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- PDB-1vsq: Solution NMR structure of the productive complex between IIAManno... -

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Basic information

Entry
Database: PDB / ID: 1vsq
TitleSolution NMR structure of the productive complex between IIAMannose and IIBMannose of the mannose transporter of the E. coli phosphotransferase system
Components
  • Mannose-specific phosphotransferase enzyme IIA component
  • Mannose-specific phosphotransferase enzyme IIB component
KeywordsTRANSFERASE / phosphotransferase / sugar transport / transferase-phosphocarrier complex / Membrane / Phosphoprotein / Phosphotransferase system
Function / homology
Function and homology information


protein-Npi-phosphohistidine-D-mannose phosphotransferase / mannose transmembrane transport / protein-N(PI)-phosphohistidine-mannose phosphotransferase system transporter activity / fructose import across plasma membrane / N-acetylglucosamine transport / protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / D-glucose import across plasma membrane / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / kinase activity ...protein-Npi-phosphohistidine-D-mannose phosphotransferase / mannose transmembrane transport / protein-N(PI)-phosphohistidine-mannose phosphotransferase system transporter activity / fructose import across plasma membrane / N-acetylglucosamine transport / protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / D-glucose import across plasma membrane / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / kinase activity / protein homodimerization activity / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Phosphotransferase system, mannose family IIA component / Phosphotransferase system, sorbose subfamily IIB component, subgroup / Fructose Permease / Phosphotransferase system, sorbose subfamily IIB component / : / Phosphotransferase system, sorbose subfamily IIB component / Phosphotransferase system, sorbose subfamily IIB component superfamily / PTS system sorbose subfamily IIB component / PTS_EIIB type-4 domain profile. / PTS system mannose/sorbose specific IIA subunit ...Phosphotransferase system, mannose family IIA component / Phosphotransferase system, sorbose subfamily IIB component, subgroup / Fructose Permease / Phosphotransferase system, sorbose subfamily IIB component / : / Phosphotransferase system, sorbose subfamily IIB component / Phosphotransferase system, sorbose subfamily IIB component superfamily / PTS system sorbose subfamily IIB component / PTS_EIIB type-4 domain profile. / PTS system mannose/sorbose specific IIA subunit / Phosphotransferase system, mannose-type IIA component / Phosphotransferase system, mannose-type IIA component / Phosphotransferase system, mannose-type IIA component superfamily / PTS system fructose IIA component / PTS_EIIA type-4 domain profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PTS system mannose-specific EIIAB component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / conjoined rigid body, torsion angle simulated annealing
AuthorsClore, G.M. / Hu, J. / Hu, K.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Solution NMR Structures of Productive and Non-productive Complexes between the A and B Domains of the Cytoplasmic Subunit of the Mannose Transporter of the Escherichia coli Phosphotransferase System.
Authors: Hu, J. / Hu, K. / Williams, D.C. / Komlosh, M.E. / Cai, M. / Clore, G.M.
History
DepositionJan 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2013Group: Derived calculations
Revision 1.3Oct 3, 2018Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Refinement description / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_nmr_exptl ...entity_src_gen / pdbx_nmr_exptl / pdbx_nmr_exptl_sample / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_refine / pdbx_nmr_representative / pdbx_nmr_sample_details / struct / struct_keywords
Item: _entity_src_gen.gene_src_genus / _entity_src_gen.host_org_genus ..._entity_src_gen.gene_src_genus / _entity_src_gen.host_org_genus / _pdbx_nmr_exptl_sample_conditions.pressure_units / _pdbx_nmr_refine.software_ordinal / _struct.pdbx_model_type_details / _struct_keywords.text
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mannose-specific phosphotransferase enzyme IIA component
B: Mannose-specific phosphotransferase enzyme IIA component
C: Mannose-specific phosphotransferase enzyme IIB component


Theoretical massNumber of molelcules
Total (without water)47,3873
Polymers47,3873
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-38 kcal/mol
Surface area19440 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)2 / 120restrained regularized mean
Representative

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Components

#1: Protein Mannose-specific phosphotransferase enzyme IIA component / EIIA-Man / PTS system mannose-specific EIIA component


Mass: 14527.425 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: manX, gptB, ptsL / Plasmid: pET32a modified / Production host: Escherichia coli (E. coli)
References: UniProt: P69797, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Protein Mannose-specific phosphotransferase enzyme IIB component / EIIB-Man / PTS system mannose-specific EIIB component


Mass: 18332.271 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: manX, gptB, ptsL / Plasmid: pET32a modified / Production host: Escherichia coli (E. coli)
References: UniProt: P69797, protein-Npi-phosphohistidine-sugar phosphotransferase
Compound detailsMODEL 1 IS PHOSPHORYLATED-HIS IN CHAIN B OF IIAMAN. MODEL 2 IS A PHOSPHORYL TRANSITION STATE ...MODEL 1 IS PHOSPHORYLATED-HIS IN CHAIN B OF IIAMAN. MODEL 2 IS A PHOSPHORYL TRANSITION STATE INVOLVING A PENTACOORDINATE PHOSPHORYL GROUP IN A TRIGONAL BIPYRAMIDAL GEOMETRY WITH THE DONOR (NE2 OF HIS10 OF CHAIN B OF IIAMAN) AND ACCEPTOR (ND1 OF HIS175 OF IIBMAN, CHAIN C) IN APICAL POSITIONS. THE STRUCTURE OF THE TRANSITION STATE IS DERIVED FROM MODEL 1. IN THIS TRANSITION STATE WITH PARTIAL DISSOCIATIVE CHARACTER THE N-P DISTANCE IS 2.5 A. THE COORDINATES OF MODEL 1 ARE IDENTICAL TO THOSE OF 2JZN (IIAMANH10E-IIBMAN COMPLEX EXCEPT THAT GLU10 OF CHAIN B OF IIAMANNOSE HAS BEEN REPLACED BY PHOSPHORYLATED HISTIDINE. MODEL 2 IS DERIVED FROM MODEL 1 BY RESTRAINED MINIMIZATION IN WHICH MINIMAL SHIFTS IN THE BACKBONE COORDINATES (AND ASSOCIATED SIDE CHAINS) OF RESIDUES 8-12 OF CHAIN B OF IIAMANNOSE AND RESIDUES 173-177 OF IIBMANNOSE (CHAIN C) ARE ALLOWED TO OCCUR IN ORDER TO ACCOMMODATE THE STEREOCHEMICAL REQUIREMENTS OF THE TRANSITION STATE. SEE PUBLICATION FOR DETAILS.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-edited/13C-edited NOE
12212C-filtered/13C-separated NOE
NMR detailsText: Triple resonance experiments for assignment. Quantitative J correlation experiments for heteronuclear scalar couplings. 3D and 2D isotope filtered/isotope-separated NOE experiments for intermolecular NOEs.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-1 mM IIAMan(H10E)+IIBMan, 90% H2O/10% D2O90% H2O/10% D2O
20.5-1 mM IIAMan(H10E)+IIBMan, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMIIAMan(H10E)+IIBMan1
20 mMsodium phosphatenatural abundance1
0.01 %sodium azidenatural abundance1
0.5 mMIIAMan(H10E)+IIBMan2
20 mMsodium phosphatenatural abundance2
0.01 %sodium azidenatural abundance2
Sample conditionsIonic strength: 20 mM phosphate / pH: 6.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMX500BrukerDMX5005001
Bruker DMX600BrukerDMX6006002
Bruker DRX600BrukerDRX6006003
Bruker DRX800BrukerDRX8008004

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.18.1Schwieters, Kuszewski, and Clorestructure solution
X-PLOR NIH2.18.1Schwieters, Kuszewski, and Clorerefinement
RefinementMethod: conjoined rigid body, torsion angle simulated annealing
Software ordinal: 2
Details: COORDINATES OF IIAMAN (1PDO) AND IIBMAN (2JZH) ARE TREATED AS RIGID BODIES WITH THE INTERFACIAL SIDE CHAINS GIVEN TORSIONAL DEGREES OF FREEDOM. RESIDUES 130- 134 OF IIAMAN ARE ALSO GIVEN ...Details: COORDINATES OF IIAMAN (1PDO) AND IIBMAN (2JZH) ARE TREATED AS RIGID BODIES WITH THE INTERFACIAL SIDE CHAINS GIVEN TORSIONAL DEGREES OF FREEDOM. RESIDUES 130- 134 OF IIAMAN ARE ALSO GIVEN TORSIONAL DEGREES OF FREEDOM SINCE INTERMOLECULAR NOES WERE OBSERVED INVOLVED THESE RESIDUES ALTHOUGH THEY ARE NOT VISIBLE IN THE ELECTRON DENSITY MAP OF THE X-RAY STRUCTURE OF FREE IIAMAN. FURTHER DETAILS IN PUBLICATION. THE COORDINATES of 1VSQ ARE DERIVED DIRECTLY FROM THOSE OF 2JZN, THE IIAMAN(H10E)-IIBMAN COMPLEX.
NMR ensembleConformer selection criteria: restrained regularized mean / Conformers calculated total number: 120 / Conformers submitted total number: 2
NMR ensemble rmsDistance rms dev: 0.02 Å

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