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

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Basic information

Entry
Database: PDB / ID: 3eza
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
  • HISTIDINE-CONTAINING PHOSPHOCARRIER PROTEIN HPR
  • PHOSPHOTRANSFERASE SYSTEM, ENZYME I
KeywordsCOMPLEX (TRANSFERASE/PHOSPHOCARRIER) / PHOSPHOTRANSFERASE / TRANSFERASE / KINASE / SUGAR TRANSPORT / COMPLEX (TRANSFERASE-PHOSPHOCARRIER) / COMPLEX (TRANSFERASE-PHOSPHOCARRIER) complex
Function / homology
Function and homology information


phosphotransferase activity, nitrogenous group as acceptor / phosphoenolpyruvate-protein phosphotransferase / phosphoenolpyruvate-protein phosphotransferase activity / regulation of carbon utilization / antisigma factor binding / positive regulation of glycogen catabolic process / phosphoenolpyruvate-dependent sugar phosphotransferase system / enzyme inhibitor activity / enzyme regulator activity / enzyme activator activity ...phosphotransferase activity, nitrogenous group as acceptor / phosphoenolpyruvate-protein phosphotransferase / phosphoenolpyruvate-protein phosphotransferase activity / regulation of carbon utilization / antisigma factor binding / positive regulation of glycogen catabolic process / phosphoenolpyruvate-dependent sugar phosphotransferase system / enzyme inhibitor activity / enzyme regulator activity / enzyme activator activity / kinase activity / phosphorylation / identical protein binding / metal ion 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. / PEP-utilising enzyme, conserved site ...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 / PEP-utilising enzyme, mobile domain / Phosphohistidine domain superfamily / PEP-utilising enzyme, mobile domain / 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. / Enzyme I; Chain A, domain 2 / Glucose Oxidase; domain 1 / Pyruvate kinase-like domain superfamily / 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 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 3, 1998Processing site: BNL
Revision 1.0May 25, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 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 1.4May 22, 2024Group: 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: PHOSPHOTRANSFERASE SYSTEM, ENZYME I
B: HISTIDINE-CONTAINING PHOSPHOCARRIER PROTEIN HPR


Theoretical massNumber of molelcules
Total (without water)36,3532
Polymers36,3532
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)1 / 40REGULARIZED MEAN STRUCTURE
Representative

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Components

#1: Protein PHOSPHOTRANSFERASE SYSTEM, ENZYME I


Mass: 27223.904 Da / Num. of mol.: 1 / Fragment: AMINO-TERMINAL DOMAIN RESIDUES 1 - 249
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 HISTIDINE-CONTAINING 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 detailsText: THE 3D STRUCTURE OF THE EIN-HPR COMPLEX WAS SOLVED BY MULTI-DIMENSIONAL HETERONUCLEAR NMR AND IS BASED ON 5475 EXPERIMENTAL NMR RESTRAINTS:' INTRAMOLECULAR EIN NOES: 746 SEQUENTIAL (|I-J|1), ...Text: THE 3D STRUCTURE OF THE EIN-HPR COMPLEX WAS SOLVED BY MULTI-DIMENSIONAL HETERONUCLEAR NMR AND IS BASED ON 5475 EXPERIMENTAL NMR RESTRAINTS:' INTRAMOLECULAR EIN NOES: 746 SEQUENTIAL (|I-J|1), 517 MEDIUM RANGE (1 < |I-J <= 5), 436 LONG RANGE (|I-J|>5) INTERRESIDUE NOES AND 486 INTRARESIDUE NOES. INTRAMOLECULAR HPR NOES: 247 SEQUENTIAL (|I-J|1), 167 MEDIUM RANGE (1 < |I-J <= 5), 246 LONG RANGE (|I-J|>5) INTERRESIDUE NOES AND 202 INTRARESIDUE NOES. INTERMOLECULAR NOES BETWEEN EIN AND HPR: 117 TORSION ANGLE RESTRAINTS 768 FOR EIN AND 170 FOR HPR. 3JHNA COUPLING CONSTANT RESTRAINTS: 34 FOR HPR 13CALPHA AND 13CBETA CHEMICAL SHIFT RESTRAINTS: 503 FOR EIN, 162 FOR HPR. ONE-BOND N-H DIPOLAR COUPLING CONSTANT RESTRAINTS: 165 FOR EIN AND 79 FOR HPR

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Sample preparation

Sample conditionspH: 7.0 / 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

Software
NameClassification
CNSrefinement
CNSphasing
NMR software
NameVersionDeveloperClassification
CNSBRUNGER, ADAMS, CLORE, DELANO, GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ,RICE,SIMONSON,WARRENrefinement
CNS (SEE ABOVE)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. FITTING TO GENERATE THE AVERAGE STRUCTURE IS WITH RESPECT BEST TO RESIDUES 1 - 250 (RESIDUES 251 - 249 ARE DISORDERED IN SOLUTION) OF ENZYME I AND RESIDUES 1-85 OF HPR. RESIDUES 251-249 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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