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- PDB-2xja: Structure of MurE from M.tuberculosis with dipeptide and ADP -

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Basic information

Entry
Database: PDB / ID: 2xja
TitleStructure of MurE from M.tuberculosis with dipeptide and ADP
ComponentsUDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE
KeywordsLIGASE / PEPTIDOGLYCAN / PEPTIDASE LIGASE
Function / homology
Function and homology information


UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase / UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / magnesium ion binding / ATP binding / plasma membrane ...UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase / UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / magnesium ion binding / ATP binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase / MurE/MurF, N-terminal domain / MurE/MurF, N-terminal / Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 / Mur ligase, N-terminal catalytic domain / Mur ligase family, catalytic domain / Mur ligase, C-terminal domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase family, glutamate ligase domain ...UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase / MurE/MurF, N-terminal domain / MurE/MurF, N-terminal / Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 / Mur ligase, N-terminal catalytic domain / Mur ligase family, catalytic domain / Mur ligase, C-terminal domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase family, glutamate ligase domain / Mur ligase, C-terminal domain superfamily / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / Protein-Tyrosine Phosphatase; Chain A / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-UAG / UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase / UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBasavannacharya, C. / Moody, P.R. / Bhakta, S. / Keep, N.
Citation
Journal: Protein Cell / Year: 2010
Title: Essential Residues for the Enzyme Activity of ATP-Dependent Mure Ligase from Mycobacterium Tuberculosis.
Authors: Basavannacharya, C. / Moody, P.R. / Munshi, T. / Cronin, N. / Keep, N.H. / Bhakta, S.
#1: Journal: Tuberculosis (Edinb) / Year: 2010
Title: ATP-Dependent Mure Ligase in Mycobacterium Tuberculosis: Biochemical and Structural Characterisation.
Authors: Basavannacharya, C. / Robertson, G. / Munshi, T. / Keep, N.H. / Bhakta, S.
History
DepositionJul 3, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE
B: UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE
C: UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE
D: UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,28922
Polymers221,8194
Non-polymers5,47018
Water724
1
A: UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8105
Polymers55,4551
Non-polymers1,3554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8346
Polymers55,4551
Non-polymers1,3805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8105
Polymers55,4551
Non-polymers1,3554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8346
Polymers55,4551
Non-polymers1,3805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.040, 76.320, 81.990
Angle α, β, γ (deg.)111.32, 91.42, 92.90
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
31D
41C
12B
22A
13B
23A
33C
43D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112B25 - 378
2112A25 - 378
3112D25 - 378
4112C25 - 378
1121B379 - 535
2121A379 - 535
1134B1400 - 1500
2134A1400 - 1500
3134C1400 - 1500
4134D1400 - 1500

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE / MURE / UDP-MURNAC-L-ALA-D-GLU\:MESO-DIAMINOPIMELATE LIGASE / MESO-DIAMINOPIMELATE-ADDING ENZYME / ...MURE / UDP-MURNAC-L-ALA-D-GLU\:MESO-DIAMINOPIMELATE LIGASE / MESO-DIAMINOPIMELATE-ADDING ENZYME / MESO-A2PM-ADDING ENZYME / UDP-N- ACETYLMURAMYL-TRIPEPTIDE SYNTHETASE / UDP-MURNAC-TRIPEPTIDE SYNTHETASE


Mass: 55454.625 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)/PLYSS
References: UniProt: P65477, UniProt: P9WJL3*PLUS, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-UAG / URIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE-D-GLUTAMATE


Mass: 879.608 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H43N5O23P2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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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: 1.96 Å3/Da / Density % sol: 37.4 % / Description: NONE
Crystal growpH: 8.5 / Details: 0.35 M MGCL2, 0.1 M TRIS PH 8.5, 16% PEG 8000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 3, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3→74.8 Å / Num. obs: 31925 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.1
Reflection shellResolution: 3→3.16 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.6 / % possible all: 95.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0077refinement
MOSFLMdata reduction
SCALAdata scaling
SCALAphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WTZ

2wtz


Resolution: 3→76.3 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.867 / SU B: 46.79 / SU ML: 0.399 / Cross valid method: THROUGHOUT / ESU R Free: 0.546 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1598 4.9 %RANDOM
Rwork0.189 ---
obs0.193 30876 95.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.12 Å2
Baniso -1Baniso -2Baniso -3
1-2.56 Å2-1.27 Å2-1.27 Å2
2---0.42 Å20.63 Å2
3----1.88 Å2
Refinement stepCycle: LAST / Resolution: 3→76.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14123 0 350 4 14477
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02214731
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8461.99420151
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.77151976
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.93122.481540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.153151991
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.15315141
X-RAY DIFFRACTIONr_chiral_restr0.1250.22452
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02111169
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4991.59709
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.926215385
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.57134899
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6084.54577
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
12A1336tight positional0.080.05
11B1336tight positional0.060.05
14C1336tight positional0.060.05
13D1336tight positional0.070.05
22A1027tight positional0.050.05
21B1027tight positional0.050.05
12A991medium positional0.080.5
11B991medium positional0.060.5
14C991medium positional0.060.5
13D991medium positional0.070.5
32A88medium positional0.280.5
31B88medium positional0.320.5
33C88medium positional0.30.5
34D88medium positional0.350.5
12A1336tight thermal2.44
11B1336tight thermal2.52
14C1336tight thermal2.78
13D1336tight thermal2.65
22A1027tight thermal2.23
21B1027tight thermal2.23
12A991medium thermal3.29
11B991medium thermal3.1
14C991medium thermal3.27
13D991medium thermal2.94
32A88medium thermal3.62
31B88medium thermal7.78
33C88medium thermal4.65
34D88medium thermal6.27
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 113 -
Rwork0.23 2286 -
obs--95.92 %
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)
17.0048-1.08781.72537.77041.01278.8993-0.0931-0.29710.1085-0.2613-0.0563-0.7513-0.12390.69640.14940.014-0.01830.02040.2720.05230.105327.46-5.346-1.37
25.53881.6027-0.69317.3502-0.86728.71460.02980.5415-0.30130.0493-0.0707-1.0346-0.10650.43810.04090.01230.02490.02460.22580.04980.249727.322-23.61120.754
37.60271.1033-0.70687.92380.28839.2897-0.04840.3646-0.36020.80570.34480.72161.2515-1.1276-0.29640.4645-0.2007-0.00270.24310.13540.3209-4.50222.44944.249
42.8009-1.00151.04986.6937-0.794111.98130.0561-0.38980.2878-0.38230.24160.7669-0.9732-0.8388-0.29770.37030.20780.17870.2490.10410.3503-4.384-2.2457.247
56.9759-1.46222.00363.0847-0.75933.39850.0859-0.1644-0.2096-0.15360.16810.69230.1951-0.3463-0.25390.2173-0.0466-0.07930.22040.06470.1935-4.074-3.134-7.755
67.79931.4914-3.26212.1613-0.09833.7644-0.030.05720.0894-0.029-0.01150.2393-0.2742-0.31310.04150.14490.0651-0.00780.19270.00350.0522-2.314-23.5131.621
76.7840.6634-0.05873.8804-0.9022.9168-0.3246-0.1460.29550.2815-0.002-0.5310.11220.36920.32660.30990.0625-0.1710.0989-0.03870.289926.15729.44544.209
85.1817-1.86570.86572.93020.32013.236-0.0916-0.0454-0.07150.10530.113-0.2551-0.32940.3204-0.02150.2678-0.13050.07360.1125-0.04510.21325.485-11.18552.441
910.9656-1.86330.00794.2417-0.70226.75920.42110.31150.9162-0.4021-0.0915-0.4766-0.54340.164-0.32960.46720.07740.24840.1659-0.02510.46-14.0015.0315.352
108.6932.0654-0.1327.5348-2.37558.80940.1185-0.3959-0.6769-0.0781-0.3271-0.37510.4430.39990.20860.3353-0.0177-0.09420.23560.04880.1828-14.984-31.7939.383
119.9094-0.1087-2.28045.02680.82126.52260.1650.38060.563-0.33920.22110.2738-0.3582-0.2427-0.3860.38130.11240.10090.44390.06230.259835.56311.66826.621
129.463-0.80296.48446.9895-2.203813.42960.5427-0.7399-0.4916-0.8396-0.07850.18791.8666-1.027-0.46420.6016-0.1886-0.02930.3199-0.05670.222439.1964.88768.722
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 139
2X-RAY DIFFRACTION2B26 - 139
3X-RAY DIFFRACTION3C26 - 139
4X-RAY DIFFRACTION4D26 - 139
5X-RAY DIFFRACTION5A140 - 379
6X-RAY DIFFRACTION5A1533 - 1535
7X-RAY DIFFRACTION6B140 - 379
8X-RAY DIFFRACTION6B1533 - 1537
9X-RAY DIFFRACTION7C140 - 379
10X-RAY DIFFRACTION7C1533 - 1536
11X-RAY DIFFRACTION8D140 - 379
12X-RAY DIFFRACTION8D1533 - 1537
13X-RAY DIFFRACTION9A380 - 533
14X-RAY DIFFRACTION10B380 - 533
15X-RAY DIFFRACTION11C380 - 533
16X-RAY DIFFRACTION12D380 - 533

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