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- PDB-5tjz: Structure of 4-Hydroxytetrahydrodipicolinate Reductase from Mycob... -

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Basic information

Entry
Database: PDB / ID: 5tjz
TitleStructure of 4-Hydroxytetrahydrodipicolinate Reductase from Mycobacterium tuberculosis with NADPH and 2,6 Pyridine Dicarboxylic Acid
Components4-hydroxy-tetrahydrodipicolinate reductase
KeywordsOXIDOREDUCTASE / Lysine Biosynthesis
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate reductase / oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor / 4-hydroxy-tetrahydrodipicolinate reductase activity / NADH binding / diaminopimelate biosynthetic process / L-lysine biosynthetic process via diaminopimelate / NADPH binding / peptidoglycan-based cell wall / NAD binding / NADP binding ...4-hydroxy-tetrahydrodipicolinate reductase / oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor / 4-hydroxy-tetrahydrodipicolinate reductase activity / NADH binding / diaminopimelate biosynthetic process / L-lysine biosynthetic process via diaminopimelate / NADPH binding / peptidoglycan-based cell wall / NAD binding / NADP binding / plasma membrane / cytosol
Similarity search - Function
Dihydrodipicolinate reductase, conserved site / Dihydrodipicolinate reductase signature. / Dihydrodipicolinate reductase, C-terminal / Dihydrodipicolinate reductase / Dihydrodipicolinate reductase, C-terminus / Dihydrodipicolinate reductase, N-terminal / Dihydrodipicolinate reductase, N-terminus / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
2-(2-ETHOXYETHOXY)ETHANOL / BENZOIC ACID / IMIDAZOLE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / PYRIDINE-2,6-DICARBOXYLIC ACID / 4-hydroxy-tetrahydrodipicolinate reductase / 4-hydroxy-tetrahydrodipicolinate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMank, N.J. / Arnette, A.K. / Klapper, V. / Chruszcz, M.
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2021
Title: Comparative structural and mechanistic studies of 4-hydroxy-tetrahydrodipicolinate reductases from Mycobacterium tuberculosis and Vibrio vulnificus.
Authors: Pote, S. / Kachhap, S. / Mank, N.J. / Daneshian, L. / Klapper, V. / Pye, S. / Arnette, A.K. / Shimizu, L.S. / Borowski, T. / Chruszcz, M.
History
DepositionOct 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 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

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Assembly

Deposited unit
A: 4-hydroxy-tetrahydrodipicolinate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,67919
Polymers25,6821
Non-polymers1,99718
Water5,657314
1
A: 4-hydroxy-tetrahydrodipicolinate reductase
hetero molecules

A: 4-hydroxy-tetrahydrodipicolinate reductase
hetero molecules

A: 4-hydroxy-tetrahydrodipicolinate reductase
hetero molecules

A: 4-hydroxy-tetrahydrodipicolinate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,71776
Polymers102,7294
Non-polymers7,98872
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
crystal symmetry operation12_555x,x-y,-z+1/31
Buried area26870 Å2
ΔGint-198 kcal/mol
Surface area34860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.157, 67.157, 251.325
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-302-

BEZ

21A-302-

BEZ

31A-302-

BEZ

41A-303-

IMD

51A-460-

HOH

61A-509-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 4-hydroxy-tetrahydrodipicolinate reductase / HTPA reductase


Mass: 25682.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra) (bacteria)
Strain: ATCC 25177 / H37Ra / Gene: dapB, MRA_2798 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A5U6C6, UniProt: P9WP23*PLUS, 4-hydroxy-tetrahydrodipicolinate reductase

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Non-polymers , 9 types, 332 molecules

#2: Chemical ChemComp-PDC / PYRIDINE-2,6-DICARBOXYLIC ACID / DIPICOLINIC ACID


Mass: 167.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5NO4
#3: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#6: Chemical ChemComp-AE3 / 2-(2-ETHOXYETHOXY)ETHANOL


Mass: 134.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O3
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 3.19 Å3/Da / Density % sol: 61.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium Chloride, 0.1 M Bis-Tris pH 6.5, 1.5 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryostream
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 52243 / % possible obs: 95.1 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.054 / Net I/av σ(I): 42.436 / Net I/σ(I): 11.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.5-1.534.30.5370.792197.8
1.53-1.5550.4270.86197.8
1.55-1.5860.3880.874197.7
1.58-1.6270.350.924197.7
1.62-1.657.80.2990.952197.4
1.65-1.6980.2560.97197.2
1.69-1.738.10.210.977196.8
1.73-1.788.10.1720.984196.5
1.78-1.838.20.1350.99196.3
1.83-1.898.20.1120.993196
1.89-1.968.20.0910.996195.7
1.96-2.048.20.0730.997195.5
2.04-2.138.20.0640.998194.8
2.13-2.248.30.0550.998194.7
2.24-2.388.30.050.999194.3
2.38-2.568.20.0470.999194
2.56-2.828.20.0520.998193.4
2.82-3.238.20.0550.998192.1
3.23-4.078.30.0430.998190.8
4.07-307.90.040.997187.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data collection
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C3V

1c3v


Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.744 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.057
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1687 2565 4.9 %RANDOM
Rwork0.1476 ---
obs0.1486 49673 95.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 92.19 Å2 / Biso mean: 29.958 Å2 / Biso min: 17.13 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å2-0.13 Å2-0 Å2
2---0.26 Å2-0 Å2
3---0.84 Å2
Refinement stepCycle: final / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1807 0 127 314 2248
Biso mean--36.14 45.39 -
Num. residues----245
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192053
X-RAY DIFFRACTIONr_angle_refined_deg2.0362.022799
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4835266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.64823.84678
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.40115304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1141514
X-RAY DIFFRACTIONr_chiral_restr0.1470.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211543
X-RAY DIFFRACTIONr_mcbond_it1.121.7311027
X-RAY DIFFRACTIONr_mcangle_it1.7182.5951297
X-RAY DIFFRACTIONr_scbond_it2.3542.1561025
LS refinement shellResolution: 1.501→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 182 -
Rwork0.205 3623 -
all-3805 -
obs--96.5 %
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)
11.55410.04180.1272.0447-1.40312.0208-0.08760.3127-0.224-0.33510.07770.0150.1759-0.1320.00990.2132-0.0593-0.02150.1936-0.03790.03992.13717.8359.306
20.25310.1247-0.2980.2673-0.18930.43740.00920.01540.0413-0.03310.01060.0251-0.0696-0.0267-0.01990.1138-0.0356-0.01150.09530.00050.02434.33823.27926.668
31.6892-1.3542-2.25731.53461.57464.18650.0718-0.0130.2152-0.00930.065-0.1629-0.25760.031-0.13680.0984-0.04410.00230.0781-0.00670.05346.58319.10837.764
40.3140.01530.11040.3208-0.09490.6743-0.0088-0.01190.0442-0.02450.0133-0.024-0.0418-0.004-0.00450.0673-0.04830.00350.0978-0.00730.01644.9211.36738.37
52.82392.09030.18042.6233-1.87433.75850.1388-0.20330.36740.1950.01360.3676-0.1692-0.3129-0.15240.07460.01650.02470.09130.0010.0656-5.96526.95226.01
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 45
2X-RAY DIFFRACTION2A46 - 134
3X-RAY DIFFRACTION3A135 - 157
4X-RAY DIFFRACTION4A158 - 226
5X-RAY DIFFRACTION5A227 - 244

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