 at 40mg/ml + 3mM UMA (BSI102034) and MgCl2: tray: 325018b1: cryo: direct, puck: tua1-2. SIN is modeled tenatively based on density only, it was not added to the crystallizaton buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 9, 2022
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 67812 / % possible obs: 100 % / Redundancy: 8.964 % / Biso Wilson estimate: 28.069 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.06 / Χ2: 0.952 / Net I/σ(I): 20.91
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.645.8310.5932.3150050.8090.653100
1.64-1.697.4920.4893.4348750.9020.526100
1.69-1.749.0810.44.8947250.9510.424100
1.74-1.799.4310.3026.6246140.9760.32100
1.79-1.859.4350.2368.5344440.9850.25100
1.85-1.919.4570.17911.3343330.990.19100
1.91-1.989.4610.13814.7541550.9940.146100
1.98-2.079.4670.10918.5840250.9960.115100
2.07-2.169.4610.09322.0538470.9970.099100
2.16-2.269.4520.08125.2336840.9970.085100
2.26-2.399.4480.07228.2135110.9980.076100
2.39-2.539.4370.06431.233040.9980.067100
2.53-2.79.3980.05733.8631150.9980.06100
2.7-2.929.3780.0537.9729080.9990.053100
2.92-3.29.2810.04641.1626850.9990.048100
3.2-3.589.1740.0445.3224100.9990.043100
3.58-4.139.10.03847.2821400.9990.04100
4.13-5.069.1340.03548.7818280.9990.037100
5.06-7.169.2860.03348.4314110.9990.035100
7.16-508.8280.03248.67930.9990.03499.4

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.20.1refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ADP-bound MurD, pdb entry 7U35, in three domains

7u35


Resolution: 1.6→41.34 Å / SU ML: 0.136 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.1236
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1689 1964 2.9 %0
Rwork0.15 65778 --
obs0.1506 67742 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.91 Å2
Refinement stepCycle: LAST / Resolution: 1.6→41.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3374 0 104 516 3994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00893651
X-RAY DIFFRACTIONf_angle_d1.04794967
X-RAY DIFFRACTIONf_chiral_restr0.0688566
X-RAY DIFFRACTIONf_plane_restr0.0091659
X-RAY DIFFRACTIONf_dihedral_angle_d14.49351387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.24941370.21724681X-RAY DIFFRACTION99.96
1.64-1.680.21371350.18174706X-RAY DIFFRACTION99.98
1.68-1.730.21360.17814671X-RAY DIFFRACTION100
1.73-1.790.19861150.1724696X-RAY DIFFRACTION99.96
1.79-1.850.20311460.17784671X-RAY DIFFRACTION100
1.85-1.930.19611330.14754683X-RAY DIFFRACTION100
1.93-2.020.17191610.14774690X-RAY DIFFRACTION100
2.02-2.120.17751340.14194731X-RAY DIFFRACTION100
2.12-2.260.15341260.14994672X-RAY DIFFRACTION100
2.26-2.430.16691440.14284705X-RAY DIFFRACTION100
2.43-2.670.18021580.16034665X-RAY DIFFRACTION100
2.67-3.060.18921270.14964751X-RAY DIFFRACTION100
3.06-3.850.14171370.14014713X-RAY DIFFRACTION100
3.86-41.340.15611750.14084743X-RAY DIFFRACTION99.94
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)
12.852158278240.146724373796-0.3080066347962.92231697210.618208085653.63450637783-0.1786649509840.02185188213440.4900785855720.04179259493940.158121948762-0.290861407974-0.352583102730.6160594041180.02212440843420.199133939258-0.0453365196218-0.06113002153950.241766420663-0.01870741093320.28928967728865.97557971529.719871048259.79152770562
21.19504512172-0.1720079593090.18969993510.7359989394440.1014775807051.04082784086-0.0275402777265-0.0064153682085-0.08243712540640.00752035208542-0.01232554699170.01028503768550.0145476776354-0.05613442603950.03733922483740.1372763623720.0004514532819980.003765419592590.0842999091304-0.001792273545820.10590813525740.3584387816-2.218285589520.367960683994
31.71598332864-0.5714946455180.04327097699051.464575206440.1605170091663.711673119880.08083183026980.03492007625420.0438033270981-0.06425032228520.0112367141856-0.0645446134090.0208101188760.0500138679297-0.07971321267580.1155024726940.008647410286750.02803927108590.0890918786101-0.008631900787860.16360119972854.7648114508-16.5788757365-18.4868892316
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 75 )3 - 751 - 73
22chain 'A' and (resid 76 through 310 )76 - 31074 - 308
33chain 'A' and (resid 311 through 448 )311 - 448309 - 446

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