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- PDB-7zd4: Crystal structure of Pseudomonas aeruginosa S-adenosyl-L-homocyst... -

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Basic information

Entry
Database: PDB / ID: 7zd4
TitleCrystal structure of Pseudomonas aeruginosa S-adenosyl-L-homocysteine hydrolase soaked with Cu+ ions
ComponentsAdenosylhomocysteinase
KeywordsHYDROLASE / REGULATION OF SAM-DEPENDENT METHYLATION REACTIONS / INHIBITION / METAL BINDING / COPPER / DISULFIDE BOND
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 / BROMIDE ION / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Adenosylhomocysteinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.14 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 ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
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)211,37221
Polymers206,9404
Non-polymers4,43217
Water25,8341434
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31430 Å2
ΔGint-176 kcal/mol
Surface area55150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.680, 133.570, 107.040
Angle α, β, γ (deg.)90.000, 105.221, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11D-505-

BR

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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 , 6 types, 1451 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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#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-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1434 / 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: 2.93 Å3/Da / Density % sol: 57.99 % / Description: 3-D plate
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.03 M sodium fluoride, 0.03 M sodium bromide, 0.03 M sodium iodide, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.1 M MOPS/HEPES-Na pH 7.5

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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: Mar 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.14→35.29 Å / Num. obs: 127941 / % possible obs: 98 % / Redundancy: 3.792 % / Biso Wilson estimate: 34.106 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.191 / Rrim(I) all: 0.221 / Χ2: 0.821 / Net I/σ(I): 5.09
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.14-2.21.690.8031.0977240.5381.06180.1
2.2-2.262.7470.8451.3889440.6541.02395.6
2.26-2.323.9960.7921.8590950.6930.91399.7
2.32-2.44.1460.6662.1988570.7720.76699.9
2.4-2.474.1530.6232.3385810.810.71699.8
2.47-2.564.1510.5412.6683300.8270.623100
2.56-2.664.1370.5192.7679850.8450.59899.9
2.66-2.774.140.3963.577510.8880.45699.8
2.77-2.894.1370.3264.0573910.9260.37599.8
2.89-3.034.1250.284.6970980.9430.323100
3.03-3.194.1190.2275.667330.9650.26199.9
3.19-3.394.080.1757.1663430.9770.20199.9
3.39-3.623.9970.1468.5159850.9840.16999.7
3.62-3.913.9220.1219.7155900.9870.14199.4
3.91-4.293.9050.10111.0651500.9910.11699.5
4.29-4.793.8580.08712.2646290.9930.10199.6
4.79-5.533.7840.09311.0141080.9910.10799.4
5.53-6.783.6720.09210.2934650.9920.10799.6
6.78-9.583.3710.0612.926920.9960.07199.2
9.58-35.293.040.03815.1214900.9970.04697.3

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Processing

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

6f3m


Resolution: 2.14→35.29 Å / SU ML: 0.2562 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.0007
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2267 1023 0.8 %
Rwork0.1831 126805 -
obs0.1834 127828 97.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.56 Å2
Refinement stepCycle: LAST / Resolution: 2.14→35.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14204 0 289 1434 15927
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002514878
X-RAY DIFFRACTIONf_angle_d0.554920190
X-RAY DIFFRACTIONf_chiral_restr0.04352275
X-RAY DIFFRACTIONf_plane_restr0.00372726
X-RAY DIFFRACTIONf_dihedral_angle_d13.35515536
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.260.34141300.300616096X-RAY DIFFRACTION87.44
2.26-2.40.28441480.24118389X-RAY DIFFRACTION99.71
2.4-2.580.261490.222518417X-RAY DIFFRACTION99.94
2.58-2.840.20341490.218450X-RAY DIFFRACTION99.89
2.84-3.250.2231490.181518486X-RAY DIFFRACTION99.91
3.25-4.10.22051480.149718430X-RAY DIFFRACTION99.63
4.1-35.290.19351500.155518537X-RAY DIFFRACTION99.21
Refinement TLS params.Method: refined / Origin x: 27.5789908827 Å / Origin y: -16.6178591426 Å / Origin z: 26.1650939867 Å
111213212223313233
T0.21996109898 Å2-0.00646176995789 Å2-0.00943724777813 Å2-0.213678399712 Å20.014143727048 Å2--0.169602951945 Å2
L0.665292042629 °20.22190934716 °2-0.0134426670277 °2-0.562850489907 °20.00206756633202 °2--0.333812673075 °2
S0.000416282090001 Å °0.0100285567861 Å °0.0106986967834 Å °-0.0116955784063 Å °-0.00945693939005 Å °-0.00199238500511 Å °-0.0199954311981 Å °0.00433021631778 Å °0.00818576728616 Å °
Refinement TLS groupSelection details: all

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