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- PDB-1vrv: Structure of phosphorylated IIB (C384(SEP)) domain of the mannito... -

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Basic information

Entry
Database: PDB / ID: 1vrv
TitleStructure of phosphorylated IIB (C384(SEP)) domain of the mannitol-specific permease enzyme II
Componentsmannitol-specific PTS system enzyme IIABC components
KeywordsTRANSFERASE / PHOSPHOTRANSFERASE / KINASE / SUGAR TRANSPORT
Function / homology
Function and homology information


protein-Npi-phosphohistidine-D-mannitol phosphotransferase / sorbitol transmembrane transport / protein-N(PI)-phosphohistidine-mannitol phosphotransferase system transmembrane transporter activity / protein-phosphocysteine-mannitol phosphotransferase system transporter activity / mannitol transmembrane transport / protein-phosphocysteine-sugar phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / plasma membrane
Similarity search - Function
Phosphotransferase system, mannitol-specific enzyme IIC / Phosphotransferase system EIIB component, mannitol-specific / : / Phosphotransferase system, EIIC component, type 2 / PTS_EIIC type-2 domain profile. / PTS EIIA domains phosphorylation site signature 2. / Phosphotransferase system, EIIB component, type 2 / PTS_EIIB type-2 domain profile. / PTS EIIA type-2 domain / Phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 2 ...Phosphotransferase system, mannitol-specific enzyme IIC / Phosphotransferase system EIIB component, mannitol-specific / : / Phosphotransferase system, EIIC component, type 2 / PTS_EIIC type-2 domain profile. / PTS EIIA domains phosphorylation site signature 2. / Phosphotransferase system, EIIB component, type 2 / PTS_EIIB type-2 domain profile. / PTS EIIA type-2 domain / Phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 2 / PTS_EIIA type-2 domain profile. / Phosphotransferase system, EIIC / Phosphotransferase system, EIIC / Phosphotransferase system, EIIB component, type 2/3 / PTS system IIB component-like superfamily / PTS system, Lactose/Cellobiose specific IIB subunit / Phosphotransferase/anion transporter / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PTS system mannitol-specific EIICBA component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsSuh, J.Y. / Tang, C. / Cai, M. / Clore, G.M.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Visualization of the Phosphorylated Active Site Loop of the Cytoplasmic B Domain of the Mannitol Transporter II(Mannitol) of the Escherichia coli Phosphotransferase System by NMR Spectroscopy ...Title: Visualization of the Phosphorylated Active Site Loop of the Cytoplasmic B Domain of the Mannitol Transporter II(Mannitol) of the Escherichia coli Phosphotransferase System by NMR Spectroscopy and Residual Dipolar Couplings.
Authors: Suh, J.Y. / Tang, C. / Cai, M. / Clore, G.M.
History
DepositionJun 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / struct_conn / struct_ref_seq_dif
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 / _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: mannitol-specific PTS system enzyme IIABC components


Theoretical massNumber of molelcules
Total (without water)11,0281
Polymers11,0281
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 / 150REGULARIZED MEAN STRUCTURE
Representative

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Components

#1: Protein mannitol-specific PTS system enzyme IIABC components / IIBMTL PHOSPHOTRANSFERASE ENZYME II / B COMPONENT / EIIB-MTL


Mass: 11028.347 Da / Num. of mol.: 1 / Fragment: IIB DOMAIN / Mutation: C384(SEP)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 / Production host: Escherichia coli (E. coli) / References: UniProt: P00550

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111(1) TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEIN
121(2) QUANTITATIVE J CORRELATION FOR COUPLING CONSTANTS
131(3) 3D HETERONUCLEAR SEPARATED NOE EXPTS
141(4) IPAP AND COUPLED HSQC EXPERIMENTS FOR DIPOLAR COUPLINGS.

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Sample preparation

Sample conditionsIonic strength: 0 EXCEPT FOR RDC MEASUREMENTS IN PHAGE PF1 WHERE IT WAS 0.5M
pH: 7.4 / Temperature: 303.00 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMX600BrukerDMX6006001
Bruker DRX600BrukerDRX6006002
Bruker DMX650BrukerDMX6507503

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Processing

NMR softwareName: X-PLOR NIH / Version: (HTTP://NMR.CIT.NIH.GOV/XPLOR_NIH) / Developer: SCHWIETERS, KUSZEWSKI, TJANDRA, CLORE / Classification: refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: THE TARGET FUNCTION COMPRISES TERMS FOR THE NOE-DERIVED INTERPROTON DISTANCE RESTRAINTS, TORSION ANGLE RESTRAINTS, AND RESIDUAL DIPOLAR COUPLINGS (N-H, N-C' AND HN-C') IN THREE ALIGNMENT ...Details: THE TARGET FUNCTION COMPRISES TERMS FOR THE NOE-DERIVED INTERPROTON DISTANCE RESTRAINTS, TORSION ANGLE RESTRAINTS, AND RESIDUAL DIPOLAR COUPLINGS (N-H, N-C' AND HN-C') IN THREE ALIGNMENT MEDIA; A QUARTIC VAN DE WAALS REPULSION TERM, AND A TORSION ANGLE DATABASE POTENTIAL OF MEAN FORCE. IN THIS ENTRY THE LAST COLUMN FOR FOR THE ACTIVE SITE LOOP (RESIDUES 383-393) REPRESENTS THE AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL 150 SIMULATED ANNEALING STRUCTURES AND THE MEAN COORDINATE POSITIONS. NOTE ONLY THE COORDINATES OF THE ACTIVE SITE LOOP (RESIDUES 383-393) HAVE BEEN REFINED; THE REMAINDER OF THE PROTEIN COORDINATES ARE HELD FIXED AT THEIR POSITIONS IN UNPHOSPHORYLATED IIBMTL (PDB ACCESSION CODE 1VKR). THE LAST COLUMN FOR RESIDUES OUTSIDE THE ACTIVE SITE REPRESENTS THE AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL 100 SIMULATED ANNEALING STRUCTURES AND THE MEAN COORDINATE POSITIONS FOR THE STRUCTURE OF THE PREVIOUSLY DETERMINED UNPHOSPHORYLATED STATE (PDB ACCESSION CODE 1VKR). EXPERIMENTAL RESTRAINTS INVOLVING THE PHOSPHORYLATED ACTIVE SITE RESIDUES 383-394: 83 NOE-DERIVED INTERPROTON DISTANCE RESTRAINTS (8 INTRARESIDUE, 17 SEQUENTIAL, 20 MEDIUM RANGE AND 38 LONG-RANGE INTERRESIDUE) 21 TORSION ANGLES (10 PHI, 9 PSI AND TWO CHI1) 11 N-H, 11 N-C' and 11 HN-C' RDCS IN PHAGE PF1 11 N-H, 6 N-C' AND 6 HN-C' RDCS IN NEUTRAL ANISOTROPIC GEL 10 N-H RDCS IN A POSITIVELY CHARGED ANISOTROPIC GEL 12 RESTRAINTS FOR 6 BACKBONE H-BONDS INVOLVING ONE ACTIVE SITE RESIDUE 2 RESTRAINTS FOR A PHOSPHORYL-NH(SER391) H-BOND DEMONSTRATED BY OBSERVATION OF A 3JNP COUPLING. THE TOTAL NUMBER OF RDCS MEASURED FOR THE WHOLE PROTEIN WAS: 192 IN PHAGE PF1, 139 IN NEUTRAL GEL, AND 55 IN POSITIVE GEL. EXCLUDING A FEW OUTLIERS INVOLVING ONLY RESIDUES 386-391 WITHIN THE ACTIVE SITE, THE REMAINING RDCS FIT THE STRUCTURE OF THE UNPHOSPHORYLATED STATE (COORDINATES 1VKR) EXTREMELY WELL INDICATING THAT THE ONLY BACKBONE CONFORMATIONAL CHANGES THAT OCCUR UPON PHOSPHORYLATION ARE LOCALIZED SPECIFICALLY TO THE ACTIVE SITE (RESIDUES 383-393). THEREFORE ONLY THE COORDINATES OF THE ACTIVE SITE WERE REFINED WITH THE COORDINATES OF THE REMAINDER OF THE PROTEIN FIXED TO THEIR POSITIONS IN 1VKR.
NMR ensembleConformer selection criteria: REGULARIZED MEAN STRUCTURE / Conformers calculated total number: 150 / Conformers submitted total number: 1

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