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- PDB-6buv: Structure of Mycobacterium tuberculosis NadD in complex with inhi... -

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Basic information

Entry
Database: PDB / ID: 6buv
TitleStructure of Mycobacterium tuberculosis NadD in complex with inhibitor [(1~{R},2~{R},5~{S})-5-methyl-2-propan-2-yl-cyclohexyl] 2-[3-methyl-2-(phenoxymethyl)benzimidazol-1-yl]ethanoate
Componentsnicotinate mononucleotide adenylyltransferase NadD
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Rossman fold / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


nicotinamide-nucleotide adenylyltransferase activity / nicotinate-nucleotide adenylyltransferase / nicotinate-nucleotide adenylyltransferase activity / NAD biosynthetic process / ATP binding
Similarity search - Function
Nicotinate/nicotinamide nucleotide adenylyltransferase / Cytidylyltransferase-like / Cytidyltransferase-like domain / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-E9A / Probable nicotinate-nucleotide adenylyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.86 Å
AuthorsRodionova, I.A. / Reed, R.W. / Sorci, L. / Osterman, A.L. / Korotkov, K.V.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R03AI117361 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103486 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM110787 United States
CitationJournal: Acs Chem.Biol. / Year: 2019
Title: Novel Antimycobacterial Compounds Suppress NAD Biogenesis by Targeting a Unique Pocket of NaMN Adenylyltransferase.
Authors: Osterman, A.L. / Rodionova, I. / Li, X. / Sergienko, E. / Ma, C.T. / Catanzaro, A. / Pettigrove, M.E. / Reed, R.W. / Gupta, R. / Rohde, K.H. / Korotkov, K.V. / Sorci, L.
History
DepositionDec 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3May 29, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.4Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry
Revision 2.0May 1, 2024Group: Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.formula / _chem_comp.name ..._chem_comp.formula / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: nicotinate mononucleotide adenylyltransferase NadD
B: nicotinate mononucleotide adenylyltransferase NadD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3409
Polymers44,7052
Non-polymers6367
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-63 kcal/mol
Surface area18100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.730, 163.730, 153.650
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein nicotinate mononucleotide adenylyltransferase NadD / Deamido-NAD(+) diphosphorylase / Deamido-NAD(+) pyrophosphorylase / Nicotinate mononucleotide ...Deamido-NAD(+) diphosphorylase / Deamido-NAD(+) pyrophosphorylase / Nicotinate mononucleotide adenylyltransferase / NaMN adenylyltransferase


Mass: 22352.281 Da / Num. of mol.: 2 / Mutation: C196R, C200T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: nadD, Rv2421c, MTCY428.26 / Plasmid: pRSF-NT / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta2(DE3)
References: UniProt: P9WJJ5, nicotinate-nucleotide adenylyltransferase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-E9A / 1-methyl-3-(2-{[(1R,2R,5S)-5-methyl-2-(propan-2-yl)cyclohexyl]oxy}-2-oxoethyl)-2-(phenoxymethyl)-1H-1,3-benzimidazol-3-ium


Mass: 435.578 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H35N2O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 4.43 Å3/Da / Density % sol: 72.25 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.1 M sodium/potassium phosphate, pH 6.2, 2.5 M sodium chloride
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 20, 2015
Details: Si(111). Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.86→52.102 Å / Num. obs: 65723 / % possible obs: 99.3 % / Redundancy: 3.773 % / Biso Wilson estimate: 33.35 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.09 / Χ2: 0.989 / Net I/σ(I): 11.08 / Num. measured all: 248001 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.86-1.913.761.1461.7248410.5471.329100
1.91-1.963.7720.8162.3547410.6620.94599.9
1.96-2.023.7760.6542.9246200.7440.758100
2.02-2.083.7890.5063.7244770.8410.586100
2.08-2.153.780.3615.0243290.9110.41899.9
2.15-2.223.7940.2846.1141850.940.32999.9
2.22-2.313.7940.2287.2240540.9610.26499.8
2.31-2.43.7940.1818.5839080.9730.2199.8
2.4-2.513.8080.1499.8837210.980.17299.5
2.51-2.633.8030.1211.4935970.9850.13999.6
2.63-2.773.8060.09813.1633820.9910.11499.5
2.77-2.943.8010.07815.4332040.9920.09199.2
2.94-3.143.780.06318.3730320.9940.07399.1
3.14-3.43.7650.05321.1428010.9950.06298.9
3.4-3.723.7570.04524.0225960.9960.05298.9
3.72-4.163.7280.04225.4123420.9960.04998.2
4.16-4.83.740.0427.2520570.9960.04797.8
4.8-5.883.6940.0426.8217360.9960.04796.9
5.88-8.323.6730.0426.8313540.9960.04796.4
8.32-52.1023.4640.04327.847460.9930.05292.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALENovember 3, 2014data scaling
PHASER2.5.7phasing
PHENIX1.13rc2_2975refinement
PDB_EXTRACT3.24data extraction
XDSNovember 3, 2014data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4S1O

4s1o


Resolution: 1.86→52.102 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0.9 / Phase error: 20.23
RfactorNum. reflection% reflectionSelection details
Rfree0.1918 5923 5.03 %RANDOM SELECTION
Rwork0.1706 ---
obs0.1716 65711 91.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 152.63 Å2 / Biso mean: 48.6118 Å2 / Biso min: 21.33 Å2
Refinement stepCycle: final / Resolution: 1.86→52.102 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2976 0 73 296 3345
Biso mean--66.72 49.56 -
Num. residues----380
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.86-1.88120.4572050.42413572377788
1.8812-1.90330.3722010.36493610381188
1.9033-1.92650.30972040.3233549375389
1.9265-1.95090.29832030.29093622382589
1.9509-1.97660.28831930.28833619381289
1.9766-2.00360.27141780.26893644382289
2.0036-2.03230.2461780.27333706388489
2.0323-2.06260.29281540.25753675382990
2.0626-2.09480.26351890.25283673386290
2.0948-2.12920.25211880.23783704389290
2.1292-2.16590.25281950.21313664385991
2.1659-2.20530.21192080.19813676388490
2.2053-2.24770.23141840.18943736392091
2.2477-2.29360.22512160.18853680389691
2.2936-2.34340.21441820.17453743392591
2.3434-2.39790.19441870.16743704389191
2.3979-2.45790.19331940.16493762395692
2.4579-2.52440.19952120.16623742395492
2.5244-2.59860.1812220.16123742396492
2.5986-2.68250.20291930.1763796398992
2.6825-2.77840.20082120.16993741395393
2.7784-2.88960.18492120.16643797400993
2.8896-3.02110.18031600.16223835399593
3.0211-3.18040.20462180.1713813403194
3.1804-3.37960.17582090.15543831404094
3.3796-3.64050.17052060.1383834404094
3.6405-4.00670.11732320.13113827405994
4.0067-4.58620.11831910.11823858404995
4.5862-5.7770.17081610.14253917407894
5.777-52.12210.23852360.18913822405894
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)
10.50290.1174-0.24212.10240.87452.4444-0.06710.0216-0.0465-0.0260.0224-0.1817-0.04610.15850.03470.20390.03480.02350.17650.02250.2192-6.659819.312264.1662
22.65170.15170.11471.898-0.45321.21110.12050.3719-0.2064-0.3178-0.1108-0.149-0.11620.0087-0.0090.33620.04780.01410.259-0.00210.2926-4.942913.785452.2647
31.00340.08040.24841.89460.93642.4020.0607-0.04140.0045-0.1365-0.0408-0.2503-0.25980.3175-0.03670.28790.02690.03130.2330.04010.3472-1.369330.092265.5305
42.25391.00250.86941.93110.26491.46350.0299-0.04080.05420.3496-0.0118-0.2165-0.33440.08580.00730.43870.01160.00350.24610.02210.2748-9.23547.678372.6054
51.41640.55180.29241.4113-0.14161.2131-0.12330.12350.25340.14930.07270.0205-0.5665-0.04810.03680.51490.06410.02390.28050.01840.3063-18.025752.139670.099
60.86550.0109-0.80135.9874-2.21921.73360.03330.0040.17740.42130.1720.4688-0.6483-0.1681-0.0530.58350.090.04130.25220.01010.3487-18.260854.596375.7435
73.9262-0.38671.47491.66180.62485.4505-0.0662-0.49660.26270.6418-0.0994-0.1313-0.1028-0.16990.10740.82130.03150.00580.3444-0.03990.3908-12.260162.918880.0749
81.2925-0.6541-0.12631.9039-1.58493.0198-0.10710.14230.18840.5014-0.1763-0.1581-0.32020.0650.30370.5423-0.048-0.03560.24460.03590.323-6.703759.901366.6921
92.081.33240.25625.15810.9423.3937-0.0747-0.11530.47640.6363-0.3023-0.0069-0.96740.03520.37410.7402-0.0934-0.09630.30050.01190.4352-3.340763.256970.8637
103.25420.863-1.39135.3291-0.71663.45150.07890.08870.44570.2325-0.1045-1.3533-0.72510.99310.03220.6057-0.0662-0.00890.46980.11840.69674.585756.900664.6204
111.34220.45320.53231.4766-0.10140.8863-0.03530.28690.113-0.27580.01490.0079-0.2163-0.0409-0.00120.3930.05920.01740.25940.02490.2711-16.07938.770459.9547
124.69330.23190.17626.4322-2.49186.9809-0.06170.2749-0.1246-0.18560.16520.4342-0.0131-0.90750.00640.36040.09280.00630.3614-0.01290.2867-27.103439.779365.1446
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 85 )A4 - 85
2X-RAY DIFFRACTION2chain 'A' and (resid 86 through 133 )A86 - 133
3X-RAY DIFFRACTION3chain 'A' and (resid 134 through 200 )A134 - 200
4X-RAY DIFFRACTION4chain 'B' and (resid 4 through 30 )B4 - 30
5X-RAY DIFFRACTION5chain 'B' and (resid 31 through 65 )B31 - 65
6X-RAY DIFFRACTION6chain 'B' and (resid 66 through 85 )B66 - 85
7X-RAY DIFFRACTION7chain 'B' and (resid 86 through 100 )B86 - 100
8X-RAY DIFFRACTION8chain 'B' and (resid 101 through 118 )B101 - 118
9X-RAY DIFFRACTION9chain 'B' and (resid 119 through 133 )B119 - 133
10X-RAY DIFFRACTION10chain 'B' and (resid 134 through 160 )B134 - 160
11X-RAY DIFFRACTION11chain 'B' and (resid 161 through 186 )B161 - 186
12X-RAY DIFFRACTION12chain 'B' and (resid 187 through 200 )B187 - 200

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