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- PDB-1glc: CATION PROMOTED ASSOCIATION (CPA) OF A REGULATORY AND TARGET PROT... -

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Basic information

Entry
Database: PDB / ID: 1glc
TitleCATION PROMOTED ASSOCIATION (CPA) OF A REGULATORY AND TARGET PROTEIN IS CONTROLLED BY PHOSPHORYLATION
Components
  • GLUCOSE-SPECIFIC PROTEIN IIIGlc
  • GLYCEROL KINASE
KeywordsPHOSPHOTRANSFERASE
Function / homology
Function and homology information


negative regulation of carbohydrate metabolic process / regulation of carbohydrate utilization / negative regulation of maltose transport / enzyme IIA-maltose transporter complex / negative regulation of transmembrane transport / glycerol-3-phosphate metabolic process / glycerol kinase / glycerol kinase activity / glycerol metabolic process / phosphoenolpyruvate-dependent sugar phosphotransferase system ...negative regulation of carbohydrate metabolic process / regulation of carbohydrate utilization / negative regulation of maltose transport / enzyme IIA-maltose transporter complex / negative regulation of transmembrane transport / glycerol-3-phosphate metabolic process / glycerol kinase / glycerol kinase activity / glycerol metabolic process / phosphoenolpyruvate-dependent sugar phosphotransferase system / glycerol catabolic process / transmembrane transporter complex / kinase activity / DNA damage response / zinc ion binding / ATP binding / identical protein binding / membrane / metal ion binding / cytosol
Similarity search - Function
: / PTS EIIA domains phosphorylation site signature 1. / Phosphotransferase system, sugar-specific permease EIIA type 1 / phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1 / PTS_EIIA type-1 domain profile. / Glucose Permease (Domain IIA) / Glucose Permease (Domain IIA) / FGGY family of carbohydrate kinases signature 1. / Glycerol kinase / FGGY family of carbohydrate kinases signature 2. ...: / PTS EIIA domains phosphorylation site signature 1. / Phosphotransferase system, sugar-specific permease EIIA type 1 / phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1 / PTS_EIIA type-1 domain profile. / Glucose Permease (Domain IIA) / Glucose Permease (Domain IIA) / FGGY family of carbohydrate kinases signature 1. / Glycerol kinase / FGGY family of carbohydrate kinases signature 2. / Carbohydrate kinase, FGGY, conserved site / Carbohydrate kinase, FGGY / Carbohydrate kinase, FGGY, N-terminal / FGGY family of carbohydrate kinases, N-terminal domain / Carbohydrate kinase, FGGY, C-terminal / FGGY family of carbohydrate kinases, C-terminal domain / Duplicated hybrid motif / ATPase, nucleotide binding domain / Distorted Sandwich / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / GLYCERALDEHYDE-3-PHOSPHATE / Glycerol kinase / PTS system glucose-specific EIIA component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.65 Å
AuthorsFeese, M.D. / Meadow, N.D. / Roseman, S. / Pettigrew, D.W. / Remington, S.J.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Cation-promoted association of a regulatory and target protein is controlled by protein phosphorylation.
Authors: Feese, M. / Pettigrew, D.W. / Meadow, N.D. / Roseman, S. / Remington, S.J.
#1: Journal: Science / Year: 1993
Title: Three-Dimensional Structure of the Regulatory Complex of Escherichia Coli III-Glc with Glycerol Kinase
Authors: Hurley, J.H. / Worthylake, D. / Faber, H.R. / Meadow, N.D. / Roseman, S. / Pettigrew, D.W. / Remington, S.J.
History
DepositionMar 7, 1994Processing site: BNL
Revision 1.0May 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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.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_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: GLUCOSE-SPECIFIC PROTEIN IIIGlc
G: GLYCEROL KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9916
Polymers74,3042
Non-polymers6874
Water75742
1
F: GLUCOSE-SPECIFIC PROTEIN IIIGlc
G: GLYCEROL KINASE
hetero molecules

F: GLUCOSE-SPECIFIC PROTEIN IIIGlc
G: GLYCEROL KINASE
hetero molecules

F: GLUCOSE-SPECIFIC PROTEIN IIIGlc
G: GLYCEROL KINASE
hetero molecules

F: GLUCOSE-SPECIFIC PROTEIN IIIGlc
G: GLYCEROL KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,96524
Polymers297,2178
Non-polymers2,74816
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
MethodPQS
2
F: GLUCOSE-SPECIFIC PROTEIN IIIGlc
G: GLYCEROL KINASE
hetero molecules

F: GLUCOSE-SPECIFIC PROTEIN IIIGlc
G: GLYCEROL KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,98212
Polymers148,6084
Non-polymers1,3748
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area9020 Å2
ΔGint-161 kcal/mol
Surface area44720 Å2
MethodPISA
3
G: GLYCEROL KINASE
hetero molecules

G: GLYCEROL KINASE
hetero molecules

F: GLUCOSE-SPECIFIC PROTEIN IIIGlc
hetero molecules

F: GLUCOSE-SPECIFIC PROTEIN IIIGlc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,98212
Polymers148,6084
Non-polymers1,3748
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation6_454-x-1/2,-y+1/2,z-1/21
crystal symmetry operation8_555x+1/2,-y+1/2,-z+1/21
Buried area10260 Å2
ΔGint-143 kcal/mol
Surface area43470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.830, 125.160, 133.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Atom site foot note1: CIS PROLINE - PRO G 354
DetailsTHE CRYSTAL CONTAINS TETRAMERS OF THE GLYCEROL KINASE/III-GLC COMPLEX WITH 222 POINT-GROUP SYMMETRY. THE TETRAMER IS LOCATED AT THE INTERSECTION OF THREE CRYSTALLOGRAPHIC TWO-FOLD AXES. THE FOLLOWING TRANSFORMATIONS WILL PRODUCE A TETRAMER OF THE COMPLEX WHEN APPLIED TO THE COORDINATES IN THIS ENTRY: TRANSFORM 1 (-X, 1-Y, Z) -1.0 0.0 0.0 0.0 0.0 -1.0 0.0 125.16 0.0 0.0 1.0 0.0 TRANSFORM 2 ( X, 1-Y, -Z) 1.0 0.0 0.0 0.0 0.0 -1.0 0.0 125.16 0.0 0.0 1.0 0.0 TRANSFORM 3 (-X, Y, -Z) -1.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 -1.0 0.0

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Components

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Protein , 2 types, 2 molecules FG

#1: Protein GLUCOSE-SPECIFIC PROTEIN IIIGlc


Mass: 18141.834 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
References: UniProt: P69783, protein-Npi-phosphohistidine-sugar phosphotransferase
#2: Protein GLYCEROL KINASE


Mass: 56162.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P0A6F3, glycerol kinase

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Non-polymers , 5 types, 46 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-G3H / GLYCERALDEHYDE-3-PHOSPHATE


Mass: 170.058 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O6P
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsTHE COMPLEX OF GLYCEROL KINASE AND III-GLC CREATES AN INTERMOLECULAR ZINC BINDING SITE. HISTIDINES ...THE COMPLEX OF GLYCEROL KINASE AND III-GLC CREATES AN INTERMOLECULAR ZINC BINDING SITE. HISTIDINES 75 AND 90 OF III-GLC AND GLUTAMATE 478 OF GLYCEROL KINASE ARE THE LIGANDS THAT CONTACT THE ZN(II) ION. A SOLVENT MOLECULE (PROBABLY A HYDROXIDE) IS BOUND TO THE ZN(II) AND ACCEPTS HYDROGEN BONDS FROM THE BACKBONE AMIDES OF III-GLC RESIDUES 95 AND 96. THERE ARE NO LARGE CONFORMATIONAL CHANGES EXCEPT FOR THE SIDE CHAIN OF GLYCEROL KINASE RESIDUE GLUTAMATED 478, WHICH ADOPTS A VERY DIFFERENT CONFORMATION FROM THAT SEEN IN OTHER STRUCTURES OF THE COMPLEX.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.48 Å3/Da / Density % sol: 64.66 %
Crystal grow
*PLUS
pH: 6.1 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mMcation chloride1reservoir
220 mMADP1reservoir
350 mMG3P1reservoir
40.6 Msodium acetate1reservoir
5100 mMMES1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2.65→14.5 Å / Rfactor obs: 0.166
Refinement stepCycle: LAST / Resolution: 2.65→14.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4909 0 39 42 4990
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.021
X-RAY DIFFRACTIONt_angle_deg2.988
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.166
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg

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