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- PDB-6dyy: Crystal structure of Helicobacter pylori 5'-methylthioadenosine/S... -

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Basic information

Entry
Database: PDB / ID: 6dyy
TitleCrystal structure of Helicobacter pylori 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with (3R,4S)-1-((4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl)-4-(((3-(1-butyl-1H-1,2,3-triazol-4-yl)propyl)thio)methyl)pyrrolidin-3-ol
Components5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / MTAN enzyme / duodenal ulcers / stomach cancer / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


aminodeoxyfutalosine nucleosidase / 6-amino-6-deoxyfutalosine hydrolase activity / adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / L-methionine salvage from S-adenosylmethionine / nucleoside catabolic process / L-methionine salvage from methylthioadenosine / menaquinone biosynthetic process / cytosol
Similarity search - Function
MTA/SAH nucleosidase / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-OS6 / adenosylhomocysteine nucleosidase / Aminodeoxyfutalosine nucleosidase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsHarijan, R.K. / Ducati, R.G. / Bonanno, J.B. / Almo, S.C. / Schramm, V.L.
CitationJournal: J. Med. Chem. / Year: 2019
Title: Selective Inhibitors of Helicobacter pylori Methylthioadenosine Nucleosidase and Human Methylthioadenosine Phosphorylase.
Authors: Harijan, R.K. / Hoff, O. / Ducati, R.G. / Firestone, R.S. / Hirsch, B.M. / Evans, G.B. / Schramm, V.L. / Tyler, P.C.
History
DepositionJul 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.2Apr 24, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
B: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
C: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
D: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,80917
Polymers107,5484
Non-polymers2,26113
Water16,015889
1
A: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
B: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,96010
Polymers53,7742
Non-polymers1,1868
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-36 kcal/mol
Surface area17730 Å2
MethodPISA
2
C: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
hetero molecules

D: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8497
Polymers53,7742
Non-polymers1,0755
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_475x-1/2,-y+5/2,-z1
Buried area4100 Å2
ΔGint-22 kcal/mol
Surface area17590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.564, 74.028, 176.887
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALGLUGLUAA1 - 22916 - 244
21VALVALGLUGLUBB1 - 22916 - 244
12VALVALGLUGLUAA1 - 22916 - 244
22VALVALGLUGLUCC1 - 22916 - 244
13GLNGLNLEULEUAA-1 - 23014 - 245
23GLNGLNLEULEUDD-1 - 23014 - 245
14VALVALLEULEUBB1 - 23016 - 245
24VALVALLEULEUCC1 - 23016 - 245
15VALVALGLUGLUBB1 - 22916 - 244
25VALVALGLUGLUDD1 - 22916 - 244
16VALVALGLUGLUCC1 - 22916 - 244
26VALVALGLUGLUDD1 - 22916 - 244

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase


Mass: 26886.875 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: BW246_00770, BZL55_04980, CEP79_03920 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A1W0VQJ9, UniProt: Q9ZMY2*PLUS, adenosylhomocysteine nucleosidase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-OS6 / (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-({[3-(1-butyl-1H-1,2,3-triazol-4-yl)propyl]sulfanyl}methyl)pyrrolidin-3-ol


Mass: 444.597 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H32N8OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 889 / 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: 2.2 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 200 mM calcium chloride, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 24, 2017 / Details: KB mirrors
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.61→88.44 Å / Num. obs: 123910 / % possible obs: 100 % / Redundancy: 7.4 % / CC1/2: 0.99 / Net I/σ(I): 11.4
Reflection shellResolution: 1.61→1.64 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5998 / CC1/2: 0.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4WKP

4wkp


Resolution: 1.61→88.44 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.941 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20328 6265 5.1 %RANDOM
Rwork0.17927 ---
obs0.18048 117541 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.601 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å20 Å2
2--1.88 Å20 Å2
3----1.47 Å2
Refinement stepCycle: 1 / Resolution: 1.61→88.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7042 0 154 894 8090
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0197388
X-RAY DIFFRACTIONr_bond_other_d0.0020.027086
X-RAY DIFFRACTIONr_angle_refined_deg1.491.9849950
X-RAY DIFFRACTIONr_angle_other_deg0.935316485
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7315934
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.43425.571289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.969151319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4171512
X-RAY DIFFRACTIONr_chiral_restr0.0850.21151
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028110
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021406
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_it1.3032.143727
X-RAY DIFFRACTIONr_mcbond_other1.3032.1393726
X-RAY DIFFRACTIONr_mcangle_it23.2034664
X-RAY DIFFRACTIONr_mcangle_other23.2034665
X-RAY DIFFRACTIONr_scbond_it2.0532.453661
X-RAY DIFFRACTIONr_scbond_other2.0532.4513662
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2613.5625287
X-RAY DIFFRACTIONr_long_range_B_refined4.88727.1288368
X-RAY DIFFRACTIONr_long_range_B_other4.88727.1338369
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A147980.05
12B147980.05
21A145720.06
22C145720.06
31A148060.05
32D148060.05
41B148820.06
42C148820.06
51B149120.06
52D149120.06
61C148860.05
62D148860.05
LS refinement shellResolution: 1.61→1.652 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 428 -
Rwork0.267 8590 -
obs--99.99 %

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