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- PDB-5m67: Crystal structure of S-adenosyl-L-homocysteine hydrolase from Bra... -

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Basic information

Entry
Database: PDB / ID: 5m67
TitleCrystal structure of S-adenosyl-L-homocysteine hydrolase from Bradyrhizobium elkanii in complex with adenine and 2'-deoxyadenosine
ComponentsAdenosylhomocysteinase
KeywordsHYDROLASE / SAHase / SAH / SAM-dependent methylation / nitrogen fixation / symbiotic bacteria / NAD / conformational transition / molecular gate / adenine / 2`-deoxyadenosine
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
Chem-3D1 / ACETATE ION / ADENINE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Adenosylhomocysteinase
Similarity search - Component
Biological speciesBradyrhizobium elkanii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 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 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 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Aug 8, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set / Item: _pdbx_related_exp_data_set.data_reference
Revision 1.4Jan 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 / refine_hist / 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_auth_seq_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 / _refine_hist.d_res_high / _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)214,92722
Polymers210,9494
Non-polymers3,97818
Water38,8402156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29950 Å2
ΔGint-136 kcal/mol
Surface area57610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.484, 174.532, 96.620
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
11D-1096-

HOH

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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 , 7 types, 2174 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


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


Mass: 135.127 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5N5
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-3D1 / (2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol / 2'-DEOXYADENOSINE


Mass: 251.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2156 / 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: 2.16 Å3/Da / Density % sol: 43.11 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.3 M sodium acetate, 14% PEG 4000, 0.1 M Tris pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.969 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 1.54→43.633 Å / Num. obs: 268793 / % possible obs: 99.6 % / Redundancy: 9.3 % / Biso Wilson estimate: 15.59 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 15.41
Reflection shellResolution: 1.54→1.63 Å / Redundancy: 9.08 % / Rmerge(I) obs: 1.021 / Mean I/σ(I) obs: 2.19 / CC1/2: 0.693 / % possible all: 98.3

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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: 1.54→43.633 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 18.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1757 1009 0.38 %Random
Rwork0.1446 ---
obs0.1447 268768 99.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.54→43.633 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14444 0 266 2156 16866
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01615264
X-RAY DIFFRACTIONf_angle_d1.50620691
X-RAY DIFFRACTIONf_dihedral_angle_d15.2779160
X-RAY DIFFRACTIONf_chiral_restr0.092273
X-RAY DIFFRACTIONf_plane_restr0.0092641
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5354-1.61630.30061400.247337244X-RAY DIFFRACTION98
1.6163-1.71760.23761440.193238123X-RAY DIFFRACTION100
1.7176-1.85020.21531430.163438105X-RAY DIFFRACTION100
1.8502-2.03640.17051450.144438229X-RAY DIFFRACTION100
2.0364-2.33110.18571440.140538317X-RAY DIFFRACTION100
2.3311-2.93680.18971450.142838494X-RAY DIFFRACTION100
2.9368-43.65060.13551480.122839247X-RAY DIFFRACTION100
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)
10.50450.3841-0.15911.2798-0.35250.42720.0098-0.05560.00650.0501-0.01120.07880.0329-0.02840.00460.16740.0027-0.02750.12150.01390.17125.76451.566537.8486
20.3675-0.02030.05730.4593-0.0370.37960.0185-0.0654-0.04580.07620.0224-0.00390.0569-0.0651-0.0470.1083-0.0064-0.00580.09490.02180.099519.192921.183432.5048
31.11210.2545-0.0560.4845-0.00750.42990.0323-0.13670.05860.0366-0.04730.0254-0.0743-0.04250.01610.13590.0121-0.01050.1252-0.02720.081516.496558.769655.2338
42.39861.53310.78742.86960.5371.99230.0468-0.3507-0.10370.1684-0.0988-0.2636-0.04840.08690.04330.13420.0069-0.0290.22090.01020.13234.14555.044167.5121
50.210.2513-0.50880.9505-0.58222.87-0.0209-0.0924-0.04610.089-0.0689-0.04780.18130.15630.10930.11570.0296-0.01620.1525-0.00680.143726.380743.846449.4799
60.8169-0.27080.02471.35150.07350.59450.0025-0.03950.08670.03850.0032-0.1537-0.04310.0777-0.00520.1005-0.0013-0.02040.1192-0.0090.114437.900549.710935.3472
70.22980.45060.44982.12410.90650.8550.0571-0.134-0.00290.2567-0.08070.02630.1433-0.14690.00810.1438-0.00560.03180.18920.02350.106511.254133.483550.2996
81.23850.0676-0.40630.70130.09631.2624-0.04830.2864-0.0663-0.24270.06070.00240.0551-0.0155-0.01810.2309-0.0495-0.01810.1876-0.01110.114718.283817.8153-9.4682
93.303-2.0362-0.49912.6170.85683.17250.03840.4029-0.1781-0.4532-0.018-0.03280.01610.1099-0.01280.3531-0.13360.0550.302-0.01320.154128.76620.295-20.5208
100.9221-0.9193-0.86161.14690.24657.83460.01140.1290.1631-0.42410.0063-0.1757-0.22030.4088-0.07590.2789-0.06280.03330.20910.03130.19624.053535.764-9.9532
110.5302-0.04640.03891.6618-0.15330.55220.01580.0643-0.0168-0.05640.0052-0.17460.04680.0455-0.0220.10140.00230.01770.1129-0.00290.11736.178227.041210.4829
122.3138-0.0241-0.19761.37530.36380.24830.02110.39720.1838-0.46330.00110.0369-0.1156-0.0933-0.03280.2473-0.0028-0.02760.20350.04240.126711.134335.0284-8.6281
132.5307-1.07640.03362.3271-0.03910.87250.03670.24070.1824-0.1567-0.01630.1056-0.0753-0.0716-0.02720.13110.0049-0.03270.14280.00340.07895.216548.554.0884
141.0583-0.37850.21150.836-0.18680.6963-0.02060.14590.2478-0.0424-0.0285-0.0355-0.1627-0.05050.0360.20290.00310.00210.1420.05840.249921.552874.33149.1725
150.5054-0.1024-0.01580.3710.11790.3102-0.00350.05960.0813-0.0556-0.0036-0.0425-0.0642-0.0549-0.00020.11990.0133-0.00740.1080.02430.10717.05954.312415.1016
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 230 )
2X-RAY DIFFRACTION2chain 'A' and (resid 231 through 473 )
3X-RAY DIFFRACTION3chain 'B' and (resid 6 through 137 )
4X-RAY DIFFRACTION4chain 'B' and (resid 138 through 198 )
5X-RAY DIFFRACTION5chain 'B' and (resid 199 through 248 )
6X-RAY DIFFRACTION6chain 'B' and (resid 249 through 393 )
7X-RAY DIFFRACTION7chain 'B' and (resid 394 through 473 )
8X-RAY DIFFRACTION8chain 'C' and (resid 6 through 162 )
9X-RAY DIFFRACTION9chain 'C' and (resid 163 through 198 )
10X-RAY DIFFRACTION10chain 'C' and (resid 199 through 230 )
11X-RAY DIFFRACTION11chain 'C' and (resid 231 through 393 )
12X-RAY DIFFRACTION12chain 'C' and (resid 394 through 439 )
13X-RAY DIFFRACTION13chain 'C' and (resid 440 through 473 )
14X-RAY DIFFRACTION14chain 'D' and (resid 4 through 230 )
15X-RAY DIFFRACTION15chain 'D' and (resid 231 through 473 )

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