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- PDB-5l6v: Crystal structure of E. coli ADP-glucose pyrophosphorylase (AGPas... -

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Basic information

Entry
Database: PDB / ID: 5l6v
TitleCrystal structure of E. coli ADP-glucose pyrophosphorylase (AGPase) in complex with a negative allosteric regulator adenosine monophosphate (AMP) - AGPase*AMP
ComponentsGlucose-1-phosphate adenylyltransferase
KeywordsTRANSFERASE
Function / homology
Function and homology information


glucose-1-phosphate adenylyltransferase complex / glucose-1-phosphate adenylyltransferase / glucose-1-phosphate adenylyltransferase activity / glycogen biosynthetic process / AMP binding / protein homotetramerization / magnesium ion binding / ATP binding / identical protein binding
Similarity search - Function
Glucose-1-phosphate adenylyltransferase GlgC, bacterial / ADP-glucose pyrophosphorylase, conserved site / Glucose-1-phosphate adenylyltransferase / ADP-glucose pyrophosphorylase signature 1. / ADP-glucose pyrophosphorylase signature 2. / ADP-glucose pyrophosphorylase signature 3. / Nucleotidyl transferase domain / Nucleotidyl transferase / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 ...Glucose-1-phosphate adenylyltransferase GlgC, bacterial / ADP-glucose pyrophosphorylase, conserved site / Glucose-1-phosphate adenylyltransferase / ADP-glucose pyrophosphorylase signature 1. / ADP-glucose pyrophosphorylase signature 2. / ADP-glucose pyrophosphorylase signature 3. / Nucleotidyl transferase domain / Nucleotidyl transferase / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Trimeric LpxA-like superfamily / 3 Solenoid / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
sucrose / ADENOSINE MONOPHOSPHATE / PHOSPHATE ION / Glucose-1-phosphate adenylyltransferase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.667 Å
AuthorsCifuente, J.O. / Albesa-Jove, D. / Comino, N. / Madariaga-Marcos, J. / Agirre, J. / Lopez-Fernandez, S. / Garcia-Alija, M. / Guerin, M.E.
CitationJournal: Structure / Year: 2016
Title: Structural Basis of Glycogen Biosynthesis Regulation in Bacteria.
Authors: Cifuente, J.O. / Comino, N. / Madariaga-Marcos, J. / Lopez-Fernandez, S. / Garcia-Alija, M. / Agirre, J. / Albesa-Jove, D. / Guerin, M.E.
History
DepositionMay 31, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucose-1-phosphate adenylyltransferase
B: Glucose-1-phosphate adenylyltransferase
C: Glucose-1-phosphate adenylyltransferase
D: Glucose-1-phosphate adenylyltransferase
E: Glucose-1-phosphate adenylyltransferase
F: Glucose-1-phosphate adenylyltransferase
G: Glucose-1-phosphate adenylyltransferase
H: Glucose-1-phosphate adenylyltransferase
I: Glucose-1-phosphate adenylyltransferase
J: Glucose-1-phosphate adenylyltransferase
K: Glucose-1-phosphate adenylyltransferase
L: Glucose-1-phosphate adenylyltransferase
M: Glucose-1-phosphate adenylyltransferase
N: Glucose-1-phosphate adenylyltransferase
O: Glucose-1-phosphate adenylyltransferase
P: Glucose-1-phosphate adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)788,52641
Polymers780,13716
Non-polymers8,38925
Water25,1851398
1
A: Glucose-1-phosphate adenylyltransferase
B: Glucose-1-phosphate adenylyltransferase
C: Glucose-1-phosphate adenylyltransferase
D: Glucose-1-phosphate adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,86110
Polymers195,0344
Non-polymers1,8266
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16770 Å2
ΔGint-53 kcal/mol
Surface area63080 Å2
MethodPISA
2
E: Glucose-1-phosphate adenylyltransferase
F: Glucose-1-phosphate adenylyltransferase
G: Glucose-1-phosphate adenylyltransferase
H: Glucose-1-phosphate adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,45011
Polymers195,0344
Non-polymers2,4167
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17550 Å2
ΔGint-39 kcal/mol
Surface area60700 Å2
MethodPISA
3
I: Glucose-1-phosphate adenylyltransferase
J: Glucose-1-phosphate adenylyltransferase
K: Glucose-1-phosphate adenylyltransferase
L: Glucose-1-phosphate adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,45011
Polymers195,0344
Non-polymers2,4167
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17560 Å2
ΔGint-40 kcal/mol
Surface area60550 Å2
MethodPISA
4
M: Glucose-1-phosphate adenylyltransferase
N: Glucose-1-phosphate adenylyltransferase
O: Glucose-1-phosphate adenylyltransferase
P: Glucose-1-phosphate adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,7669
Polymers195,0344
Non-polymers1,7315
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17220 Å2
ΔGint-46 kcal/mol
Surface area62710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.883, 148.193, 180.164
Angle α, β, γ (deg.)90.00, 115.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glucose-1-phosphate adenylyltransferase / ADP-glucose pyrophosphorylase / ADPGlc PPase / ADP-glucose synthase


Mass: 48758.590 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: glgC, b3430, JW3393 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0A6V1, glucose-1-phosphate adenylyltransferase
#2: Polysaccharide
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1398 / 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: 2.58 Å3/Da / Density % sol: 52.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10mM EDTA, 10% D-(+)-Sucrose, 50mM MgCl2, 5mM ADP, 16% (w/v) PEG 10000, 100mM Imidazole pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.667→45.271 Å / Num. obs: 224803 / % possible obs: 100 % / Redundancy: 3.2 % / Biso Wilson estimate: 30.64 Å2 / CC1/2: 0.959 / Rmerge(I) obs: 0.2 / Net I/σ(I): 5.69
Reflection shellResolution: 2.667→2.762 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.7832 / Mean I/σ(I) obs: 1.74 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_2219: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YP2

1yp2


Resolution: 2.667→45.271 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 0.44 / Phase error: 28.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2634 21150 5.01 %Random selection
Rwork0.2388 ---
obs0.24 422567 95.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.667→45.271 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms51529 0 557 1398 53484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00353273
X-RAY DIFFRACTIONf_angle_d0.59172380
X-RAY DIFFRACTIONf_dihedral_angle_d11.81232275
X-RAY DIFFRACTIONf_chiral_restr0.0478081
X-RAY DIFFRACTIONf_plane_restr0.0049585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6666-2.69690.39986420.369113197X-RAY DIFFRACTION93
2.6969-2.72860.37137540.342113293X-RAY DIFFRACTION95
2.7286-2.76190.37297430.349413353X-RAY DIFFRACTION95
2.7619-2.79690.36877320.340113292X-RAY DIFFRACTION95
2.7969-2.83370.36686610.338613405X-RAY DIFFRACTION95
2.8337-2.87250.3617340.332213307X-RAY DIFFRACTION95
2.8725-2.91350.34577050.3313434X-RAY DIFFRACTION95
2.9135-2.9570.35857090.326113015X-RAY DIFFRACTION93
2.957-3.00320.35087120.31912842X-RAY DIFFRACTION92
3.0032-3.05240.33217370.304213248X-RAY DIFFRACTION95
3.0524-3.1050.33696700.302313511X-RAY DIFFRACTION96
3.105-3.16150.33076790.298113607X-RAY DIFFRACTION96
3.1615-3.22230.32846830.300413353X-RAY DIFFRACTION95
3.2223-3.2880.30746710.285513342X-RAY DIFFRACTION94
3.288-3.35950.3027500.276113456X-RAY DIFFRACTION96
3.3595-3.43760.28977170.260813538X-RAY DIFFRACTION96
3.4376-3.52360.28277100.249613290X-RAY DIFFRACTION95
3.5236-3.61880.26676500.24313502X-RAY DIFFRACTION95
3.6188-3.72520.26997560.238913042X-RAY DIFFRACTION93
3.7252-3.84540.24037100.214713356X-RAY DIFFRACTION95
3.8454-3.98280.2317200.201913545X-RAY DIFFRACTION96
3.9828-4.14210.216880.194513460X-RAY DIFFRACTION96
4.1421-4.33050.20017290.183213533X-RAY DIFFRACTION96
4.3305-4.55860.1897220.167213567X-RAY DIFFRACTION97
4.5586-4.84390.19756540.165213609X-RAY DIFFRACTION96
4.8439-5.21740.18876890.184213369X-RAY DIFFRACTION95
5.2174-5.74150.22127500.190813586X-RAY DIFFRACTION97
5.7415-6.57020.21276590.204613629X-RAY DIFFRACTION96
6.5702-8.26950.2076900.178713300X-RAY DIFFRACTION95
8.2695-45.27750.17637240.161613436X-RAY DIFFRACTION96

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