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- PDB-7o5m: Crystal structure of S-adenosyl-L-homocysteine hydrolase from Syn... -

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Basic information

Entry
Database: PDB / ID: 7o5m
TitleCrystal structure of S-adenosyl-L-homocysteine hydrolase from Synechocystis sp. PCC 6803 cocrystallized with adenosine in the presence of Na+ cations
ComponentsAdenosylhomocysteinase
KeywordsHYDROLASE / REGULATION OF SAM-DEPENDENT METHYLATION REACTIONS
Function / homology
Function and homology information


L-homocysteine biosynthetic process / adenosylhomocysteinase / adenosylhomocysteinase activity / S-adenosylmethionine cycle / one-carbon metabolic process / cytosol
Similarity search - Function
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 domain superfamily
Similarity search - Domain/homology
ADENOSINE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Adenosylhomocysteinase
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMalecki, P.H. / Imiolczyk, B. / Barciszewski, J. / Czyrko-Horczak, J. / Brzezinski, K.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2013/09/B/NZ1/01880 Poland
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Biochemical and structural insights into an unusual, alkali-metal-independent S-adenosyl-L-homocysteine hydrolase from Synechocystis sp. PCC 6803.
Authors: Malecki, P.H. / Imiolczyk, B. / Barciszewski, J. / Czyrko-Horczak, J. / Sliwiak, J. / Gawel, M. / Wozniak, K. / Jaskolski, M. / Brzezinski, K.
History
DepositionApr 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2022Group: 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 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenosylhomocysteinase
C: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4378
Polymers92,5342
Non-polymers1,9036
Water8,809489
1
A: Adenosylhomocysteinase
C: Adenosylhomocysteinase
hetero molecules

A: Adenosylhomocysteinase
C: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,87416
Polymers185,0674
Non-polymers3,80712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area25870 Å2
ΔGint-163 kcal/mol
Surface area52810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.770, 197.130, 82.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-862-

HOH

21A-903-

HOH

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Components

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Protein , 1 types, 2 molecules AC

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


Mass: 46266.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / Gene: ahcY, sll1234 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): CodonPlus(DE3)-RIPL / References: UniProt: P74008, adenosylhomocysteinase

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Non-polymers , 5 types, 495 molecules

#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4 / Feature type: SUBJECT OF INVESTIGATION
#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.: 489 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.64 Å3/Da / Density % sol: 53.49 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 7.5
Details: 0.2MSodium fluoride, 0.1MBis-Tris propane pH 7.5, 20% w/vPEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.89429 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jan 15, 2016
RadiationMonochromator: Single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89429 Å / Relative weight: 1
ReflectionResolution: 2.2→42.27 Å / Num. obs: 46913 / % possible obs: 93.3 % / Redundancy: 4.388 % / Biso Wilson estimate: 22.7 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.216 / Rrim(I) all: 0.243 / Χ2: 0.827 / Net I/σ(I): 5.92 / Num. measured all: 205840 / Scaling rejects: 26
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.2-2.262.9070.7971.327870368927070.5380.93673.4
2.26-2.323.2230.7421.569362358929050.5830.8680.9
2.32-2.383.4960.6681.8910941345131300.6920.76690.7
2.38-2.464.1820.6072.3613780340732950.7340.68996.7
2.46-2.544.6880.5612.815044327932090.8130.62997.9
2.54-2.634.6580.5073.0714588320331320.8210.56997.8
2.63-2.734.7130.4583.3514100306229920.8680.51497.7
2.73-2.844.6980.4083.8413610297428970.8860.45797.4
2.84-2.964.6970.3324.5913047285327780.9250.37297.4
2.96-3.114.7260.2835.212348269526130.950.31797
3.11-3.284.720.2256.3211900260425210.9650.25296.8
3.28-3.484.7270.1767.8711236246023770.9770.19796.6
3.48-3.724.7280.1419.5510624233222470.9840.15896.4
3.72-4.014.7430.11211.539762214420580.990.12596
4.01-4.44.7090.09313.098999199819110.9920.10495.6
4.4-4.924.7280.08414.728198182217340.9930.09495.2
4.92-5.684.7230.10811.897226161315300.990.12194.9
5.68-6.954.7060.1210.826099137812960.9890.13594
6.95-9.834.590.07416.014654109010140.9960.08393
9.83-42.274.3250.06719.724526425670.9910.07688.3

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Processing

Software
NameVersionClassification
PHENIX1.19refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ONF

3onf


Resolution: 2.2→42.27 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2487 1032 2.2 %
Rwork0.1924 45865 -
obs0.1936 46897 93.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.43 Å2 / Biso mean: 29.8547 Å2 / Biso min: 9.85 Å2
Refinement stepCycle: final / Resolution: 2.2→42.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6323 0 126 497 6946
Biso mean--21.94 31.14 -
Num. residues----827
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.310.30681210.24875356547777
2.31-2.460.29121460.23586476662293
2.46-2.650.29851530.21546803695698
2.65-2.920.23591530.21046798695197
2.92-3.340.30671520.19516789694197
3.34-4.20.19661530.15856783693696
4.2-42.270.22061540.17636860701494
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)
10.5371-0.3427-0.57781.663-0.20971.9964-0.0793-0.06760.15030.07320.0526-0.1371-0.00790.24520.02330.1059-0.0138-0.03970.2028-0.00520.187823.041471.982642.4912
25.81571.1309-1.11536.5942-0.53662.0237-0.1103-0.4848-0.08360.25250.05320.2034-0.25-0.090.07660.15750.0445-0.01880.1792-0.03130.168411.541382.931849.7967
30.66880.48180.13340.544-0.17490.6189-0.007-0.00360.12210.0176-0.07050.0395-0.0311-0.00850.08070.13410.00630.01010.1505-0.00020.14991.377470.116533.5679
42.12890.2485-0.21424.0218-0.83942.34270.0396-0.18710.06570.3243-0.04410.0783-0.0707-0.1093-0.00610.1428-0.01380.01940.201-0.03150.1155-7.974461.241746.3473
56.21632.3365-3.14351.2188-1.49371.92670.2237-0.3101-0.00840.1515-0.14830.0868-0.0620.1305-0.0920.2234-0.037-0.00870.181-0.0260.13710.431857.991148.2173
61.076-0.767-0.426.06582.16092.31230.08510.12690.1747-0.1614-0.1863-0.1306-0.30280.10610.0720.1277-0.0345-0.02570.17020.04250.172316.240680.860827.2866
76.1584-4.40681.31873.5551-0.77460.34620.19860.58410.6535-0.1444-0.3348-0.4567-0.26540.33620.07480.2425-0.01350.04590.17160.02830.281812.082775.9672.5183
80.5585-0.48410.34342.2980.97652.552-0.026-0.1561-0.09020.31310.081-0.3010.36130.2716-0.06330.3425-0.0149-0.01650.39140.0890.43611.329127.719745.4876
91.21140.10130.27330.53960.15760.71880.0148-0.0649-0.23940.0415-0.0278-0.05860.1876-0.00450.0240.17930.01420.01540.1350.01470.151111.586539.444628.4131
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 110 )A9 - 110
2X-RAY DIFFRACTION2chain 'A' and (resid 111 through 143 )A111 - 143
3X-RAY DIFFRACTION3chain 'A' and (resid 144 through 262 )A144 - 262
4X-RAY DIFFRACTION4chain 'A' and (resid 263 through 323 )A263 - 323
5X-RAY DIFFRACTION5chain 'A' and (resid 324 through 355 )A324 - 355
6X-RAY DIFFRACTION6chain 'A' and (resid 356 through 402 )A356 - 402
7X-RAY DIFFRACTION7chain 'A' and (resid 403 through 422 )A403 - 422
8X-RAY DIFFRACTION8chain 'C' and (resid 9 through 193 )C9 - 193
9X-RAY DIFFRACTION9chain 'C' and (resid 194 through 421 )C194 - 421

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