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- PDB-7zd2: Crystal structure of Pseudomonas aeruginosa S-adenosyl-L-homocyst... -

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Basic information

Entry
Database: PDB / ID: 7zd2
TitleCrystal structure of Pseudomonas aeruginosa S-adenosyl-L-homocysteine hydrolase inhibited by Co2+ ions.
ComponentsAdenosylhomocysteinase
KeywordsHYDROLASE / REGULATION OF SAM-DEPENDENT METHYLATION REACTIONS / INHIBITION / METAL BINDING / COBALT
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 ...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-BUTANEDIOL / : / HEXANE-1,6-DIOL / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 1,3-PROPANDIOL / Adenosylhomocysteinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsMalecki, P.H. / Gawel, M. / Brzezinski, K.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science CentreSONATA BIS 2018/30/E/NZ1/00729 Poland
CitationJournal: Chem.Commun.(Camb.) / Year: 2024
Title: A closer look at molecular mechanisms underlying inhibition of S -adenosyl-L-homocysteine hydrolase by transition metal cations.
Authors: Gawel, M. / Malecki, P.H. / Sliwiak, J. / Stepniewska, M. / Imiolczyk, B. / Czyrko-Horczak, J. / Jakubczyk, D. / Marczak, L. / Plonska-Brzezinska, M.E. / Brzezinski, K.
History
DepositionMar 29, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 30, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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 / _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
B: Adenosylhomocysteinase
C: Adenosylhomocysteinase
D: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,38439
Polymers206,9404
Non-polymers5,44335
Water31,1121727
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32940 Å2
ΔGint-212 kcal/mol
Surface area56870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.150, 134.210, 109.610
Angle α, β, γ (deg.)90.000, 106.080, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-510-

CL

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 51735.031 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: ahcY, sahH, PA0432 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: Q9I685, adenosylhomocysteinase

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Non-polymers , 9 types, 1762 molecules

#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


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


Mass: 267.241 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N5O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O2
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2
#8: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1727 / 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: 3.1 Å3/Da / Density % sol: 60.31 % / Description: 3-D plate
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.02 M 1,6-hexanediol, 0.02 M 1-butanol, 0.02 M (RS)-1,2-propanediol, 0.02 M 2-propanol, 0.02 M 1,4-butanediol, 0.02 M 1,3-propanediol, 10% w/v PEG 20 000, 20% v/v PEG MME 550, 0.1 M bicine/Trizma base pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Feb 1, 2021
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.16→29.32 Å / Num. obs: 130661 / % possible obs: 98.5 % / Redundancy: 3.111 % / Biso Wilson estimate: 29.74 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.134 / Rrim(I) all: 0.162 / Χ2: 0.839 / Net I/σ(I): 6.59 / Num. measured all: 406543 / Scaling rejects: 350
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
2.16-2.213.1160.8011.4129317974694100.6040.96596.6
2.21-2.273.1590.6471.8230124956995360.6850.77999.7
2.27-2.343.1530.5552.1629177927392550.7510.66999.8
2.34-2.413.1750.4732.4928452898189620.8040.56999.8
2.41-2.493.1560.4222.7427489872987090.8490.50999.8
2.49-2.583.170.3663.226724845784290.8680.4499.7
2.58-2.673.1590.3353.4225672814881260.8910.40399.7
2.67-2.783.1670.2564.4124781785978250.9310.30799.6
2.78-2.913.1570.215.1123604751574760.9590.25399.5
2.91-3.053.1570.1835.8622720723371960.9660.2299.5
3.05-3.213.1490.1437.1421445685368110.9790.17299.4
3.21-3.413.1270.1039.6620049646064120.9880.12499.3
3.41-3.643.0890.08211.6118660609660410.9920.09999.1
3.64-3.933.0640.06813.5217344572256610.9940.08198.9
3.93-4.313.0330.05915.5115559523051300.9950.07198.1
4.31-4.822.9970.0541713780473945980.9950.06597
4.82-5.562.9980.0615.311957419939880.9950.07295
5.56-6.812.9350.06214.559665352932930.9950.07593.3
6.81-9.642.7160.04617.696847276325210.9960.05791.2
9.64-29.322.4780.03720.663177155412820.9960.04682.5

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.19.2.4158refinement
PDB_EXTRACT3.27data extraction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F3M

6f3m


Resolution: 2.16→29.32 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2265 1045 0.8 %
Rwork0.1799 129518 -
obs0.1803 130563 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.29 Å2 / Biso mean: 37.2308 Å2 / Biso min: 16.69 Å2
Refinement stepCycle: final / Resolution: 2.16→29.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14208 0 315 1742 16265
Biso mean--34.71 42.04 -
Num. residues----1844
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 (%)
2.16-2.270.30841480.2606183511849998
2.27-2.410.28671510.22561864518796100
2.41-2.60.28861500.21161869218842100
2.6-2.860.22921510.19921869718848100
2.86-3.270.27511510.187186861883799
3.27-4.120.211500.155185901874099
4.12-29.320.1651440.1492178571800194
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)
12.08770.2050.15041.26780.27430.6212-0.02530.0925-0.3525-0.00870.01850.13050.2001-0.11840.00920.2737-0.07250.00610.2254-00.28587.4377-49.796228.8222
21.9780.3283-0.86860.8729-0.07730.3991-0.06260.38980.1696-0.14850.09360.18090.0238-0.0544-0.00740.2794-0.043-0.04040.29370.02660.21266.927-32.943923.8878
31.0629-0.5256-0.10780.9576-0.43360.6708-0.03120.3526-0.066-0.22140.01710.0410.0977-0.07950.01230.2936-0.076-0.03750.3558-0.0230.195417.6435-26.49418.7593
42.00420.10410.30031.6289-0.97713.7817-0.12440.6397-0.3686-0.5909-0.0677-0.22370.46270.02140.14580.4245-0.07180.05190.4104-0.0860.263723.2705-38.13926.3947
50.61490.57980.1271.1639-0.01640.29240.0332-0.14360.0450.2161-0.05980.28780.0472-0.15020.03540.2609-0.05660.04780.2863-0.01070.26171.4738-29.646840.2161
61.37990.683-0.05211.2011-0.11171.1029-0.16040.3418-0.4955-0.26060.1193-0.56110.2240.27480.03550.3357-0.0080.12360.3983-0.12790.512652.0625-39.393315.23
71.23040.6849-0.19512.0071-0.14560.78780.0032-0.1097-0.2360.1727-0.0213-0.29330.05990.10070.01710.21970.0009-0.03670.21890.0230.254338.5364-33.449839.2025
80.6102-0.84120.11051.1377-0.04130.7039-0.33150.5796-0.0301-0.36490.2661-0.8503-0.0410.46550.08060.331-0.08590.19040.5646-0.1170.663561.7822-28.315911.2856
91.0119-0.02230.15121.5342-0.30350.9338-0.02980.44510.0559-0.44420.0947-0.4301-0.20910.2331-0.06840.384-0.0910.09580.41160.00640.292648.2673-10.38478.7374
101.86010.3365-0.30870.70420.00260.4250.01070.03660.3144-0.03870.0361-0.076-0.12810.0865-0.04190.2787-0.0748-0.01130.2398-0.0010.3548.496111.5132.5785
111.1652-0.3148-0.15221.27650.74990.95890.0130.32390.2618-0.3833-0.0164-0.049-0.2517-0.0351-0.00230.355-0.0742-0.00690.33590.09030.265631.38461.895412.3448
120.80720.95220.07881.23740.23650.22020.0043-0.0731-0.13580.04420.041-0.37870.00720.1925-0.03890.2317-0.0426-0.04060.3008-0.00480.350856.7956-7.700336.5034
131.48730.49660.20031.3679-0.00461.0007-0.01650.05240.52810.0079-0.00820.4547-0.2788-0.31910.02040.3230.0598-0.01360.33890.02350.49071.78897.597931.3622
141.10940.42860.17652.07260.20260.5690.0388-0.17390.16680.3058-0.04970.1023-0.0088-0.0610.01960.2511-0.02930.02130.2208-0.03790.192820.9206-5.934546.9189
150.54240.11510.32381.65140.19531.01740.00670.10910.1014-0.1523-0.0580.5249-0.0524-0.33090.06220.2208-0.0172-0.07870.37710.04050.3612-3.3305-9.580720.0115
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 165 )A10 - 165
2X-RAY DIFFRACTION2chain 'A' and (resid 166 through 215 )A166 - 215
3X-RAY DIFFRACTION3chain 'A' and (resid 216 through 350 )A216 - 350
4X-RAY DIFFRACTION4chain 'A' and (resid 351 through 383 )A351 - 383
5X-RAY DIFFRACTION5chain 'A' and (resid 384 through 469 )A384 - 469
6X-RAY DIFFRACTION6chain 'B' and (resid 10 through 215 )B10 - 215
7X-RAY DIFFRACTION7chain 'B' and (resid 216 through 383 )B216 - 383
8X-RAY DIFFRACTION8chain 'B' and (resid 384 through 424 )B384 - 424
9X-RAY DIFFRACTION9chain 'B' and (resid 425 through 469 )B425 - 469
10X-RAY DIFFRACTION10chain 'C' and (resid 9 through 215 )C9 - 215
11X-RAY DIFFRACTION11chain 'C' and (resid 216 through 383 )C216 - 383
12X-RAY DIFFRACTION12chain 'C' and (resid 384 through 469 )C384 - 469
13X-RAY DIFFRACTION13chain 'D' and (resid 10 through 215 )D10 - 215
14X-RAY DIFFRACTION14chain 'D' and (resid 216 through 383 )D216 - 383
15X-RAY DIFFRACTION15chain 'D' and (resid 384 through 469 )D384 - 469

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