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- PDB-9pcs: Crystal structure of Dihydrodipicolinate Synthase from Mycobacter... -

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Basic information

Entry
Database: PDB / ID: 9pcs
TitleCrystal structure of Dihydrodipicolinate Synthase from Mycobacterium tuberculosis in complex with pyruvate
Components4-hydroxy-tetrahydrodipicolinate synthase
KeywordsLYASE / Complex / Substrate
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / plasma membrane / cytosol
Similarity search - Function
4-hydroxy-tetrahydrodipicolinate synthase, DapA / Schiff base-forming aldolase, conserved site / Dihydrodipicolinate synthase signature 1. / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase-type TIM barrel
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PYRUVIC ACID / 4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsRosa, L.V.S. / Dias, M.V.B.
Funding support Brazil, 5items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)22/03967-9 Brazil
Sao Paulo Research Foundation (FAPESP)20/03850-9 Brazil
Sao Paulo Research Foundation (FAPESP)22/12234-5 Brazil
Sao Paulo Research Foundation (FAPESP)2021/10577-0 Brazil
Sao Paulo Research Foundation (FAPESP)2024/22643-5 Brazil
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Crystal structure of dihydrodipicolinate synthase from Mycobacterium tuberculosis in complex with pyruvate and insights into allosteric regulation.
Authors: Rosa, L.V.S. / Blaszczyk, B. / Blundell, T. / Dias, M.V.B.
History
DepositionJun 29, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4-hydroxy-tetrahydrodipicolinate synthase
B: 4-hydroxy-tetrahydrodipicolinate synthase
C: 4-hydroxy-tetrahydrodipicolinate synthase
D: 4-hydroxy-tetrahydrodipicolinate synthase
E: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
G: 4-hydroxy-tetrahydrodipicolinate synthase
H: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,05458
Polymers247,1068
Non-polymers2,94850
Water49,4872747
1
A: 4-hydroxy-tetrahydrodipicolinate synthase
B: 4-hydroxy-tetrahydrodipicolinate synthase
C: 4-hydroxy-tetrahydrodipicolinate synthase
D: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,07929
Polymers123,5534
Non-polymers1,52625
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14400 Å2
ΔGint-106 kcal/mol
Surface area36680 Å2
MethodPISA
2
E: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
G: 4-hydroxy-tetrahydrodipicolinate synthase
H: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,97529
Polymers123,5534
Non-polymers1,42225
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13570 Å2
ΔGint-157 kcal/mol
Surface area37170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.470, 87.016, 141.059
Angle α, β, γ (deg.)90.00, 107.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

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


Mass: 30888.221 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: dapA, Rv2753c, MTV002.18c / Production host: Escherichia coli (E. coli)
References: UniProt: P9WP25, 4-hydroxy-tetrahydrodipicolinate synthase

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Non-polymers , 7 types, 2797 molecules

#2: Chemical
ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2747 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.26 Å3/Da / Density % sol: 45.7 % / Description: Thin plates
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 28% PEG4000, 170 mM MgCl2, 100 mM Tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.97718 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97718 Å / Relative weight: 1
ReflectionResolution: 1.5→47.86 Å / Num. obs: 347369 / % possible obs: 98.54 % / Redundancy: 6.6 % / Biso Wilson estimate: 15.68 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.03 / Rrim(I) all: 0.08 / Net I/σ(I): 13.97
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.663 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 11409 / CC1/2: 0.742 / CC star: 0.923 / Rpim(I) all: 0.307 / Rrim(I) all: 0.732 / % possible all: 90.76

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
pointless1.12.14data scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→47.86 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1685 3939 0.58 %
Rwork0.151 --
obs0.1511 347360 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→47.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17056 0 168 2747 19971
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00617769
X-RAY DIFFRACTIONf_angle_d0.89424256
X-RAY DIFFRACTIONf_dihedral_angle_d7.1172685
X-RAY DIFFRACTIONf_chiral_restr0.0552931
X-RAY DIFFRACTIONf_plane_restr0.0073185
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.31551270.272222339X-RAY DIFFRACTION91
1.52-1.540.3121370.25522837X-RAY DIFFRACTION92
1.54-1.560.2681270.240622991X-RAY DIFFRACTION93
1.56-1.580.25831410.223223409X-RAY DIFFRACTION95
1.58-1.60.21691410.206623603X-RAY DIFFRACTION96
1.6-1.630.18331320.19723915X-RAY DIFFRACTION97
1.63-1.650.17951170.187724237X-RAY DIFFRACTION98
1.65-1.680.20591600.180624570X-RAY DIFFRACTION99
1.68-1.710.2031540.181424662X-RAY DIFFRACTION100
1.71-1.740.19921340.177524524X-RAY DIFFRACTION100
1.74-1.770.23081260.176624714X-RAY DIFFRACTION100
1.77-1.810.20291700.175524623X-RAY DIFFRACTION100
1.81-1.850.21651360.176424635X-RAY DIFFRACTION100
1.85-1.890.20351330.164724686X-RAY DIFFRACTION100
1.89-1.940.18781430.157324682X-RAY DIFFRACTION100
1.94-1.990.16261410.148324744X-RAY DIFFRACTION100
1.99-2.050.18911480.148824563X-RAY DIFFRACTION100
2.05-2.110.17871320.147724718X-RAY DIFFRACTION100
2.11-2.190.16711570.144724594X-RAY DIFFRACTION100
2.19-2.280.17981430.142124671X-RAY DIFFRACTION100
2.28-2.380.16061400.142924628X-RAY DIFFRACTION100
2.38-2.510.17751410.142524643X-RAY DIFFRACTION100
2.51-2.660.14551350.145324646X-RAY DIFFRACTION100
2.66-2.870.16691470.146624715X-RAY DIFFRACTION100
2.87-3.160.16181420.140624583X-RAY DIFFRACTION100
3.16-3.610.11821440.128224653X-RAY DIFFRACTION100
3.61-4.550.10881460.117824531X-RAY DIFFRACTION99
4.55-47.860.17221450.144524487X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -5.9989 Å / Origin y: 0.1332 Å / Origin z: 41.8896 Å
111213212223313233
T0.1403 Å20.0051 Å20.004 Å2-0.145 Å20.006 Å2--0.1503 Å2
L0.0346 °20.0141 °20.0129 °2-0.0559 °20.0531 °2--0.0917 °2
S-0.0026 Å °0.0021 Å °0.0059 Å °-0.0161 Å °-0.0091 Å °0.0055 Å °-0.0071 Å °-0.0252 Å °0.013 Å °
Refinement TLS groupSelection details: all

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