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- PDB-3onf: Crystal structure of Lupinus luteus S-adenosyl-L-homocysteine hyd... -

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Basic information

Entry
Database: PDB / ID: 3onf
TitleCrystal structure of Lupinus luteus S-adenosyl-L-homocysteine hydrolase in complex with cordycepin
ComponentsAdenosylhomocysteinase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Plant protein / enzyme-inhibitor complex / NAD cofactor / Regulation of SAM-dependent methylation reactions / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


adenosylhomocysteinase / adenosylhomocysteinase activity / S-adenosylmethionine cycle / one-carbon metabolic process / 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'-DEOXYADENOSINE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Adenosylhomocysteinase
Similarity search - Component
Biological speciesLupinus luteus (yellow lupine)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBrzezinski, K. / Jaskolski, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: High-resolution structures of complexes of plant S-adenosyl-L-homocysteine hydrolase (Lupinus luteus).
Authors: Brzezinski, K. / Dauter, Z. / Jaskolski, M.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Purification, crystallization and preliminary crystallographic studies of plant S-adenosyl-L-homocysteine hydrolase (Lupinus luteus).
Authors: Brzezinski, K. / Bujacz, G. / Jaskolski, M.
#2: Journal: Acta Biochim.Pol. / Year: 2001
Title: Sequence determination and analysis of S-adenosyl-L-homocysteine hydrolase from yellow lupine (Lupinus luteus).
Authors: Brzezinski, K. / Janowski, R. / Podkowinski, J. / Jaskolski, M.
#3: Journal: Nat.Struct.Biol. / Year: 1998
Title: Structure determination of selenomethionyl S-adenosylhomocysteine hydrolase using data at a single wavelength.
Authors: Turner, M.A. / Yuan, C.S. / Borchardt, R.T. / Hershfield, M.S. / Smith, G.D. / Howell, P.L.
#4: Journal: Biochemistry / Year: 1999
Title: Crystal structure of S-adenosylhomocysteine hydrolase from rat liver.
Authors: Hu, Y. / Komoto, J. / Huang, Y. / Gomi, T. / Ogawa, H. / Takata, Y. / Fujioka, M. / Takusagawa, F.
#5: Journal: J.Mol.Biol. / Year: 2004
Title: Crystal structure of S-adenosyl-L-homocysteine hydrolase from the human malaria parasite Plasmodium falciparum.
Authors: Tanaka, N. / Nakanishi, M. / Kusakabe, Y. / Shiraiwa, K. / Yabe, S. / Ito, Y. / Kitade, Y. / Nakamura, K.T.
#6: Journal: Protein Sci. / Year: 2008
Title: Crystal structures of Mycobacterium tuberculosis S-adenosyl-L-homocysteine hydrolase in ternary complex with substrate and inhibitors.
Authors: Reddy, M.C. / Kuppan, G. / Shetty, N.D. / Owen, J.L. / Ioerger, T.R. / Sacchettini, J.C.
#7: Journal: MOL.PHYLOGENET.EVOL. / Year: 2005
Title: Bayesian phylogenetic analysis reveals two-domain topology of S-adenosylhomocysteine hydrolase protein sequences.
Authors: Stepkowski, T. / Brzezinski, K. / Legocki, A.B. / Jaskolski, M. / Bena, G.
History
DepositionAug 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Database references
Revision 1.2Feb 19, 2014Group: Database references
Revision 1.3Sep 6, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: Adenosylhomocysteinase
B: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,3449
Polymers107,3472
Non-polymers1,9977
Water11,476637
1
A: Adenosylhomocysteinase
B: Adenosylhomocysteinase
hetero molecules

A: Adenosylhomocysteinase
B: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,68818
Polymers214,6934
Non-polymers3,99514
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area29360 Å2
ΔGint-169 kcal/mol
Surface area62350 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10400 Å2
ΔGint-56 kcal/mol
Surface area35450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.623, 122.623, 126.622
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe asymmetric unit contains a dimer, which corresponds to the biological unit

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 53673.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lupinus luteus (yellow lupine) / Gene: SAHH, SHH, ssh-1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIPL / References: UniProt: Q9SP37, adenosylhomocysteinase

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Non-polymers , 5 types, 644 molecules

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


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-3AD / 3'-DEOXYADENOSINE


Mass: 251.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 637 / 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: 2.22 Å3/Da / Density % sol: 44.49 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG 4000, 10% isopropanol, 0.1 M Tris-HCl pH 8.0, 2 mM cordycepin, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 19, 2009
RadiationMonochromator: DOUBLE CRYSTAL SI(111), HORIZONTALLY FOCUSING
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 65547 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 10.5 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 17.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.686 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.4.0077refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V8B

1v8b


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.932 / SU B: 7.899 / SU ML: 0.098
Isotropic thermal model: Isotropic atomic displacement parameters
Cross valid method: R FREE / ESU R: 0.165 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGEN ATOMS WERE ADDED AT RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.201 1119 1.7 %RANDOM
Rwork0.156 ---
obs0.157 64344 99.8 %-
all-65729 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0.11 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7500 0 134 637 8271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0227953
X-RAY DIFFRACTIONr_bond_other_d0.0010.025330
X-RAY DIFFRACTIONr_angle_refined_deg1.4791.98610824
X-RAY DIFFRACTIONr_angle_other_deg1.2363.00213040
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.27851023
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.93525.06332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.944151406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5791534
X-RAY DIFFRACTIONr_chiral_restr0.0840.21232
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218792
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021476
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7561.54907
X-RAY DIFFRACTIONr_mcbond_other0.1841.52014
X-RAY DIFFRACTIONr_mcangle_it1.4342.57939
X-RAY DIFFRACTIONr_scbond_it3.57653046
X-RAY DIFFRACTIONr_scangle_it5.427102860
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 100 -
Rwork0.247 4659 -
obs--99.94 %
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)
10.6356-0.2431-0.29151.44830.80040.8661-0.0298-0.04380.17670.02150.04260.0245-0.13460.0456-0.01280.1094-0.0129-0.03560.03550.03340.10589.030844.7607-2.4922
20.5760.03210.21490.373-0.25020.9271-0.0245-0.05970.12320.0793-0.01010.0595-0.1457-0.06770.03470.0576-0.0087-0.01120.0218-0.01220.03365.303325.42329.0391
30.86650.56910.00132.17890.53760.7606-0.09270.06080.2245-0.2411-0.02760.3824-0.163-0.11580.12030.07830.0158-0.07360.08110.02210.1196-12.639325.0096-14.5283
41.444-0.35560.64211.1079-0.1680.75790.05320.0586-0.023-0.071-0.04530.27340.0716-0.19-0.00780.0379-0.03110.0280.1667-0.02990.1103-37.214-1.69290.2054
50.46090.1272-0.17910.720.16020.9443-0.0220.07170.0516-0.0804-0.01480.1112-0.0554-0.13750.03670.0211-0.0165-0.01760.06160.00030.021-17.00421.6307-10.3868
61.7250.3940.8241.17740.20851.1924-0.1209-0.28030.35620.1316-0.06540.2691-0.1998-0.23970.18630.11210.01950.02190.1123-0.06040.1497-18.494921.20212.1378
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 193
2X-RAY DIFFRACTION2A194 - 424
3X-RAY DIFFRACTION3A425 - 485
4X-RAY DIFFRACTION4B-2 - 193
5X-RAY DIFFRACTION5B194 - 424
6X-RAY DIFFRACTION6B425 - 485

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