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- PDB-5m66: Crystal structure of S-adenosyl-L-homocysteine hydrolase from Bra... -

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Basic information

Entry
Database: PDB / ID: 5m66
TitleCrystal structure of S-adenosyl-L-homocysteine hydrolase from Bradyrhizobium elkanii in complex with adenosine
ComponentsAdenosylhomocysteinase
KeywordsHYDROLASE / SAHase / SAH / SAM-dependent methylation / nitrogen fixation / symbiotic bacteria / NAD / conformational transition / molecular gate / adenosine
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 / 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
ADENOSINE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Adenosylhomocysteinase
Similarity search - Component
Biological speciesBradyrhizobium elkanii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.951 Å
AuthorsManszewski, T. / Jaskolski, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
National Science Centre2013/10/MZ/NZ1/00251 Poland
Citation
Journal: IUCrJ / Year: 2017
Title: Crystallographic and SAXS studies of S-adenosyl-l-homocysteine hydrolase from Bradyrhizobium 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 8, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set / Item: _pdbx_related_exp_data_set.data_reference
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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

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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)215,29421
Polymers210,9494
Non-polymers4,34517
Water16,141896
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29670 Å2
ΔGint-129 kcal/mol
Surface area57950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.437, 173.622, 97.425
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 52737.238 Da / Num. of mol.: 4
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 , 5 types, 913 molecules

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


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N5O4
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 896 / 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: 2.13 Å3/Da / Density % sol: 42.37 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.3 sodium acetate, 16% PEG 4000, 0.1 M Tris pH 9.0

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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: Apr 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.95→46.9 Å / Num. obs: 130113 / % possible obs: 98.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 26.09 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 13.01
Reflection shellResolution: 1.96→2.07 Å / Redundancy: 3.67 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1.93 / CC1/2: 0.729 / % possible all: 96

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Processing

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

4lvc


Resolution: 1.951→46.9 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 22.41
Details: Riding H atoms were added. TLS parameters were included.
RfactorNum. reflection% reflectionSelection details
Rfree0.2108 1009 0.78 %Random
Rwork0.1694 ---
obs0.1698 130052 98.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.951→46.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14397 0 291 896 15584
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01715122
X-RAY DIFFRACTIONf_angle_d1.53920482
X-RAY DIFFRACTIONf_dihedral_angle_d17.4069067
X-RAY DIFFRACTIONf_chiral_restr0.0792288
X-RAY DIFFRACTIONf_plane_restr0.0092608
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9513-2.05420.28111380.244717654X-RAY DIFFRACTION96
2.0542-2.18290.3261440.218218369X-RAY DIFFRACTION100
2.1829-2.35140.24741430.20618389X-RAY DIFFRACTION99
2.3514-2.58810.21351440.181118497X-RAY DIFFRACTION100
2.5881-2.96250.23971460.174718563X-RAY DIFFRACTION100
2.9625-3.73220.211460.154218614X-RAY DIFFRACTION100
3.7322-46.9150.15741480.141918957X-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)
11.11510.7537-0.30171.8569-0.45780.77860.0458-0.1165-0.0437-0.0579-0.06860.09730.0757-0.0310.02140.22120.03450.00620.16790.04370.240525.60120.530737.5076
20.41250.0401-0.0960.75830.04360.48940.003-0.0829-0.02740.0271-0.03470.06570.0773-0.0590.02020.1824-0.0030.0220.16970.00910.17319.169120.816733.9036
31.73440.22920.22930.9958-0.040.78950.0331-0.2673-0.00120.1512-0.0775-0.0455-0.09680.06670.05460.2074-0.00460.00270.2585-0.0890.234121.566258.023459.3169
41.84141.49012.74512.86492.82567.26170.16420.0349-0.360.1810.1122-0.50320.18760.3576-0.20910.1884-0.0081-0.00070.2821-0.02350.303325.355541.627156.8573
50.75570.0030.07092.2979-0.41610.89360.0234-0.11170.15390.0271-0.0343-0.1285-0.11580.10780.00630.1457-0.0157-0.00270.1935-0.04140.189637.195649.309235.1717
60.42220.3566-0.32221.1689-0.16630.686-0.0083-0.1658-0.00760.1267-0.04410.05970.0028-0.01680.06560.16580.01420.01170.2328-0.03620.213214.813238.284248.7132
71.74320.0452-0.98991.06960.32221.8213-0.07650.4055-0.0451-0.3576-0.0028-0.08490.0061-0.1770.07680.4051-0.02990.02230.3072-0.02060.180620.532219.3299-11.2962
80.43080.04670.04821.2228-0.09590.74720.01030.13660.0101-0.1796-0.01-0.16720.05270.08040.01180.22280.0080.06630.17030.01360.167234.18228.12458.7485
90.933-0.27160.24361.57970.30080.7196-0.00550.27810.1483-0.4514-0.09110.1599-0.1066-0.05220.08650.32850.028-0.07190.26850.04320.19148.269941.5339-1.5712
101.6326-0.11070.70472.2831-0.14851.3766-0.14120.15140.4913-0.3674-0.00780.5181-0.4541-0.2410.09390.51330.0331-0.07220.29680.08460.635221.275974.27779.1262
110.6545-0.0823-0.22850.77790.29480.71860.01870.07640.1778-0.2225-0.04210.0154-0.1843-0.09660.01010.23780.0391-0.04280.16820.03430.202216.71854.316515.2857
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 210 )
2X-RAY DIFFRACTION2chain 'A' and (resid 211 through 473 )
3X-RAY DIFFRACTION3chain 'B' and (resid 6 through 190 )
4X-RAY DIFFRACTION4chain 'B' and (resid 191 through 233 )
5X-RAY DIFFRACTION5chain 'B' and (resid 234 through 373 )
6X-RAY DIFFRACTION6chain 'B' and (resid 374 through 473 )
7X-RAY DIFFRACTION7chain 'C' and (resid 6 through 210 )
8X-RAY DIFFRACTION8chain 'C' and (resid 211 through 393 )
9X-RAY DIFFRACTION9chain 'C' and (resid 394 through 473 )
10X-RAY DIFFRACTION10chain 'D' and (resid 6 through 230 )
11X-RAY DIFFRACTION11chain 'D' and (resid 231 through 473 )

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