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- PDB-3eze: COMPLEX OF THE AMINO TERMINAL DOMAIN OF ENZYME I AND THE HISTIDIN... -

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Entry
Database: PDB / ID: 3eze
TitleCOMPLEX OF THE AMINO TERMINAL DOMAIN OF ENZYME I AND THE HISTIDINE-CONTAINING PHOSPHOCARRIER PROTEIN HPR FROM ESCHERICHIA COLI NMR, RESTRAINED REGULARIZED MEAN STRUCTURE
Components
  • PROTEIN (PHOSPHOTRANSFERASE SYSTEM, ENZYME I)
  • PROTEIN (PHOSPHOTRANSFERASE SYSTEM, HPR)
KeywordsTRANSFERASE / PHOSPHOTRANSFERASE / KINASE / SUGAR TRANSPORT
Function / homology
Function and homology information


phosphotransferase activity, nitrogenous group as acceptor / phosphoenolpyruvate-protein phosphotransferase / phosphoenolpyruvate-protein phosphotransferase activity / N-acetylglucosamine transport / antisigma factor binding / regulation of carbon utilization / positive regulation of glycogen catabolic process / phosphoenolpyruvate-dependent sugar phosphotransferase system / enzyme inhibitor activity / enzyme regulator activity ...phosphotransferase activity, nitrogenous group as acceptor / phosphoenolpyruvate-protein phosphotransferase / phosphoenolpyruvate-protein phosphotransferase activity / N-acetylglucosamine transport / antisigma factor binding / regulation of carbon utilization / positive regulation of glycogen catabolic process / phosphoenolpyruvate-dependent sugar phosphotransferase system / enzyme inhibitor activity / enzyme regulator activity / enzyme activator activity / kinase activity / metal ion binding / identical protein binding / cytosol
Similarity search - Function
PtsI, HPr-binding domain / Phosphotransferase system, enzyme I / Phosphotransferase system, enzyme I-like / Phosphotransferase system, enzyme I N-terminal / PtsI, HPr-binding domain superfamily / : / PEP-utilising enzyme, N-terminal / Phosphohistidine domain / PEP-utilising enzyme, active site / PEP-utilizing enzymes phosphorylation site signature. ...PtsI, HPr-binding domain / Phosphotransferase system, enzyme I / Phosphotransferase system, enzyme I-like / Phosphotransferase system, enzyme I N-terminal / PtsI, HPr-binding domain superfamily / : / PEP-utilising enzyme, N-terminal / Phosphohistidine domain / PEP-utilising enzyme, active site / PEP-utilizing enzymes phosphorylation site signature. / PEP-utilising enzyme, conserved site / PEP-utilizing enzymes signature 2. / PEP-utilising enzyme, C-terminal / PEP-utilising enzyme, PEP-binding domain / Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / PEP-utilising enzyme, mobile domain / Phosphohistidine domain superfamily / PEP-utilising enzyme, mobile domain / HPr-like / Phosphocarrier protein HPr-like / HPr-like superfamily / : / PTS HPr component phosphorylation site / PTS HPR domain profile. / Histidine-containing Protein; Chain: A; / PTS HPR domain serine phosphorylation site signature. / Glucose Oxidase; domain 1 / Pyruvate kinase-like domain superfamily / Enzyme I; Chain A, domain 2 / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / 3-Layer(bba) Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHITE ION / Phosphoenolpyruvate-protein phosphotransferase / Phosphocarrier protein HPr
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsClore, G.M. / Garrett, D.S. / Gronenborn, A.M.
Citation
Journal: Nat.Struct.Biol. / Year: 1999
Title: Solution structure of the 40,000 Mr phosphoryl transfer complex between the N-terminal domain of enzyme I and HPr.
Authors: Garrett, D.S. / Seok, Y.J. / Peterkofsky, A. / Gronenborn, A.M. / Clore, G.M.
#1: Journal: Protein Sci. / Year: 1998
Title: Tautomeric State and pKa of the Phosphorylated Active Site Histidine in the N-Terminal Domain of Enzyme I of the Escherichia coli Phosphoenolpyruvate: Sugar Phosphotransferase System
Authors: Garrett, D.S. / Seok, Y.J. / Peterkofsky, A. / Clore, G.M. / Gronenborn, A.M.
#2: Journal: Biochemistry / Year: 1997
Title: Solution Structure of the 30 kDa N-Terminal Domain of Enzyme I of the Escherichia Coli Phosphoenolpyruvate:Sugar Phosphotransferase System by Multidimensional NMR
Authors: Garrett, D.S. / Seok, Y.J. / Liao, D.I. / Peterkofsky, A. / Gronenborn, A.M. / Clore, G.M.
#3: Journal: Biochemistry / Year: 1997
Title: Identification by NMR of the Binding Surface for the Histidine-Containing Phosphocarrier Protein HPr on the N-Terminal Domain of Enzyme I of the Escherichia Coli Phosphotransferase System
Authors: Garrett, D.S. / Seok, Y.J. / Peterkofsky, A. / Clore, G.M. / Gronenborn, A.M.
History
DepositionNov 4, 1998Processing site: RCSB
Revision 1.0Dec 16, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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: PROTEIN (PHOSPHOTRANSFERASE SYSTEM, ENZYME I)
B: PROTEIN (PHOSPHOTRANSFERASE SYSTEM, HPR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5903
Polymers37,5112
Non-polymers791
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 40REGULARIZED MEAN STRUCTURE
Representative

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Components

#1: Protein PROTEIN (PHOSPHOTRANSFERASE SYSTEM, ENZYME I)


Mass: 28381.316 Da / Num. of mol.: 1 / Fragment: AMINO-TERMINAL DOMAIN RESIDUES 1 - 259
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: GI698 / Plasmid: PLP2 / Production host: Escherichia coli (E. coli)
References: UniProt: P08839, phosphoenolpyruvate-protein phosphotransferase
#2: Protein PROTEIN (PHOSPHOTRANSFERASE SYSTEM, HPR)


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 / Plasmid: PSP100 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AA04
#3: Chemical ChemComp-PO3 / PHOSPHITE ION


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 3D STRUCTURE OF THE EIN-HPR COMPLEX WAS SOLVED BY MULTI HETERONUCLEAR NMR AND IS BASED ON 5475

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Sample preparation

Sample conditionspH: 7 / Temperature: 313 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 DMX750BrukerDMX7507503

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Processing

NMR software
NameDeveloperClassification
CNSBRUNGERrefinement
CNS (SEE ABOVE)structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129-136 USING THE PROGRAM CNS MODIFIED TO INCORPORATE COUPLING CONSTANT ...Details: THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129-136 USING THE PROGRAM CNS MODIFIED TO INCORPORATE COUPLING CONSTANT RESTRAINTS (GARRETT ET AL. (1984) J. MAGN. RESON. SERIES B 104, 99-103), CARBON CHEMICAL SHIFT RESTRAINTS, (KUSZEWSKI ET AL. (1995) J. MAGN. RESON. SERIES B 106, 92-96) RESTRAINTS, AND RESIDUAL DIPOLAR COUPLING RESTRAINTS (CLORE ET AL. J. MAGN. RESON 131, 159-162 (1998); J. MAGN 133, 216-221 (1998)). IN THIS ENTRY THE LAST COLUMN REPRESENTS THE AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL SIMULATED ANNEALING STRUCTURES AND THE MEAN COORDINATE POSITIONS. THE LAST COLUMN IN THE INDIVIDUAL SA STRUCTURES HAS NO MEANING. BEST FITTING TO GENERATE THE AVERAGE STRUCTURE IS WITH RESPECT TO RESIDUES 1 - 250 (RESIDUES 251 - 259 ARE DISORDERED IN SOLUTION) OF ENZYME I AND RESIDUES 301-385 OF HPR. RESIDUES 251-259 ARE OMITTED FROM THE MEAN STRUCTURE
NMR ensembleConformer selection criteria: REGULARIZED MEAN STRUCTURE / Conformers calculated total number: 40 / Conformers submitted total number: 1

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