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- PDB-2zj0: Crystal structure of Mycobacterium tuberculosis S-Adenosyl-L-homo... -

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Basic information

Entry
Database: PDB / ID: 2zj0
TitleCrystal structure of Mycobacterium tuberculosis S-Adenosyl-L-homocysteine hydrolase in ternary complex with NAD and 2-fluoroadenosine
ComponentsAdenosylhomocysteinase
KeywordsHYDROLASE / Protein-substrate complex / dimer of dimers / NAD binding domain / 37 amino acid insertional region / One-carbon metabolism
Function / homology
Function and homology information


adenosylhomocysteinase / L-methionine catabolic process / entry of bacterium into host cell / adhesion of symbiont to host cell / adenosine metabolic process / L-homocysteine biosynthetic process / adenosylhomocysteinase / adenosylhomocysteinase activity / S-adenosylmethionine cycle / zymogen binding ...adenosylhomocysteinase / L-methionine catabolic process / entry of bacterium into host cell / adhesion of symbiont to host cell / adenosine metabolic process / L-homocysteine biosynthetic process / adenosylhomocysteinase / adenosylhomocysteinase activity / S-adenosylmethionine cycle / zymogen binding / NAD+ binding / one-carbon metabolic process / peptidoglycan-based cell wall / extracellular region / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Adenosylhomocysteinase-like / Adenosylhomocysteinase-like / S-adenosyl-L-homocysteine hydrolase, conserved site / Adenosylhomocysteinase-like superfamily / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase signature 1. / S-adenosyl-L-homocysteine hydrolase signature 2. / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase, NAD binding domain ...Adenosylhomocysteinase-like / Adenosylhomocysteinase-like / S-adenosyl-L-homocysteine hydrolase, conserved site / Adenosylhomocysteinase-like superfamily / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase signature 1. / S-adenosyl-L-homocysteine hydrolase signature 2. / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-2FA / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Adenosylhomocysteinase / Adenosylhomocysteinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsReddy, M.C.M. / Gokulan, K. / Shetty, N.D. / Owen, J.L. / Ioerger, T.R. / Sacchettini, J.C.
CitationJournal: Protein Sci. / Year: 2008
Title: Crystal structures of Mycobacterium tuberculosis S-adenosyl-L-homocysteine hydrolase in ternary complex with substrate and inhibitors.
Authors: Reddy, M.C. / Kuppan, G. / Shetty, N.D. / Owen, J.L. / Ioerger, T.R. / Sacchettini, J.C.
History
DepositionFeb 29, 2008Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Aug 30, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Adenosylhomocysteinase
B: Adenosylhomocysteinase
C: Adenosylhomocysteinase
D: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,34412
Polymers217,5504
Non-polymers3,7958
Water12,809711
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20930 Å2
ΔGint-83.7 kcal/mol
Surface area64150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.254, 112.079, 100.451
Angle α, β, γ (deg.)90.00, 95.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Adenosylhomocysteinase / S-adenosyl-L-homocysteine hydrolase / AdoHcyase


Mass: 54387.410 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: ahcY, sahH, Rv3248c, MT3346, MTCY20B11.23c / Plasmid: pET28TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P60176, UniProt: P9WGV3*PLUS, adenosylhomocysteinase
#2: Chemical
ChemComp-2FA / 2-(6-AMINO-2-FLUORO-PURIN-9-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL / 2-FLUOROADENOSINE


Mass: 285.232 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H12FN5O4
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 711 / 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: 2.49 Å3/Da / Density % sol: 50.53 %
Crystal growTemperature: 291.5 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M Magnesium chloride, 0.1 M Tris-HCl pH 8.5, 25% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291.5K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.964 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 4, 2005 / Details: Mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.964 Å / Relative weight: 1
ReflectionResolution: 2.42→100 Å / Num. all: 74187 / Num. obs: 70373 / % possible obs: 91.9 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 35.92 Å2 / Rmerge(I) obs: 0.0809 / Rsym value: 0.0809 / Net I/σ(I): 10.52
Reflection shellResolution: 2.42→2.49 Å / Rmerge(I) obs: 0.406 / Rsym value: 0.406 / % possible all: 79.54

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3CE6

3ce6


Resolution: 2.42→33.15 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.889 / SU B: 10.628 / SU ML: 0.244 / Cross valid method: THROUGHOUT / ESU R: 0.769 / ESU R Free: 0.338 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27993 3728 5 %RANDOM
Rwork0.19373 ---
obs0.19804 70373 91.91 %-
all-70373 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.276 Å2
Baniso -1Baniso -2Baniso -3
1-2.49 Å20 Å20.33 Å2
2---1.09 Å20 Å2
3----1.34 Å2
Refinement stepCycle: LAST / Resolution: 2.42→33.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14996 0 256 711 15963
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02215578
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6991.97721176
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0151936
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.61424.798692
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.656152599
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1081584
X-RAY DIFFRACTIONr_chiral_restr0.1080.22368
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211748
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2420.28065
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.210422
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2788
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.270.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7021.59868
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.204215436
X-RAY DIFFRACTIONr_scbond_it1.96736585
X-RAY DIFFRACTIONr_scangle_it3.0744.55740
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.42→2.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 240 -
Rwork0.267 4454 -
obs--79.52 %

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