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- PDB-5tow: Crystal structure of the inactive form of S-adenosyl-L-homocystei... -

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Basic information

Entry
Database: PDB / ID: 5tow
TitleCrystal structure of the inactive form of S-adenosyl-L-homocysteine hydrolase from Thermotoga maritima in ternary complex with NADH and Adenosine
ComponentsAdenosylhomocysteinase
KeywordsHYDROLASE / REGULATION OF SAM-DEPENDENT METHYLATION REACTIONS
Function / homology
Function and homology information


adenosylhomocysteinase / adenosylhomocysteinase activity / S-adenosylmethionine cycle / one-carbon metabolic process / 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
ADENOSINE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Adenosylhomocysteinase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsCzyrko, J. / Brzezinski, K.
Funding support Poland, 1items
OrganizationGrant numberCountry
National Science Centre, PolandUMO-2013/09/B/NZ1/01880 Poland
CitationJournal: Int. J. Biol. Macromol. / Year: 2017
Title: S-adenosyl-L-homocysteine hydrolase from a hyperthermophile (Thermotoga maritima) is expressed in Escherichia coli in inactive form - Biochemical and structural studies.
Authors: Brzezinski, K. / Czyrko, J. / Sliwiak, J. / Nalewajko-Sieliwoniuk, E. / Jaskolski, M. / Nocek, B. / Dauter, Z.
History
DepositionOct 19, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.2Jan 17, 2024Group: 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: Adenosylhomocysteinase
B: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,4797
Polymers90,3582
Non-polymers1,1225
Water10,467581
1
A: Adenosylhomocysteinase
B: Adenosylhomocysteinase
hetero molecules

A: Adenosylhomocysteinase
B: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,95914
Polymers180,7154
Non-polymers2,24410
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area21060 Å2
ΔGint-178 kcal/mol
Surface area56150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.381, 105.509, 85.535
Angle α, β, γ (deg.)90.00, 108.76, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 45178.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ...Details: SNAMNTGEMKINWVSRYMPLLNKIAEEYSREKPLSGFTVGMSIHLEAKTAYLAITLSKLGAKVVITGSNPLSTQDDVAEALRSKGITVYARRTHDESIYRENLMKVLDERPDFIIDDGGDLTVISHTEREEVLENLKGVSEETTTGVRRLKALEETGKLRVPVIAVNDSKMKYLFDNRYGTGQSTWDAIMRNTNLLVAGKNVVVAGYGWCGRGIALRAAGLGARVIVTEVDPVKAVEAIMDGFTVMPMKEAVKIADFVITASGNTDVLSKEDILSLKDGAVLANAGHFNVEIPVRVLEEIAVEKFEARPNVTGYTLENGKTVFLLAEGRLVNLAAGDGHPVEIMDLSFALQIFAVLYLLENHRKMSPKVYMLPDEIDERVARMKLDSLGVKIDELTEKQRRYLRSWQ
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: ahcY, TM_0172 / Plasmid: pMCSG9 / Details (production host): pMCSG9 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): CodonPlus RIPL / References: UniProt: O51933, adenosylhomocysteinase

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Non-polymers , 5 types, 586 molecules

#2: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 581 / 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: 2.9 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2 M CaCl2, 0.1 M sodium acetate pH 4.6 and 30% (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 101542 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 21.92
Reflection shellResolution: 1.75→1.81 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LI4

1li4


Resolution: 1.75→30 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / SU B: 4.178 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.087 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18812 1169 1.2 %RANDOM
Rwork0.16551 ---
obs0.16577 100299 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 39.529 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å2-0 Å2-0.68 Å2
2--0.36 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5943 0 73 581 6597
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0196417
X-RAY DIFFRACTIONr_bond_other_d0.0020.026331
X-RAY DIFFRACTIONr_angle_refined_deg1.6741.9748758
X-RAY DIFFRACTIONr_angle_other_deg1.021314541
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3375868
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.70223.636253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.624151154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6021552
X-RAY DIFFRACTIONr_chiral_restr0.1060.21046
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027384
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021382
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9563.2463257
X-RAY DIFFRACTIONr_mcbond_other1.9553.2463256
X-RAY DIFFRACTIONr_mcangle_it2.7787.2794087
X-RAY DIFFRACTIONr_mcangle_other2.7797.2794088
X-RAY DIFFRACTIONr_scbond_it2.8473.6713160
X-RAY DIFFRACTIONr_scbond_other2.8473.6723161
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3288.0244633
X-RAY DIFFRACTIONr_long_range_B_refined7.25515.6967605
X-RAY DIFFRACTIONr_long_range_B_other7.12915.1347345
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å
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)
11.63970.745-0.20083.0212-1.18982.8278-0.03520.15180.0437-0.1321-0.0823-0.26810.01160.34070.11750.04740.04650.00660.11840.01840.039925.321296.490414.7486
21.21421.07491.16562.86951.53633.5552-0.04320.24530.1344-0.41250.03160.0644-0.43870.1790.01160.11690.02880.01170.08110.03150.036158.281978.584123.9483
30.5253-0.42331.04622.3319-0.96223.2248-0.0923-0.13340.11520.48310.043-0.1354-0.3360.10280.04940.1341-0.0010.00930.1901-0.06220.073925.099795.559934.586
42.65941.35840.07771.55470.17191.2664-0.01960.1265-0.09040.0288-0.02210.10.0689-0.20130.04170.09390.0614-0.01930.1216-0.06060.05444.770946.797514.3187
51.1540.04350.92893.1748-1.00033.05470.17680.0598-0.0821-0.4049-0.14520.17560.1899-0.1391-0.03150.08380.0386-0.03970.0383-0.02360.020225.978263.022529.4493
60.93420.46831.0910.5872-0.07313.04220.1572-0.0571-0.18910.1077-0.0082-0.00550.2796-0.0638-0.14910.1120.05490.01170.06770.00960.141357.380746.87530.6515
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 169
2X-RAY DIFFRACTION2A175 - 331
3X-RAY DIFFRACTION3A332 - 400
4X-RAY DIFFRACTION4B1 - 172
5X-RAY DIFFRACTION5B173 - 329
6X-RAY DIFFRACTION6B330 - 404

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