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- PDB-4xtu: Mycobacterium tuberculosis biotin ligase complexed with bisubstra... -

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Basic information

Entry
Database: PDB / ID: 4xtu
TitleMycobacterium tuberculosis biotin ligase complexed with bisubstrate inhibitor (N-({[(1R,2S,3R,4R)-4-(6-amino-9H-purin-9-yl)-2,3-dihydroxycyclopentyl]methyl}sulfamoyl)-5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamide)
ComponentsBifunctional ligase/repressor BirA
KeywordsLIGASE/LIGASE INHIBITOR / biotin-protein ligase / bisubstrate inhibitor / LIGASE-LIGASE INHIBITOR COMPLEX
Function / homology
Function and homology information


biotin-[biotin carboxyl-carrier protein] ligase / biotin--[biotin carboxyl-carrier protein] ligase activity / biotin binding / protein modification process / positive regulation of cell population proliferation / protein homodimerization activity / protein-containing complex / ATP binding / cytoplasm
Similarity search - Function
Biotin protein ligase, C-terminal / Biotin protein ligase C terminal domain / Biotin--acetyl-CoA-carboxylase ligase / Biotin/lipoate A/B protein ligase family / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain / SH3 type barrels. - #100 / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / SH3 type barrels. ...Biotin protein ligase, C-terminal / Biotin protein ligase C terminal domain / Biotin--acetyl-CoA-carboxylase ligase / Biotin/lipoate A/B protein ligase family / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain / SH3 type barrels. - #100 / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / SH3 type barrels. / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-44J / biotin--[biotin carboxyl-carrier protein] ligase / Biotin--[acetyl-CoA-carboxylase] ligase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65002988236 Å
AuthorsDe la Mora-Rey, T. / Finzel, B.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI091790-01 United States
Citation
Journal: To be Published
Title: Mycobacterium tuberculosis biotin ligase complexed with bisubstrate inhibitor (N-({[(1R,2S,3R,4R)-4-(6-amino-9H-purin-9-yl)-2,3-dihydroxycyclopentyl]methyl}sulfamoyl)-5-[(3aS,4S,6aR)-2- ...Title: Mycobacterium tuberculosis biotin ligase complexed with bisubstrate inhibitor (N-({[(1R,2S,3R,4R)-4-(6-amino-9H-purin-9-yl)-2,3-dihydroxycyclopentyl]methyl}sulfamoyl)-5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamide)
Authors: Bockman, M.R. / Kalinda, A.S. / Petrelli, R. / De la Mora-Rey, T. / Tawari, D. / Liu, F. / Schnappinger, D. / Finzel, B.C. / Aldrich, C.C.
#1: Journal: J.Med.Chem. / Year: 2015
Title: Targeting Mycobacterium tuberculosis Biotin Protein Ligase (MtBPL) with Nucleoside-Based Bisubstrate Adenylation Inhibitors.
Authors: Bockman, M.R. / Kalinda, A.S. / Petrelli, R. / De la Mora-Rey, T. / Tiwari, D. / Liu, F. / Dawadi, S. / Nandakumar, M. / Rhee, K.Y. / Schnappinger, D. / Finzel, B.C. / Aldrich, C.C.
History
DepositionJan 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bifunctional ligase/repressor BirA
B: Bifunctional ligase/repressor BirA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2084
Polymers57,0692
Non-polymers1,1392
Water10,287571
1
A: Bifunctional ligase/repressor BirA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1042
Polymers28,5341
Non-polymers5701
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bifunctional ligase/repressor BirA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1042
Polymers28,5341
Non-polymers5701
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.684, 68.735, 115.282
Angle α, β, γ (deg.)90.0, 90.0, 90.0
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
DetailsThe biological unit is a monomer

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Components

#1: Protein Bifunctional ligase/repressor BirA / Biotin--acetyl-CoA-carboxylase ligase / Biotin-protein ligase / BirA protein


Mass: 28534.428 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: birA, CH81_03124, CH82_03406, CH84_03412, CH85_03111, CH87_01691, CH88_02592, CO60_3782, ER17_17395, FF22_02902, FI98_01129, IQ38_01820, IQ39_01720, IQ40_01775, IQ41_01700, IQ42_01770, IQ43_ ...Gene: birA, CH81_03124, CH82_03406, CH84_03412, CH85_03111, CH87_01691, CH88_02592, CO60_3782, ER17_17395, FF22_02902, FI98_01129, IQ38_01820, IQ39_01720, IQ40_01775, IQ41_01700, IQ42_01770, IQ43_01710, IQ44_01750, IQ45_01765, IQ46_01705, IQ47_01735, IQ48_01770, IU12_01860, IU13_01785, IU14_01730, IU16_01770, IU17_01745, IU18_01730, IU19_01775, IU20_01750, IU22_01755, IU23_01750, IU24_01735, IZ84_17515, JE53_17495, LJ70_17695, T209_01770
Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): MACH I
References: UniProt: A0A045H8W3, UniProt: I6YFP0*PLUS, biotin-[biotin carboxyl-carrier protein] ligase
#2: Chemical ChemComp-44J / N-({[(1R,2S,3R,4R)-4-(6-amino-9H-purin-9-yl)-2,3-dihydroxycyclopentyl]methyl}sulfamoyl)-5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamide


Mass: 569.658 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H31N9O6S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 571 / 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: 2.21 Å3/Da / Density % sol: 44.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 17-24% PEG2000 MME, 100 mM Tris, pH 8.5, 100 mM triethylamine N-oxide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→115.282 Å / Num. obs: 60393 / % possible obs: 98 % / Redundancy: 6.7 % / Biso Wilson estimate: 16.8945173982 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 22.7 / Num. measured all: 401702
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
1.65-1.65670.4054.7411658897.2
7.658-115.28260.0284298715100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3RUX

3rux


Resolution: 1.65002988236→36.2926409498 Å / SU ML: 0.155321051552 / Cross valid method: FREE R-VALUE / σ(F): 1.35451531767 / Phase error: 21.0654598191
RfactorNum. reflection% reflectionSelection details
Rfree0.2132 3062 5.075 %Random selection
Rwork0.1814 57267 --
obs0.183 60329 97.9064898814 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.4277466564 Å2
Refinement stepCycle: LAST / Resolution: 1.65002988236→36.2926409498 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3925 0 76 571 4572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002597559842824144
X-RAY DIFFRACTIONf_angle_d0.9553025451765673
X-RAY DIFFRACTIONf_chiral_restr0.0331632791711670
X-RAY DIFFRACTIONf_plane_restr0.00351816993818749
X-RAY DIFFRACTIONf_dihedral_angle_d13.24803603731556
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.67580.27821300.23052550X-RAY DIFFRACTION96.472
1.6758-1.70330.2849556999611280.2172589622882555X-RAY DIFFRACTION97.1749366172
1.7033-1.73270.2599839371621370.2137956509432537X-RAY DIFFRACTION96.9191736136
1.7327-1.76420.2558110420471260.21957953942571X-RAY DIFFRACTION97.1191933741
1.7642-1.79810.2623275468641380.2160950908792538X-RAY DIFFRACTION97.238372093
1.7981-1.83480.2591450342151440.2046818785222552X-RAY DIFFRACTION97.5045207957
1.8348-1.87470.2670440364031360.2122313321462547X-RAY DIFFRACTION96.8242511729
1.8747-1.91830.2479992898791490.1976187928882559X-RAY DIFFRACTION97.7264525442
1.9183-1.96630.2236015296851390.1988800724442561X-RAY DIFFRACTION97.9680696662
1.9663-2.01940.2234120628051330.1985474090022586X-RAY DIFFRACTION97.981981982
2.0194-2.07880.2486801417861550.2041222402742574X-RAY DIFFRACTION97.7785739878
2.0788-2.14590.2293484222891210.1975539251772603X-RAY DIFFRACTION97.8448275862
2.1459-2.22260.2193159040761400.1915818676032598X-RAY DIFFRACTION97.9606440072
2.2226-2.31160.2335778876711270.18655376482606X-RAY DIFFRACTION98.1681034483
2.3116-2.41680.2119287972081410.1909874870642594X-RAY DIFFRACTION98.3459187343
2.4168-2.54420.2096727058531500.183048903812613X-RAY DIFFRACTION97.8746014878
2.5442-2.70350.2240235445121270.1890791353822623X-RAY DIFFRACTION98.8852930601
2.7035-2.91220.2276730998731420.1845743510252657X-RAY DIFFRACTION98.4869809993
2.9122-3.20510.1825535822121680.1746079068332619X-RAY DIFFRACTION98.86484569
3.2051-3.66850.1855658874791410.1676588226982664X-RAY DIFFRACTION98.6633837496
3.6685-4.62040.1730768489851430.1441733067352718X-RAY DIFFRACTION98.7914364641
4.6204-36.30140.1999647382281470.1622376848392842X-RAY DIFFRACTION99.2363877822

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