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- PDB-1ggr: COMPLEX OF ENZYME IIAGLC AND THE HISTIDINE-CONTAINING PHOSPHOCARR... -

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Basic information

Entry
Database: PDB / ID: 1ggr
TitleCOMPLEX OF ENZYME IIAGLC AND THE HISTIDINE-CONTAINING PHOSPHOCARRIER PROTEIN HPR FROM ESCHERICHIA COLI NMR, RESTRAINED REGULARIZED MEAN STRUCTURE
Components
  • PHOSPHOCARRIER PROTEIN HPR
  • PTS SYSTEM, GLUCOSE-SPECIFIC IIA COMPONENT
KeywordsTRANSFERASE / PHOSPHOTRANSFERASE / KINASE / SUGAR TRANSPORT / COMPLEX (TRANSFERASE-PHOSPHOCARRIER)
Function / homology
Function and homology information


negative regulation of carbohydrate metabolic process / phosphotransferase activity, nitrogenous group as acceptor / regulation of carbon utilization / antisigma factor binding / negative regulation of maltose transport / enzyme IIA-maltose transporter complex / negative regulation of transmembrane transport / positive regulation of glycogen catabolic process / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex ...negative regulation of carbohydrate metabolic process / phosphotransferase activity, nitrogenous group as acceptor / regulation of carbon utilization / antisigma factor binding / negative regulation of maltose transport / enzyme IIA-maltose transporter complex / negative regulation of transmembrane transport / positive regulation of glycogen catabolic process / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / enzyme inhibitor activity / enzyme activator activity / enzyme regulator activity / kinase activity / phosphorylation / 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) / Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / PTS HPR domain serine phosphorylation site signature. ...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) / Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / PTS HPR domain serine phosphorylation site signature. / HPr-like / Histidine-containing Protein; Chain: A; / Phosphocarrier protein HPr-like / HPr-like superfamily / PTS HPr component phosphorylation site / PTS HPR domain profile. / Duplicated hybrid motif / Distorted Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHITE ION / Phosphocarrier protein HPr / PTS system glucose-specific EIIA component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / RIGID BODY MINIMIZATION, CONSTRAINED, RESTRAINED SIMULATED ANNEALING
AuthorsClore, G.M. / Wang, G.
CitationJournal: EMBO J. / Year: 2000
Title: Solution structure of the phosphoryl transfer complex between the signal transducing proteins HPr and IIA(glucose) of the Escherichia coli phosphoenolpyruvate:sugar phosphotransferase system.
Authors: Wang, G. / Louis, J.M. / Sondej, M. / Seok, Y.J. / Peterkofsky, A. / Clore, G.M.
History
DepositionSep 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PTS SYSTEM, GLUCOSE-SPECIFIC IIA COMPONENT
B: PHOSPHOCARRIER PROTEIN HPR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3503
Polymers27,2712
Non-polymers791
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)3 / 30REGULARIZED MEAN STRUCTURES
Representative

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Components

#1: Protein PTS SYSTEM, GLUCOSE-SPECIFIC IIA COMPONENT / EIIA-GLC / PHOSPHOTRANSFERASE ENZYME II / A COMPONENT


Mass: 18141.834 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: GI698 / Production host: Escherichia coli (E. coli)
References: UniProt: P69783, protein-Npi-phosphohistidine-sugar phosphotransferase
#2: Protein PHOSPHOCARRIER PROTEIN HPR / HISTIDINE-CONTAINING PROTEIN


Mass: 9129.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: GI698 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AA04
#3: Chemical ChemComp-PO3 / PHOSPHITE ION / Phosphite ester


Mass: 78.972 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: THE FOLLOWING EXPERIMENTS WERE CONDUCTED: (1) TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEIN; (2) QUANTITATIVE J CORRELATION FOR COUPLING CONSTANTS; (3) 3D AND 4D HETERONUCLEAR SEPARATED AND ...Text: THE FOLLOWING EXPERIMENTS WERE CONDUCTED: (1) TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEIN; (2) QUANTITATIVE J CORRELATION FOR COUPLING CONSTANTS; (3) 3D AND 4D HETERONUCLEAR SEPARATED AND FILTERED NOE EXPERIMENTS; (4) IPAP EXPERIMENTS FOR DIPOLAR COUPLINGS. DIPOLAR COUPLINGS WERE MEASURED IN A NEMATIC PHASE OF A COLLOIDAL SUSPENSION OF TMV (CLORE ET AL. 1998 J.AM.CHEM.SOC. 120, 105-106).

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Sample preparation

Sample conditionsIonic strength: 10 mM SODIUM PHOSPHATE / pH: 7.1 / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMX500BrukerDMX5005001
Bruker DMX600BrukerDMX6006002
Bruker DRX750BrukerDRX7507503
Bruker DRX800BrukerDRX8008004

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Processing

NMR softwareName: X-PLOR / Version: NIH / Developer: Brunger / Classification: refinement
RefinementMethod: RIGID BODY MINIMIZATION, CONSTRAINED, RESTRAINED SIMULATED ANNEALING
Software ordinal: 1
Details: THE STRUCTURES WERE CALCULATED BY RIGID BODY MINIMIZATION (CLORE (2000) PROC.NATL.ACAD. SCI. 97, 9021-9025; BEWLEY AND CLORE (2000) J.AM.CHEM.SOC. 122, 6009-6016) FOLLOWED BY ...Details: THE STRUCTURES WERE CALCULATED BY RIGID BODY MINIMIZATION (CLORE (2000) PROC.NATL.ACAD. SCI. 97, 9021-9025; BEWLEY AND CLORE (2000) J.AM.CHEM.SOC. 122, 6009-6016) FOLLOWED BY CONSTRAINED/RESTRAINED SIMULATED ANNEALING TO REFINE THE INTERFACIAL SIDECHAIN POSITIONS AND FINE TUNE THE RELATIVE ORIENTATION OF THE TWO PROTEINS (WANG ET AL. (2000) EMBO J. IN PRESS). THE TARGET FUNCTIONS COMPRISES TERMS FOR THE NOE RESTRAINTS, THE DIPOLAR COUPLING RESTRAINTS (CLORE ET AL. J.MAGN.RESON. 131, 159-162 (1998); J.MAGN.RESON. 133, 216-221(1998)), THE RADIUS OF GYRATION (KUSZEWSKI ET AL. (1999), AND A QUARTIC VAN DER WAALS REPULSION TERM (NILGES ET AL. (1988) FEBS LETT. 229, 129-136). THE STARTING COORDINATES COME FROM THE X-RAY STRUCTURES (WITH PROTONS ADDED) OF E. COLI HPR (1POH, JIA ET AL. (1993) J.BIOL.CHEM. 268, 22940-22501; RESOLUTION 1.5 A) AND IIAGLC (MOLECULE 2 OF 2F3G, FEESE ET AL. BIOCHEMISTRY 36, 16087-16096; RESOLUTION 2.0 A) IN SEVERAL DIFFERENT ORIENTATIONS WITH THE CA-CA DISTANCE BETWEEN THE ACTIVE SITE HISTIDINES RANGING FROM 28 TO 95 A, INCLUDING ORIENTATIONS WHERE THE TWO ACTIVE SITE HISTIDINES ARE NOT OPPOSED AND WHERE HPR IS DIRECTED TOWARDS THE FACE OF IIAGLC OPPOSITE TO THE IIAGLC ACTIVE SITE. ONLY THE INTERFACIAL SIDECHAINS ARE ALLOWED TO ALTER THEIR CONFORMATION; THE BACKBONE AND NON-INTERFACIAL SIDECHAINS OF ONE MOLECULE (IIAGLC) ARE HELD COMPLETELY FIXED; THE SECOND MOLECULE (HPR) CAN ROTATE AND TRANSLATE BUT THE RELATIVE COORDINATES OF ITS BACKBONE AND NON-INTERFACIAL SIDECHAINS ARE HELD FIXED. IN THIS ENTRY THE LAST COLUMN REPRESENTS THE AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL SIMULATED ANNEALING STRUCTURES AND THE MEAN COORDINATE POSITIONS. IT IS IMPORTANT TO NOTE THAT THE VALUES GIVEN FOR THE BACKBONE ATOMS AND NON-INTERFACIAL SIDECHAINS PROVIDE ONLY A MEASURE OF THE PRECISION WITH WHICH THE RELATIVE OF THE TWO PROTEINS HAVE BEEN DETERMINED AND DOES NOT TAKE INTO ACCOUNT THE ERRORS IN THE X-RAY COORDINATES OF HPR AND IIAGLC. THREE SETS OF COORDINATES ARE GIVEN: MODEL 1: RESTRAINED MINIMIZED MEAN COORDINATES OF THE UNPHOSPHORYLATED HPR-IIAGLC COMPLEX SOLVED ON THE BASIS OF 82 INTERMOLECULAR DISTANCE RESTRAINTS (74 NOE DERIVED INTERPROTON DISTANCE AND 8 AMBIGUOUS INTERMOLECULAR SALT BRIDGE RESTRAINTS), 12 INTRAMOLECULAR INTERPROTON DISTANCE RESTRAINTS (RELATED SPECIFICALLY TO NOES INVOLVING RESIDUES 315 AND 317 OF HPR), 61 NMR DERIVED SIDECHAIN TORSION ANGLE RESTRAINTS, AND 195 1DNH DIPOLAR COUPLINGS (118 FOR IIAGLC AND 77 FOR HPR). CROSS-VALIDATION WAS USED FOR THE DIPOLAR COUPLINGS (CLORE AND GARRETT (1999) J. AM. CHEM. SOC. 121, 9008-9012). MODEL 2: RESTRAINED MINIMIZED MEAN COORDINATES FOR THE MODEL OF THE DISSOCIATIVE PHOSPHORYL TRANSITION STATE HPR-IIAGLC COMPLEX. EXPERIMENTAL RESTRAINTS ARE TO THOSE USED FOR MODEL 1, EXCEPT THAT ONE INTRAMOLECULAR INTERPROTON DISTANCE RESTRAINT INVOLVING HIS15 WAS REMOVED TO PERMIT A TRANSITION STATE TO FORM. IN ADDITION, COVALENT GEOMETRY RESTRAINTS ARE INCLUDED RELATING TO THE TRIGONAL BIPYRAMIDAL AT THE PHOSPHORUS. NO DISTANCE RESTRAINT IS INCLUDED FOR THE N-P BOND LENGTHS. THE CA-CA DISTANCE BETWEEN HIS315 (HPR) and HIS90 (IIAGLC) REMAINS UNCHANGED FROM MODEL 1, BUT THE ND1-NE2 DISTANCE BETWEEN HIS315 AND HIS90 IS REDUCED TO 6 A, WITH ESSENTIALLY IDEALIZED GEOMETRY OF THE PHOSPHORYL TRANSITION STATE. THE ND1-NE2 DISTANCE CORRESPONDS TO A DISSOCIATIVE TRANSITION STATE. THE RMS DIFFERENCE BETWEEN THE MEAN STRUCTURES OF THE UNPHOSPHORYLATED COMPLEX (MODEL 1) AND THE TRANSITION STATE COMPLEX IS 0.03 A FOR THE BACKBONE ATOMS AND 0.2 A FOR THE INTERFACIAL SIDECHAINS (EXCLUDING HIS315 AND HIS90). MODEL 3: RESTRAINED MINIMIZED MEAN COORDINATES FOR THE MODEL OF THE ASSOCIATIVE PHOSPHORYL TRANSITION STATE HPR-IIAGLC COMPLEX. MODEL 3 IS DERIVED FROM MODEL 2 BY CONSTRAINED/RESTRAINED MINIMIZATION IN WHICH THE COORDINATES OF ALL BACKBONE ATOMS, WITH THE OF RESIDUES 313-317 OF HPR AND RESIDUES 89-91 OF IIAGLC, AND ALL NON-INTERFACIAL SIDECHAINS ARE HELD COMPLETELY FIXED, AND IN WHICH THE N-P DISTANCES ARE RESTRAINED TO CA. 2 A, CORRESPONDING TO AN SN2 ASSOCIATIVE TRANSITION STATE. HPR-IIAGLC COMPLEX DEVIATIONS FROM IDEALIZED GEOMETRY: BONDS 0.014 A, ANGLES 1.74 A, IMPROPER TORSIONS 1.66 A RMS DEVIATIONS FROM NOE DISTANCE RESTRAINTS: 0.057 A RMS DEVIATIONS FROM SIDECHAIN TORSION ANGLE RESTRAINTS: 0.16 DEG. DIPOLAR COUPLING R-FACTORS (CLORE AND GARRETT (1999) J. AM. CHEM. SOC. 121, 9008-9012): 16.9% FOR HPR and 15.2% FOR IIAGLC (NOTE ONLY ONE ALIGNMENT TENSOR IS USED FOR BOTH HPR AND IIAGLC; FOR REFERENCE THE DIPOLAR COUPLING R-FACTORS FOR THE FREE X-RAY STRUCTURES OF HPR AND IIAGLC (USING INDIVIDUAL ALIGNMENT TENSORS FOR THE TWO PROTEINS) ARE 16.7% and 15.0%, RESPECTIVELY).
NMR ensembleConformer selection criteria: REGULARIZED MEAN STRUCTURES / Conformers calculated total number: 30 / Conformers submitted total number: 3

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