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- PDB-6s83: Crystal structure of methionine adenosyltransferase from Pyrococc... -

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Basic information

Entry
Database: PDB / ID: 6s83
TitleCrystal structure of methionine adenosyltransferase from Pyrococcus furiosus in complex with AMPPCP, SAM, and PCP
ComponentsS-adenosylmethionine synthase
KeywordsTRANSFERASE / S-adenosyl methionine synthesis / cofactor biosynthesis / cytoplasmic
Function / homology
Function and homology information


methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / one-carbon metabolic process / magnesium ion binding / ATP binding
Similarity search - Function
S-adenosylmethionine synthetase, N-terminal domain / S-adenosylmethionine synthetase, archaea / S-adenosylmethionine synthase / S-adenosylmethionine synthetase, domain 3 / S-adenosylmethionine synthetase (AdoMet synthetase) / GMP Synthetase; Chain A, domain 3 - #10 / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / METHYLENEDIPHOSPHONIC ACID / PHOSPHATE ION / S-ADENOSYLMETHIONINE / S-adenosylmethionine synthase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.336 Å
AuthorsDegano, M. / Minici, C. / Porcelli, M.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Association for Cancer Research Italy
CitationJournal: J.Struct.Biol. / Year: 2020
Title: Structures of catalytic cycle intermediates of the Pyrococcus furiosus methionine adenosyltransferase demonstrate negative cooperativity in the archaeal orthologues.
Authors: Minici, C. / Mosca, L. / Ilisso, C.P. / Cacciapuoti, G. / Porcelli, M. / Degano, M.
History
DepositionJul 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name
Revision 1.2Jan 24, 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_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 / _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: S-adenosylmethionine synthase
B: S-adenosylmethionine synthase
C: S-adenosylmethionine synthase
D: S-adenosylmethionine synthase
E: S-adenosylmethionine synthase
F: S-adenosylmethionine synthase
G: S-adenosylmethionine synthase
H: S-adenosylmethionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)359,50147
Polymers354,7098
Non-polymers4,79239
Water8,179454
1
A: S-adenosylmethionine synthase
B: S-adenosylmethionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,09313
Polymers88,6772
Non-polymers1,41511
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8530 Å2
ΔGint-84 kcal/mol
Surface area28860 Å2
MethodPISA
2
C: S-adenosylmethionine synthase
D: S-adenosylmethionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,67011
Polymers88,6772
Non-polymers9939
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7530 Å2
ΔGint-67 kcal/mol
Surface area29910 Å2
MethodPISA
3
E: S-adenosylmethionine synthase
F: S-adenosylmethionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,06812
Polymers88,6772
Non-polymers1,39110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8530 Å2
ΔGint-72 kcal/mol
Surface area28960 Å2
MethodPISA
4
G: S-adenosylmethionine synthase
H: S-adenosylmethionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,67011
Polymers88,6772
Non-polymers9939
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7590 Å2
ΔGint-71 kcal/mol
Surface area29750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.196, 111.430, 400.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 7 or resid 9...
21(chain B and (resid 2 through 7 or resid 9...
31(chain C and (resid 2 through 7 or resid 9...
41(chain D and (resid 2 through 7 or resid 9...
51(chain E and (resid 2 through 7 or resid 9...
61(chain F and (resid 2 through 7 or resid 9...
71(chain G and (resid 2 through 7 or resid 9...
81(chain H and (resid 2 through 7 or resid 9...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 2 through 7 or resid 9...A2 - 7
121(chain A and (resid 2 through 7 or resid 9...A9 - 58
131(chain A and (resid 2 through 7 or resid 9...A60
141(chain A and (resid 2 through 7 or resid 9...A62
151(chain A and (resid 2 through 7 or resid 9...A207 - 401
161(chain A and (resid 2 through 7 or resid 9...A0
171(chain A and (resid 2 through 7 or resid 9...A301 - 313
181(chain A and (resid 2 through 7 or resid 9...A315 - 351
191(chain A and (resid 2 through 7 or resid 9...A353 - 401
211(chain B and (resid 2 through 7 or resid 9...B2 - 7
221(chain B and (resid 2 through 7 or resid 9...B9 - 58
231(chain B and (resid 2 through 7 or resid 9...B0
241(chain B and (resid 2 through 7 or resid 9...B207 - 248
251(chain B and (resid 2 through 7 or resid 9...B301 - 313
261(chain B and (resid 2 through 7 or resid 9...B2 - 505
271(chain B and (resid 2 through 7 or resid 9...B301 - 313
281(chain B and (resid 2 through 7 or resid 9...B315 - 351
291(chain B and (resid 2 through 7 or resid 9...B353 - 401
311(chain C and (resid 2 through 7 or resid 9...C2 - 7
321(chain C and (resid 2 through 7 or resid 9...C9 - 58
331(chain C and (resid 2 through 7 or resid 9...C60
341(chain C and (resid 2 through 7 or resid 9...C2 - 205
351(chain C and (resid 2 through 7 or resid 9...C207 - 248
361(chain C and (resid 2 through 7 or resid 9...C2 - 505
371(chain C and (resid 2 through 7 or resid 9...C2 - 505
381(chain C and (resid 2 through 7 or resid 9...C2 - 505
391(chain C and (resid 2 through 7 or resid 9...C315 - 351
3101(chain C and (resid 2 through 7 or resid 9...C353 - 401
411(chain D and (resid 2 through 7 or resid 9...D2 - 7
421(chain D and (resid 2 through 7 or resid 9...D9 - 58
431(chain D and (resid 2 through 7 or resid 9...D60
441(chain D and (resid 2 through 7 or resid 9...D62
451(chain D and (resid 2 through 7 or resid 9...D207 - 504
461(chain D and (resid 2 through 7 or resid 9...D0
471(chain D and (resid 2 through 7 or resid 9...D301 - 313
481(chain D and (resid 2 through 7 or resid 9...D315 - 351
491(chain D and (resid 2 through 7 or resid 9...D353 - 401
511(chain E and (resid 2 through 7 or resid 9...E2 - 7
521(chain E and (resid 2 through 7 or resid 9...E9 - 58
531(chain E and (resid 2 through 7 or resid 9...E60
541(chain E and (resid 2 through 7 or resid 9...E62
551(chain E and (resid 2 through 7 or resid 9...E162 - 205
561(chain E and (resid 2 through 7 or resid 9...E207 - 248
571(chain E and (resid 2 through 7 or resid 9...E250 - 299
581(chain E and (resid 2 through 7 or resid 9...E301 - 313
591(chain E and (resid 2 through 7 or resid 9...E315 - 351
5101(chain E and (resid 2 through 7 or resid 9...E353 - 401
611(chain F and (resid 2 through 7 or resid 9...F2 - 7
621(chain F and (resid 2 through 7 or resid 9...F9 - 58
631(chain F and (resid 2 through 7 or resid 9...F60
641(chain F and (resid 2 through 7 or resid 9...F62
651(chain F and (resid 2 through 7 or resid 9...F162 - 205
661(chain F and (resid 2 through 7 or resid 9...F207 - 248
671(chain F and (resid 2 through 7 or resid 9...F250 - 299
681(chain F and (resid 2 through 7 or resid 9...F301 - 313
691(chain F and (resid 2 through 7 or resid 9...F315 - 351
6101(chain F and (resid 2 through 7 or resid 9...F353 - 401
711(chain G and (resid 2 through 7 or resid 9...G2 - 7
721(chain G and (resid 2 through 7 or resid 9...G9 - 58
731(chain G and (resid 2 through 7 or resid 9...G60
741(chain G and (resid 2 through 7 or resid 9...G62
751(chain G and (resid 2 through 7 or resid 9...G162 - 205
761(chain G and (resid 2 through 7 or resid 9...G207 - 248
771(chain G and (resid 2 through 7 or resid 9...G250 - 299
781(chain G and (resid 2 through 7 or resid 9...G301 - 313
791(chain G and (resid 2 through 7 or resid 9...G315 - 351
7101(chain G and (resid 2 through 7 or resid 9...G353 - 401
811(chain H and (resid 2 through 7 or resid 9...H2 - 7
821(chain H and (resid 2 through 7 or resid 9...H9 - 58
831(chain H and (resid 2 through 7 or resid 9...H60
841(chain H and (resid 2 through 7 or resid 9...H62
851(chain H and (resid 2 through 7 or resid 9...H162 - 205
861(chain H and (resid 2 through 7 or resid 9...H207 - 248
871(chain H and (resid 2 through 7 or resid 9...H250 - 299
881(chain H and (resid 2 through 7 or resid 9...H301 - 313
891(chain H and (resid 2 through 7 or resid 9...H315 - 351
8101(chain H and (resid 2 through 7 or resid 9...H353 - 401

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
S-adenosylmethionine synthase / AdoMet synthase / Methionine adenosyltransferase


Mass: 44338.660 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea)
Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: mat, PF1866 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8TZW1, methionine adenosyltransferase

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Non-polymers , 6 types, 493 molecules

#2: Chemical
ChemComp-MDN / METHYLENEDIPHOSPHONIC ACID


Mass: 176.002 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH6O6P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#6: Chemical
ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.46 Å3/Da / Density % sol: 49.98 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M Bis Tris pH 6.5, 5 mM MgCl2, 28% v/v PEG 600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2014 / Details: Mirrors
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.336→200.2 Å / Num. obs: 149431 / % possible obs: 100 % / Redundancy: 13.6 % / Biso Wilson estimate: 46.24 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.27 / Rpim(I) all: 0.076 / Rrim(I) all: 0.281 / Net I/σ(I): 6.9
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
2.34-2.4613.93.016300679215560.4510.8333.130.9
7.39-200.212.60.0926495351590.9960.0270.09622.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.2data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6S81

6s81


Resolution: 2.336→74.466 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.05
RfactorNum. reflection% reflection
Rfree0.2398 7500 5.03 %
Rwork0.2071 --
obs0.2088 149249 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 193.23 Å2 / Biso mean: 69.6637 Å2 / Biso min: 25.24 Å2
Refinement stepCycle: final / Resolution: 2.336→74.466 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24872 0 383 454 25709
Biso mean--79.14 47.75 -
Num. residues----3200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00925717
X-RAY DIFFRACTIONf_angle_d0.5134746
X-RAY DIFFRACTIONf_chiral_restr0.0474022
X-RAY DIFFRACTIONf_plane_restr0.0024492
X-RAY DIFFRACTIONf_dihedral_angle_d8.67315687
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A18841X-RAY DIFFRACTION9.867TORSIONAL
12B18841X-RAY DIFFRACTION9.867TORSIONAL
13C18841X-RAY DIFFRACTION9.867TORSIONAL
14D18841X-RAY DIFFRACTION9.867TORSIONAL
15E18841X-RAY DIFFRACTION9.867TORSIONAL
16F18841X-RAY DIFFRACTION9.867TORSIONAL
17G18841X-RAY DIFFRACTION9.867TORSIONAL
18H18841X-RAY DIFFRACTION9.867TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.3361-2.36260.4152330.36664712
2.3626-2.39040.38222280.35464621
2.3904-2.41960.36662500.35064690
2.4196-2.45020.38782560.33454638
2.4502-2.48250.37212740.32244634
2.4825-2.51650.33032540.29814687
2.5165-2.55240.32492460.2924641
2.5524-2.59050.31972410.27974709
2.5905-2.6310.33572480.2844658
2.631-2.67420.3072590.27974702
2.6742-2.72030.32542400.26364689
2.7203-2.76970.29962640.25834632
2.7697-2.8230.30282390.26484699
2.823-2.88060.31742350.25414715
2.8806-2.94330.30012450.24784694
2.9433-3.01170.30482500.244739
3.0117-3.08710.26672670.234651
3.0871-3.17050.25462660.22354672
3.1705-3.26380.27862500.22544735
3.2638-3.36920.22822430.21814705
3.3692-3.48960.24392270.2134763
3.4896-3.62930.23792460.19754698
3.6293-3.79450.23742500.18084742
3.7945-3.99450.19512620.16774778
3.9945-4.24480.19652460.16834730
4.2448-4.57250.17842550.15294795
4.5725-5.03250.16822500.14434801
5.0325-5.76050.21022610.17154798
5.7605-7.25660.21312580.18854896
7.2566-74.4660.18132570.17525125
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)
10.8995-0.27420.27270.9842-0.43472.3461-0.0062-0.0554-0.1144-0.02410.02280.09430.0959-0.113-0.0220.3167-0.0467-0.05980.36310.04830.4451-3.3091-22.629316.6484
21.2476-0.087-0.21490.75280.08742.6767-0.0128-0.16160.22220.0160.0445-0.0447-0.33890.1715-0.03620.30560.02050.01470.3381-0.00080.44986.1466-5.331468.9797
31.2143-0.1202-0.78070.96280.05172.99470.1418-0.21370.26360.1340.0531-0.1277-0.62330.4639-0.15880.4603-0.12870.01720.4108-0.05530.460342.0134-68.656484.5865
40.9827-0.18820.33030.9122-1.42673.3840.17180.05770.0695-0.2477-0.1092-0.01020.07190.2946-0.06290.4693-0.0362-0.00990.3450.04780.389848.8845-70.150833.3105
50.7172-0.2160.25430.59220.00812.7724-0.0029-0.0180.0628-0.0491-0.0474-0.0585-0.28460.21690.04880.3446-0.088-0.02930.35040.07670.412813.1813-5.270318.0004
61.006-0.2665-0.23161.0403-1.17352.98240.10680.1832-0.0492-0.49940.40940.36740.6932-0.7277-0.26240.7196-0.2545-0.24790.57430.16280.526727.7169-81.170531.8504
71.1144-0.262-1.2481.0850.70663.6223-0.03130.04840.0170.05650.08070.19480.0433-0.3948-0.03810.2425-0.0194-0.0080.40520.04940.405826.2737-85.952682.579
81.4271-0.4022-1.35530.71750.33593.2427-0.04710.15-0.07320.03620.0020.12020.2713-0.49950.02960.32790.00510.0250.49720.03330.4237-2.9108-27.099867.6431
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'C' and resid 2 through 401)C2 - 401
2X-RAY DIFFRACTION2(chain 'A' and resid 2 through 401)A2 - 401
3X-RAY DIFFRACTION3(chain 'B' and resid 2 through 401)B2 - 401
4X-RAY DIFFRACTION4(chain 'D' and resid 2 through 401)D2 - 401
5X-RAY DIFFRACTION5(chain 'E' and resid 2 through 401)E2 - 401
6X-RAY DIFFRACTION6(chain 'F' and resid 2 through 401)F2 - 401
7X-RAY DIFFRACTION7(chain 'G' and resid 2 through 401)G2 - 401
8X-RAY DIFFRACTION8(chain 'H' and resid 2 through 401)H2 - 401

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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