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- PDB-7q8e: Crystal Structure of the MurT-GatD Enzyme Complex from Staphyloco... -

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Basic information

Entry
Database: PDB / ID: 7q8e
TitleCrystal Structure of the MurT-GatD Enzyme Complex from Staphylococcus aureus COL strain
Components
  • Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD
  • Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT
KeywordsLIGASE / Essential Glutamine Amidotransferase / Glutaminase/Ligase / Bacterial Peptidoglycan Amidation.
Function / homology
Function and homology information


lipid II isoglutaminyl synthase (glutamine-hydrolysing) / carbon-nitrogen ligase activity on lipid II / acid-amino acid ligase activity / glutaminase / cobalamin biosynthetic process / glutaminase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / zinc ion binding / ATP binding
Similarity search - Function
Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT, C-terminal / Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT / MurT ligase C-terminal / CobB/CobQ-like glutamine amidotransferase / Cobyric acid synthase, glutamine amidotransferase type 1 / Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD / CobB/CobQ-like glutamine amidotransferase domain / CobBQ-type GATase domain profile. / Mur ligase, central / Mur-like, catalytic domain superfamily ...Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT, C-terminal / Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT / MurT ligase C-terminal / CobB/CobQ-like glutamine amidotransferase / Cobyric acid synthase, glutamine amidotransferase type 1 / Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD / CobB/CobQ-like glutamine amidotransferase domain / CobBQ-type GATase domain profile. / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD / Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus COL (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.90001720351 Å
AuthorsLeisico, F. / Romao, M.J. / Santos-Silva, T.
Funding support Portugal, 4items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPD/BD/105737/2014 Portugal
Fundacao para a Ciencia e a TecnologiaUIDP/04378/2020 Portugal
Fundacao para a Ciencia e a TecnologiaUIDB/04378/2020 Portugal
Fundacao para a Ciencia e a TecnologiaLA/P/0140/2020 Portugal
CitationJournal: To Be Published
Title: Crystal Structure of the MurT-GatD Enzyme Complex from Staphylococcus aureus COL strain
Authors: Leisico, F. / Romao, M.J. / Santos-Silva, T.
History
DepositionNov 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT
C: Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT
B: Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD
D: Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,7747
Polymers155,6084
Non-polymers1663
Water1,35175
1
A: Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT
B: Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9054
Polymers77,8042
Non-polymers1012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT
D: Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8703
Polymers77,8042
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.094, 111.094, 112.424
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPGLUGLUchain 'A'AA38 - 43338 - 433
221ASPASPGLUGLUchain 'C'CB38 - 43338 - 433
132METMETARGARGchain 'B'BC1 - 2431 - 243
242METMETARGARGchain 'D'DD1 - 2431 - 243

NCS ensembles :
ID
1
2

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Components

#1: Protein Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT


Mass: 49264.910 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus COL (bacteria)
Gene: murT, SACOL1951 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0H2WZQ7, lipid II isoglutaminyl synthase (glutamine-hydrolysing)
#2: Protein Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD / Lipid II isoglutaminyl synthase glutaminase subunit


Mass: 28539.184 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus COL (bacteria)
Gene: gatD, SACOL1950 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0H2WZ38, lipid II isoglutaminyl synthase (glutamine-hydrolysing), glutaminase
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.09 Å3/Da / Density % sol: 42.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30 % (w/v) PEG 4,000, 100 mM Tris-HCl pH 8.5 and 200 mM MgCl2;

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 2.9→49.31 Å / Num. obs: 30388 / % possible obs: 99.99 % / Redundancy: 6.9 % / Biso Wilson estimate: 62.9479579287 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.113 / Net I/σ(I): 6.7
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 17 / Num. unique obs: 4366 / CC1/2: 0.58 / Rpim(I) all: 0.696 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GS2

6gs2


Resolution: 2.90001720351→49.3089437971 Å / SU ML: 0.442344360262 / Cross valid method: FREE R-VALUE / σ(F): 1.33648315019 / Phase error: 30.4477447237
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.264522858175 1492 4.92539284299 %Random selection
Rwork0.239532981111 28800 --
obs0.2407687704 30292 99.7398834414 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.5780373074 Å2
Refinement stepCycle: LAST / Resolution: 2.90001720351→49.3089437971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10056 0 3 75 10134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0018964829501610234
X-RAY DIFFRACTIONf_angle_d0.48569217531513812
X-RAY DIFFRACTIONf_chiral_restr0.04311318451021536
X-RAY DIFFRACTIONf_plane_restr0.004370218969741800
X-RAY DIFFRACTIONf_dihedral_angle_d13.43061449736168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.90001720351-2.99360.3956820996251470.3735009094022547X-RAY DIFFRACTION99.70392302
2.9936-3.10060.4333466451511270.3739630268922586X-RAY DIFFRACTION99.926335175
3.1006-3.22470.386231984221150.3329704858132618X-RAY DIFFRACTION99.8903508772
3.2247-3.37140.3276522177511070.2940587942412618X-RAY DIFFRACTION99.7437774524
3.3714-3.54910.3013743308381690.2667550504882543X-RAY DIFFRACTION99.9263080324
3.5491-3.77140.307533155311650.2529836892152577X-RAY DIFFRACTION99.636627907
3.7714-4.06250.2262868016531410.2346829859812597X-RAY DIFFRACTION99.8177178272
4.0625-4.47110.2448571071940.2087741842832660X-RAY DIFFRACTION99.7464686708
4.4711-5.11750.236681467311320.2008182705572631X-RAY DIFFRACTION99.5675675676
5.1175-6.44520.2136967065211410.2273163640142664X-RAY DIFFRACTION99.9287495547
6.4452-49.30894379710.2085291650871540.1884735954692759X-RAY DIFFRACTION99.31810433
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)
12.166853004840.7309248425030.3223163573964.497572462770.7437650195161.392716998180.09821071569070.243318345275-0.399020912305-0.3877805225810.12865851149-0.02192956762430.2759138551770.0980260748818-0.2428368504370.459017330970.0220709387254-0.1045522838630.546139889366-0.08249891964280.43821411163643.06339606122.13213558021.7354449144
21.684550751311.05055020646-0.2534741172224.89245303552-1.122974049531.033407015180.007547075888350.2091366023980.277001137664-0.354576702386-0.01153266303671.024936685560.00932518829992-0.07276895376160.02368558897760.4433896854550.01824841325-0.1785059623320.568656850544-0.05033644840110.83219560880812.0166790723-2.858837280253.91663369558
33.22216873245-0.05518558035370.7735288685973.690858446860.6273152848813.65381419698-0.0119977047627-0.2988730565890.04359768887130.562990996307-0.3391179334150.7320047829550.213783691941-0.5104418386160.1396414046610.53278221324-0.0747068179890.1687163308440.451390037088-0.1226356742570.71549183724831.179129639939.769444105326.8708801111
42.54953679936-0.4806660458870.1004713832313.098233416620.6986829499614.74813399914-0.14744227291-0.213387370910.2048225911070.1988660857870.007046695250740.1547810376470.04225188697530.2446773501720.1765275788020.4563911802080.02563959770640.006719016167160.417909025458-0.06678376382430.73261449457227.180566153-40.596290949827.0000242424
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 38 through 434)
2X-RAY DIFFRACTION2(chain 'C' and resid 38 through 433)
3X-RAY DIFFRACTION3(chain 'B' and resid 1 through 243)
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 243)

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