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- PDB-2few: Complex of enzyme IIAMTL and phosphorylated enzyme IIBMTL from Es... -

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Basic information

Entry
Database: PDB / ID: 2few
TitleComplex of enzyme IIAMTL and phosphorylated enzyme IIBMTL from Escherichia coli NMR, restrained regularized mean structure
Components
  • PTS system mannitol-specific EIICBA component
  • mannitol-specific PTS system enzyme IIABC components
KeywordsTRANSFERASE / PHOSPHOTRANSFERASE / KINASE / SUGAR TRANSPORT / COMPLEX (TRANSFERASE-PHOSPHOCARRIER)
Function / homology
Function and homology information


protein-Npi-phosphohistidine-D-mannitol phosphotransferase / 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 / phosphorylation / 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 / Phosphotransferase system, EIIC / 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 / Phosphotransferase system, EIIC / Phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 2 / Phosphotransferase system, EIIC / PTS_EIIA type-2 domain profile. / Phosphotransferase system, EIIB component, type 2/3 / PTS system IIB component-like superfamily / PTS system, Lactose/Cellobiose specific IIB subunit / Mannitol-specific EII; Chain A / Mannitol-specific EII; Chain A / 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)
Escherichia coli O157:H7 (bacteria)
MethodSOLUTION NMR / CONJOINED RIGID BODY, TORSION ANGLE DYNAMICS
AuthorsClore, G.M. / Suh, J.Y.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Solution Structure of a Post-transition State Analog of the Phosphotransfer Reaction between the A and B Cytoplasmic Domains of the Mannitol Transporter IIMannitol of the Escherichia coli Phosphotransferase System
Authors: Suh, J.Y. / Cai, M. / Williams Jr., D.C. / Clore, G.M.
History
DepositionDec 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PTS system mannitol-specific EIICBA component
B: mannitol-specific PTS system enzyme IIABC components


Theoretical massNumber of molelcules
Total (without water)27,3672
Polymers27,3672
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 200REGULARIZED MEAN STRUCTURE
Representative

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Components

#1: Protein PTS system mannitol-specific EIICBA component


Mass: 16338.529 Da / Num. of mol.: 1
Fragment: EIIA-MTL, PHOSPHOTRANSFERASE ENZYME II, A DOMAIN COMPONENT
Mutation: H65Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: GI698 / Gene: mtlA / Production host: Escherichia coli (E. coli)
References: UniProt: P00550, protein-Npi-phosphohistidine-sugar phosphotransferase
#2: Protein mannitol-specific PTS system enzyme IIABC components


Mass: 11028.347 Da / Num. of mol.: 1
Fragment: EIIB-MTL, PHOSPHOTRANSFERASE ENZYME II, B DOMAIN COMPONENT
Mutation: C384(SEP)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Species: Escherichia coli / Strain: GI698 / Production host: Escherichia coli (E. coli)
References: GenBank: 13363950, UniProt: P00550*PLUS, protein-Npi-phosphohistidine-sugar phosphotransferase
Sequence detailsRESIDUE NUMBERING: IIAMTL: 4-147 (RESIDUES 1-3 ARE DISORDERED IN SOLUTION AND NOT VISIBLE IN THE ...RESIDUE NUMBERING: IIAMTL: 4-147 (RESIDUES 1-3 ARE DISORDERED IN SOLUTION AND NOT VISIBLE IN THE ELECTRON DENSITY MAP OF THE CRYSTAL STRUCTURE OF THE FREE PROTEIN). IN INTACT ENZYME IIMTL, THESE COORESPOND TO RESIDUES 493-636 OF INTACT ENZYME IIMTL. IIBMTL: 375-471 (CORRESPONDS TO NUMBERING IN INTACT IIMTL) PHOSPHATE: RESIDUE 200

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: THE FOLLOWING EXPERIMENTS WERE CONDUCTED: (1) TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEINS; (2) QUANTITATIVE J CORRELATION FOR COUPLING CONSTANTS; (3) 3D AND 4D HETERONUCLEAR SEPARATED AND ...Text: THE FOLLOWING EXPERIMENTS WERE CONDUCTED: (1) TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEINS; (2) QUANTITATIVE J CORRELATION FOR COUPLING CONSTANTS; (3) 3D AND 4D HETERONUCLEAR SEPARATED AND FILTERED NOE EXPERIMENTS; (4) IPAP EXPERIMENTS FOR DIPOLAR COUPLINGS. DIPOLAR COUPLINGS WERE MEASURED IN A NEUTRAL AXIALLY STRETCHED POLYACRYLAMIDE GEL.

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Sample preparation

Sample conditionsIonic strength: 20 mM TRIS-D11 / pH: 7.4 / Temperature: 303.00 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMX500BrukerDMX5005001
Bruker DMX600BrukerDMX6006002
Bruker DRX600BrukerDRX6007503
Bruker DRX750BrukerDRX7508004
Bruker DRX800BrukerDRX8008005

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Processing

NMR softwareName: Xplor-NIH / Developer: SCHWIETERS,KUSZEWSKI,TJANDRA,CLORE / Classification: refinement
RefinementMethod: CONJOINED RIGID BODY, TORSION ANGLE DYNAMICS / Software ordinal: 1
Details: THE STRUCTURES WERE CALCULATED BY CONJOINED RIGID BODY/TORSION ANGLE DYNAMICS (SCHWIETERS & CLORE (2001) J.MAGN.RESON 152, 288-302) THE TARGET FUNCTIONS COMPRISES TERMS FOR THE EXPERIMENTAL ...Details: THE STRUCTURES WERE CALCULATED BY CONJOINED RIGID BODY/TORSION ANGLE DYNAMICS (SCHWIETERS & CLORE (2001) J.MAGN.RESON 152, 288-302) THE TARGET FUNCTIONS COMPRISES TERMS FOR THE EXPERIMENTAL NOE RESTRAINTS AND SIDECHAIN TORSION ANGLE RESTRAINTS; A QUARTIC VAN DER WAALS REPULSION TERM (NILGES ET AL. (1988) FEBS LETT. 229, 129-136); A MULTIIMENSIONAL TORSION ANGLE DATABASE POTENTIAL OF MEAN FORCE (CLORE & KUSZEWSKI (2002) J.AM.CHEM.SOC. 124, 2866-2867); AND A RADIUS OF GYRATION POTENTIAL (KUSZEWSKI ET AL (1999) J.AM.CHEM.SOC. 121, 2337-2338). THE STARTING COORDINATES OF PHOSPHOIIBMTL ARE TAKEN FROM THE NMR STRUCTURE ((PDB ACCESSION CODE 1VRV, SUH ET AL. (2005) J.MOL.BIOL. 353, 1129-1136). THE STARTING STRUCTURE FOR IIAMTL IS TAKEN FROM THE COORDINATES OF IIAMTL IN THE IIAMTL-HPR COMPLEX (PDB ACCESSION CODE 1J6T; CORNILESCU ET AL. (2002) J.BIOL.CHEM. 277,42289-42298). THE COORDINATES OF IIAMTL IN THIS COMPLEX ARE DERIVED FROM MOLECULE D OF THE 1.8A RESOLUTION CRYSTAL STRUCTURE OF IIAMTL PDB ACCESSION CODE 1A3A, VAN MONTFORT ET AL. STRUCTURE 5, 217-225 (1998)). IN THE STRUCTURE DETERMINATION OF THE IIAMTL-PHOSPHOIIBMTL COMPLEX, THE BACKBONE COORDINATES AND NON-INTERFACIAL SIDECHAINS ARE TREATED AS RIGID BODIES THROUGHOUT WITH IIAMTL HELD FIXED AND PHOSPHOIIBMTL ALLOWED TO ROTATE AND TRANSLATE. THE INTERFACIAL SIDECHAINS ARE GIVEN FULL TORSIONAL DEGREES OF FREEDOM. IN THIS ENTRY THE LAST COLUMN REPRESENTS THE AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL SIMULATED ANNEALING STRUCTURES (TOTAL OF 200) AND THE MEAN COORDINATE POSITIONS. IT IS IMPORTANT TO NOTE THAT THE VALUES GIVEN FOR THE BACKBONE ATOMS AND NON-INTERFACIAL SIDECHAINS PROVIDE ONLY A MEASURE OF THE PRECISION WITH WHICH THE RELATIVE OF THE TWO PROTEINS HAVE BEEN DETERMINED AND DOES NOT TAKE INTO ACCOUNT THE ERRORS IN THE NMR COORDINATES OF PHOSPHOIIBMTL AND THE XRAY/NMR COORDINATES OF IIAMTL. THE COORDINATES DEPOSITED CORRESPOND TO THE RESTRAINED REGULARIZED MEAN COORDINATES. THE STRUCTURE IS BASED ON 84 INTERMOLECULAR NOE RESTRAINTS BETWEEN IIAMTL AND IIBMTL; 37 INTRAMOLECULAR NOE RESTRAINTS FOR IIAMTL AND 46 46 INTRAMOLECULAR NOE RESTRAINTS FOR IIBMTL RELATED ONLY TO INTERFACIAL SIDECHAINS; AND 55 SIDECHAIN TORSION ANGLE RESTRAINTS (36 FOR IIAMTL AND 19 FOR IIBMTL) RELATED TO INTERFACIAL SIDECHAINS ONLY. DEVIATIONS FROM NOE DISTANCE RESTRAINTS: 0.009 A DEVIATIONS FROM SIDECHAIN TORSION ANGLE RESTRAINTS: 0.31 DEG DEVIATIONS FROM IDEALIZED GEOMETRY: BONDS 0.006A, ANGLES: 0.9 DEG, IMPROPER TORSIONS 1.3 DEG.
NMR ensembleConformer selection criteria: REGULARIZED MEAN STRUCTURE / Conformers calculated total number: 200 / Conformers submitted total number: 1

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