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- PDB-5m65: Crystal structure of S-adenosyl-L-homocysteine hydrolase from Bra... -

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Basic information

Entry
Database: PDB / ID: 5m65
TitleCrystal structure of S-adenosyl-L-homocysteine hydrolase from Bradyrhizobium elkanii in complex with adenine
ComponentsAdenosylhomocysteinase
KeywordsHYDROLASE / SAHase / SAH / SAM-dependent methylation / nitrogen fixation / symbiotic bacteria / NAD / conformational transition / molecular gate / adenine
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
ADENINE / BROMIDE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Adenosylhomocysteinase
Similarity search - Component
Biological speciesBradyrhizobium elkanii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.945 Å
AuthorsManszewski, T. / Jaskolski, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
National Science Centre2013/10/M/NZ1/00251 Poland
Citation
Journal: IUCrJ / Year: 2017
Title: Crystallographic and SAXS studies ofS-adenosyl-l-homocysteine hydrolase fromBradyrhizobium elkanii.
Authors: Manszewski, T. / Szpotkowski, K. / Jaskolski, M.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2015
Title: An enzyme captured in two conformational states: crystal structure of S-adenosyl-L-homocysteine hydrolase from Bradyrhizobium elkanii.
Authors: Manszewski, T. / Singh, K. / Imiolczyk, B. / Jaskolski, M.
#2: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2012
Title: High-resolution structures of complexes of plant S-adenosyl-L-homocysteine hydrolase (Lupinus luteus).
Authors: Brzezinski, K. / Dauter, Z. / Jaskolski, M.
#3: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
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.
#4: 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.
History
DepositionOct 24, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Aug 1, 2018Group: Data collection / Database references / Category: citation / pdbx_related_exp_data_set
Item: _citation.title / _pdbx_related_exp_data_set.data_reference / _pdbx_related_exp_data_set.data_set_type
Revision 1.3Jan 17, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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_conn.ptnr2_symmetry

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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)107,58815
Polymers105,4742
Non-polymers2,11313
Water10,269570
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10870 Å2
ΔGint-40 kcal/mol
Surface area33610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.665, 103.051, 90.654
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-713-

HOH

21A-835-

HOH

31A-852-

HOH

41A-863-

HOH

51A-882-

HOH

61B-684-

HOH

71B-851-

HOH

81B-883-

HOH

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 52737.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium elkanii (bacteria) / Gene: ahcY, BeSAHase / Production host: Escherichia coli (E. coli) / References: UniProt: A0A087WNH6, adenosylhomocysteinase

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Non-polymers , 6 types, 583 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-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5N5
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 570 / 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: 2.23 Å3/Da / Density % sol: 44.82 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.09 M halogens (iodine, bromide, chloride), 40% Ethylene glycol, 20% PEG 8000, 0.1 M imidazole, 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.945→45.87 Å / Num. obs: 69284 / % possible obs: 99.1 % / Redundancy: 4.1 % / Biso Wilson estimate: 20.22 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 10.06
Reflection shellResolution: 1.945→2.06 Å / Redundancy: 4.06 % / Rmerge(I) obs: 0.739 / Mean I/σ(I) obs: 2.17 / CC1/2: 0.729 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LVC

4lvc


Resolution: 1.945→45.866 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 21.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2125 1008 1.46 %random
Rwork0.1769 ---
obs0.1775 69240 99.04 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.945→45.866 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7241 0 132 570 7943
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087568
X-RAY DIFFRACTIONf_angle_d0.9810241
X-RAY DIFFRACTIONf_dihedral_angle_d18.0784551
X-RAY DIFFRACTIONf_chiral_restr0.0521140
X-RAY DIFFRACTIONf_plane_restr0.0061308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9448-2.04730.28431390.25469414X-RAY DIFFRACTION97
2.0473-2.17550.27571430.22369694X-RAY DIFFRACTION100
2.1755-2.34350.2791440.20439759X-RAY DIFFRACTION100
2.3435-2.57930.26571440.18859743X-RAY DIFFRACTION100
2.5793-2.95250.21251450.17849776X-RAY DIFFRACTION100
2.9525-3.71960.15651440.1619795X-RAY DIFFRACTION99
3.7196-45.87910.17851490.143410051X-RAY DIFFRACTION98
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)
10.56360.53190.10510.69550.20890.5366-0.08780.659-0.2363-0.09990.4491-0.20940.050.4857-0.00170.224-0.0423-0.00760.6412-0.13330.199924.53210.5687-20.6313
20.47350.27990.20830.2680.03210.35050.01280.5038-0.26290.01490.1387-0.21160.0680.2518-0.12590.1590.0839-0.01970.2707-0.14920.226511.8127-10.2733-6.9252
30.98310.36550.27130.55720.33321.47510.09290.10550.21120.07730.04670.054-0.09870.2289-0.1730.182-0.04090.02940.13480.01990.186120.879521.64461.814
40.90090.0523-0.02520.15470.26380.7840.2859-0.4090.05530.1452-0.1518-0.0755-0.18230.216-0.08290.3547-0.1916-0.03680.32830.00680.174525.58238.045737.0398
51.05720.70140.21630.4997-0.00720.80160.2922-0.23340.14370.1668-0.17340.0177-0.05420.1749-0.07380.2358-0.07860.03130.0632-0.03760.128111.66289.379220.7127
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 230 )
2X-RAY DIFFRACTION2chain 'A' and (resid 231 through 393 )
3X-RAY DIFFRACTION3chain 'A' and (resid 394 through 473 )
4X-RAY DIFFRACTION4chain 'B' and (resid 6 through 230 )
5X-RAY DIFFRACTION5chain 'B' and (resid 231 through 473 )

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