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- PDB-1k0u: Inhibition of S-adenosylhomocysteine Hydrolase by "acyclic sugar"... -

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Basic information

Entry
Database: PDB / ID: 1k0u
TitleInhibition of S-adenosylhomocysteine Hydrolase by "acyclic sugar" Adenosine Analogue D-eritadenine
ComponentsS-ADENOSYL-L-HOMOCYSTEINE HYDROLASE
KeywordsHYDROLASE / S-adenosylhomocysteine / D-eritadenine / inhibitor
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
D-ERITADENINE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Adenosylhomocysteinase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsTakusagawa, F. / Huang, Y. / Komoto, J. / Takata, Y. / Gomi, T. / Ogawa, H. / Fujioka, M. / Powell, D.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Inhibition of S-adenosylhomocysteine hydrolase by acyclic sugar adenosine analogue D-eritadenine. Crystal structure of S-adenosylhomocysteine hydrolase complexed with D-eritadenine.
Authors: Huang, Y. / Komoto, J. / Takata, Y. / Powell, D.R. / Gomi, T. / Ogawa, H. / Fujioka, M. / Takusagawa, F.
History
DepositionSep 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2001Provider: repository / Type: Initial release
SupersessionMar 14, 2006ID: 1D4G
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S-ADENOSYL-L-HOMOCYSTEINE HYDROLASE
B: S-ADENOSYL-L-HOMOCYSTEINE HYDROLASE
C: S-ADENOSYL-L-HOMOCYSTEINE HYDROLASE
D: S-ADENOSYL-L-HOMOCYSTEINE HYDROLASE
E: S-ADENOSYL-L-HOMOCYSTEINE HYDROLASE
F: S-ADENOSYL-L-HOMOCYSTEINE HYDROLASE
G: S-ADENOSYL-L-HOMOCYSTEINE HYDROLASE
H: S-ADENOSYL-L-HOMOCYSTEINE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)387,05924
Polymers379,7268
Non-polymers7,33316
Water8,539474
1
A: S-ADENOSYL-L-HOMOCYSTEINE HYDROLASE
B: S-ADENOSYL-L-HOMOCYSTEINE HYDROLASE
C: S-ADENOSYL-L-HOMOCYSTEINE HYDROLASE
D: S-ADENOSYL-L-HOMOCYSTEINE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,52912
Polymers189,8634
Non-polymers3,6678
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25800 Å2
ΔGint-133 kcal/mol
Surface area50560 Å2
MethodPISA
2
E: S-ADENOSYL-L-HOMOCYSTEINE HYDROLASE
F: S-ADENOSYL-L-HOMOCYSTEINE HYDROLASE
G: S-ADENOSYL-L-HOMOCYSTEINE HYDROLASE
H: S-ADENOSYL-L-HOMOCYSTEINE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,52912
Polymers189,8634
Non-polymers3,6678
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26020 Å2
ΔGint-135 kcal/mol
Surface area50490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.87, 177.37, 112.16
Angle α, β, γ (deg.)90, 107.6, 90
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit contains two tetrameric enzymes, i.e., contains eight identical subunits.

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Components

#1: Protein
S-ADENOSYL-L-HOMOCYSTEINE HYDROLASE / ADENOSYLHOMOCYSTEINASE


Mass: 47465.711 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: P10760, adenosylhomocysteinase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-DEA / D-ERITADENINE


Mass: 253.215 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C9H11N5O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 474 / 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: 2.24 Å3/Da / Density % sol: 45.17 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: PEG 4000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 mMsodium D-eritadenine1drop
222 %(w/v)PEG40001drop
350 mMTris-HCl1drop
410 %(v/v)isopropyl alcohol1drop
510 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: Aug 20, 1999 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→10 Å / Num. all: 59076 / Num. obs: 56933 / % possible obs: 85 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 2.1 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 6.2
Reflection shellResolution: 3→3.1 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.19 / % possible all: 82
Reflection
*PLUS
Lowest resolution: 10 Å / Num. obs: 59048 / % possible obs: 91.5 % / Num. measured all: 241990

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1D4F

1d4f


Resolution: 3→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 5100 -RANDOM
Rwork0.183 ---
all0.231 56313 --
obs0.183 47879 85 %-
Displacement parametersBiso mean: 5.3 Å2
Baniso -1Baniso -2Baniso -3
1-5.3 Å20 Å20 Å2
2--5.3 Å20 Å2
3---5.3 Å2
Refine analyzeLuzzati sigma a obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26552 0 496 474 27522
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.12
X-RAY DIFFRACTIONx_dihedral_angle_d25.8
LS refinement shellResolution: 3→10 Å / Rfactor Rfree error: 0.01
RfactorNum. reflection% reflection
Rfree0.265 5100 -
Rwork0.208 --
obs-51000 85 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 10 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 5.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.8
LS refinement shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 10 Å / Rfactor Rfree: 0.265 / Rfactor Rwork: 0.208

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