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- PDB-1ky5: D244E mutant S-Adenosylhomocysteine hydrolase refined with noncry... -

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Basic information

Entry
Database: PDB / ID: 1ky5
TitleD244E mutant S-Adenosylhomocysteine hydrolase refined with noncrystallographic restraints
ComponentsS-adenosylhomocysteine hydrolase
KeywordsHYDROLASE / S-adenosylhomocysteine
Function / homology
Function and homology information


S-adenosylhomocysteine catabolic process / adenosylselenohomocysteinase activity / Sulfur amino acid metabolism / circadian sleep/wake cycle / adenyl nucleotide binding / chronic inflammatory response to antigenic stimulus / Methylation / adenosylhomocysteinase / adenosylhomocysteinase activity / S-adenosylmethionine cycle ...S-adenosylhomocysteine catabolic process / adenosylselenohomocysteinase activity / Sulfur amino acid metabolism / circadian sleep/wake cycle / adenyl nucleotide binding / chronic inflammatory response to antigenic stimulus / Methylation / adenosylhomocysteinase / adenosylhomocysteinase activity / S-adenosylmethionine cycle / one-carbon metabolic process / response to nutrient / NAD binding / melanosome / response to hypoxia / copper ion binding / endoplasmic reticulum / identical protein binding / nucleus / 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
3'-OXO-ADENOSINE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Adenosylhomocysteinase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTakata, Y. / Takusagawa, F.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Catalytic Mechanism of S-adenosylhomocysteine hydrolase. Site-directed mutagenesis of Asp-130, Lys-185, Asp-189, and Asn-190.
Authors: Takata, Y. / Yamada, T. / Huang, Y. / Komoto, J. / Gomi, T. / Ogawa, H. / Fujioka, M. / Takusagawa, F.
History
DepositionFeb 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S-adenosylhomocysteine hydrolase
B: S-adenosylhomocysteine hydrolase
C: S-adenosylhomocysteine hydrolase
D: S-adenosylhomocysteine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,64212
Polymers189,9194
Non-polymers3,7238
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27840 Å2
ΔGint-125 kcal/mol
Surface area51500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.00, 223.00, 91.20
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a homotetramer

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Components

#1: Protein
S-adenosylhomocysteine hydrolase / Adenosylhomocysteinase / AdoHcyase


Mass: 47479.738 Da / Num. of mol.: 4 / Mutation: D244E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: liver / Production host: Escherichia coli (E. coli) / References: UniProt: P10760, adenosylhomocysteinase
#2: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical
ChemComp-ADY / 3'-OXO-ADENOSINE


Mass: 265.225 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H11N5O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.44 Å3/Da / Density % sol: 49.49 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: PEG 6000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal grow
*PLUS
Temperature: 22 ℃
Details: used seeding, Komoto, J., (2000) J.Biol.Chem., 275, 32147.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 %(w/v)PEG40001reservoir
250 mMTris-HCl1reservoir
32 %(v/v)glycerol1reservoir
45 %(v/v)isopropanol1reservoir
51 mMdithiothreitol1reservoir
610 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 1, 2000 / Details: Yale mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 46142 / Num. obs: 43000 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 11
Reflection shellResolution: 2.8→2.92 Å / Redundancy: 3 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 5 / Num. unique all: 430 / Rsym value: 0.14 / % possible all: 83
Reflection
*PLUS
Rmerge(I) obs: 0.07
Reflection shell
*PLUS
Rmerge(I) obs: 0.14

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2929 4039 RANDOM
Rwork0.2151 --
all0.2211 40173 -
obs0.2155 36134 -
Refine analyzeLuzzati coordinate error obs: 0.04 Å
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13280 0 252 252 13784
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d27
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
2.8-2.920.35984300.25730.024401487
2.92-80.288336090.2120.0123212098
Refinement
*PLUS
Num. reflection Rfree: 4017 / Rfactor all: 0.2211 / Rfactor obs: 0.2155 / Rfactor Rfree: 0.287 / Rfactor Rwork: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27
LS refinement shell
*PLUS
Rfactor Rfree: 0.3598 / Rfactor Rwork: 0.2573

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