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

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Basic information

Entry
Database: PDB / ID: 3ezb
TitleCOMPLEX OF THE AMINO TERMINAL DOMAIN OF ENZYME I AND THE HISTIDINE-CONTAINING PHOSPHOCARRIER PROTEIN HPR FROM ESCHERICHIA COLI
Components
  • PROTEIN (PHOSPHOCARRIER PROTEIN HPR)
  • PROTEIN (PHOSPHOTRANSFER SYSTEM, ENZYME I)
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
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 Acti Histidine in the N- Terminal Domain of Enzyme I of T Eschrichia Coli Phosphoenolpyruvate:Sugar Phosphotr 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 Th Histidine-Containing Phosphocarrier Protein Hpr on N-Terminal Domain of Enzyme I of the Escherichia Co Phosphotransferase System
Authors: Garrett, D.S. / Seok, Y.J. / Peterkofsky, A. / Clore, G.M. / Gronenborn, A.M.
History
DepositionNov 3, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 16, 1999Provider: repository / Type: Initial release
SupersessionDec 29, 1999ID: 3ezc
SupersessionDec 29, 1999ID: 3ezd
Revision 1.1Apr 27, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (PHOSPHOTRANSFER SYSTEM, ENZYME I)
B: PROTEIN (PHOSPHOCARRIER PROTEIN HPR)


Theoretical massNumber of molelcules
Total (without water)37,5112
Polymers37,5112
Non-polymers00
Water00
1


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

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Components

#1: Protein PROTEIN (PHOSPHOTRANSFER 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 (PHOSPHOCARRIER PROTEIN 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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111) TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEIN. (2) QUANTITATIVE J CORRELATION FOR COUPLING CONSTANTS. (3) 3D
1214D HETERONUCLEAR SEPARATED
131FILTERED NOE E (4) IPAP EXPTS FOR DIPOLAR COUPLINGS DIPOLAR COUPLINGS WERE MEASURED IN A NEMATIC PHASE OF A CO SUSPENSION OF PHAGE FD (CLORE ET AL. 1998 J. AM. CHEM. SOC
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
CNSBRUNGER,ADAMS, CLORE, DELANO, GROS, GROSSE-KUNSTLEVE, JIANG, KUSZEWSKI, NILGES, PANNU, READ, RICE WARRENrefinement
CNSstructure 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)).
NMR ensembleConformer selection criteria: REGULARIZED MEAN STRUCTURE / Conformers calculated total number: 40 / Conformers submitted total number: 40

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