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- PDB-1vrc: Complex of enzyme IIAmannose and the histidine-containing phospho... -

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Entry
Database: PDB / ID: 1vrc
TitleComplex of enzyme IIAmannose and the histidine-containing phosphocarrier protein HPr from escherichia coli nmr, restrained regularized mean structure
Components
  • PTS system, mannose-specific IIAB component
  • Phosphocarrier protein HPr
KeywordsTRANSFERASE / PHOSPHOTRANSFERASE / KINASE / SUGAR TRANSPORT / COMPLEX (TRANSFERASE-PHOSPHOCARRIER)
Function / homology
Function and homology information


protein-Npi-phosphohistidine-D-mannose phosphotransferase / mannose transmembrane transport / protein-N(PI)-phosphohistidine-mannose phosphotransferase system transporter activity / phosphotransferase activity, nitrogenous group as acceptor / regulation of carbon utilization / antisigma factor binding / glucose import across plasma membrane / positive regulation of glycogen catabolic process / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex ...protein-Npi-phosphohistidine-D-mannose phosphotransferase / mannose transmembrane transport / protein-N(PI)-phosphohistidine-mannose phosphotransferase system transporter activity / phosphotransferase activity, nitrogenous group as acceptor / regulation of carbon utilization / antisigma factor binding / glucose import across plasma membrane / positive regulation of glycogen catabolic process / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / enzyme inhibitor activity / enzyme activator activity / enzyme regulator activity / kinase activity / phosphorylation / protein homodimerization activity / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Phosphotransferase system, mannose family IIA component / Phosphotransferase system, sorbose subfamily IIB component, subgroup / 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 ...Phosphotransferase system, mannose family IIA component / Phosphotransferase system, sorbose subfamily IIB component, subgroup / 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. / Phosphotransferase system, HPr histidine phosphorylation site / 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. / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHITE ION / Phosphocarrier protein HPr / PTS system mannose-specific EIIAB component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / CONJOINED RIGID BODY, TORSION ANGLE DYNAMICS
AuthorsClore, G.M. / Williams, D.C.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Solution NMR structure of the 48-kDa IIAMannose-HPr complex of the Escherichia coli mannose phosphotransferase system.
Authors: Williams, D.C. / Cai, M. / Suh, J.Y. / Peterkofsky, A. / Clore, G.M.
History
DepositionFeb 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jun 30, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / entity ...atom_site / entity / pdbx_database_remark / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_torsion / struct_asym / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.pdbx_PDB_model_num / _atom_site.type_symbol / _entity.pdbx_number_of_molecules / _pdbx_database_remark.text / _pdbx_nmr_software.authors / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_close_contact.dist / _pdbx_validate_torsion.PDB_model_num / _pdbx_validate_torsion.auth_asym_id / _pdbx_validate_torsion.auth_comp_id / _pdbx_validate_torsion.auth_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_ref_seq_dif.details
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 7 IN THIS ENTRY THE LAST COLUMN REPRESENTS THE AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL ... IN THIS ENTRY THE LAST COLUMN REPRESENTS THE AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL SIMULATED ANNEALING STRUCTURES 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 ORIENTATION OF THE TWO PROTEINS HAVE BEEN DETERMINED AND DOES NOT TAKE INTO ACCOUNT THE ERRORS IN THE X-RAY COORDINATES OF HPR AND IIAMAN. RESIDUE NUMBERING: IIAMAN: 1-136 (THE N-TERMINAL METHIONINE IS CLEAVED AND RESIDUES 131-136 WERE DISORDERED. RESIDUES 134-136 ARE CLONING ARTIFACTS; SEE REMARKS IN THE 1PDO CRYSTAL STRUCTURE.) HPR: 201-285 (CORRESPONDING TO RESIDUES 1-85). PHOSPHATES: RESIDUES 401 AND 402. TWO SETS OF COORDINATES ARE GIVEN: MODEL 1: RESTRAINED REGULARIZED MEAN COORDINATES FOR THE MODEL OF THE ASSOCIATIVE PHOSPHORYL TRANSITION STATE HPR-IIAMTL COMPLEX. EXPERIMENTAL RESTRAINTS ARE IDENTICAL TO THOSE USED FOR MODEL 2, BUT COVALENT GEOMETRY RESTRAINTS ARE INCLUDED RELATING TO THE PENTACOORDINATE PHOSPHORYL GROUP IN A TRIGONAL BIPYRAMIDAL GEOMETRY. THE STRUCTURE IS DERIVED FROM MODEL 2 BY RESTRAINED REGULARIZATION IN WHICH ONLY THE ACTIVE SITE HISTIDINES, THE BACKBONE IMMIEDIATELY ADJACENT (ONE RESIDUE ON EITHER SIDE) TO THE ACTIVE SITE HISTIDINES, AND THE INTERFACIAL SIDECHAINS ARE ALLOWED TO MOVE. THE N-P BOND LENGTHS ARE RESTRAINED TO 2 A. IIAMAN-HPR COMPLEX RMS DEVIATIONS FROM NOE DISTANCE RESTRAINTS: 0.009 A RMS DEVIATIONS FROM SIDECHAIN TORSION ANGLE RESTRAINTS: 0.0 DEG. DIPOLAR COUPLING R-FACTORS (CLORE AND GARRETT (1999) J. AM. CHEM. SOC. 121, 9008-9012): IIAMAN HPr NH 11.6 18.5/12.4 MODEL 2: RESTRAINED REGULARIZED MEAN COORDINATES OF THE UNPHOSPHORYLATED IIAMAN-HPR COMPLEX SOLVED ON THE BASIS OF 58x2 INTERMOLECULAR INTERPROTON DISTANCE DISTANCE RESTRAINTS BETWEEN THE TWO MOLECULES OF HPR AND THE IIAMAN DIMER, 47x2 INTRA AND 16x2 INTER-SUBUNIT IIAMAN DISTANCE RESTRAINTS RELATING ONLY TO INTERFACIAL SIDECHAINS, 39x2 INTRAMOLECULAR HPR cwDISTANCE RESTRAINTS RELATING ONLY TO INTERFACIAL SIDECHAINS, 29x2 INTERFACIAL SIDECHAIN TORSION ANGLE RESTRAINTS, 92X2 RESIDUAL DIPOLAR COUPLINGS FOR IIAMAN AND 66X2 RESIDUAL DIPOLAR COUPLINGS FOR HPR. WAS USED FOR THE DIPOLAR COUPLINGS (CLORE AND GARRETT (1999) J. AM. CHEM. SOC. 121, 9008-9012). NOTE THE NH DIPOLAR COUPLINGS FOR FULLY BOUND HPR (I.E. BOTH BIDNING SITES ON IIAMAN FULLY SATURATED) ARE BACKCALCULATED FROM THE DIPOLAR COUPLINGS MEASURED FOR A SAMPLE WITH A THREE-FOLD MOLAR EXCESS OF HPR OVER IIAMAN BINDING SITES AND A SAMPLE OF FREE HPR. THE FIRST VALUE OF THE R-FACTOR USES DIPOLAR COUPLINGS FOR THE FULLY BOUND STATE BACK-CALCULATED USING THE MEASURED VALUES OF THE DIPOLAR OUPLINGS FOR FREE HPR; WHILE THE SECOND NUMBER USES THE CALCULATED VALUES OF THE DIPOLAR COUPLINGS FOR FREE HPR DERIVED FROM THE MEASURED VALUES AND THE CRYSTAL STRUCTURE OF FREE HPR USING SINGULAR VALUE DECOMPOSITION. NOTE A SINGLE ALIGNMENT TENSOR IS USED. THE DIPOLAR COUPLING R-FACTOR OBTAINED BY SINGULAR VALUE DECOMPOSITION AGAINST THE CRYSTAL STRUCTURES OF IIAMAN AND HPR INDIVIDUAL ARE THE SAME AS THOSE OBTAINED FOR THE COMPLEX AS A WHOLE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PTS system, mannose-specific IIAB component
B: PTS system, mannose-specific IIAB component
C: Phosphocarrier protein HPr
D: Phosphocarrier protein HPr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9286
Polymers47,7704
Non-polymers1582
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area6300 Å2
ΔGint-45 kcal/mol
Surface area17510 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)2 / 100REGULARIZED MEAN STRUCTURES
Representative

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Components

#1: Protein PTS system, mannose-specific IIAB component / EIIAB-Man / Mannose-permease IIAB component / Phosphotransferase enzyme II / AB component / EIII-Man


Mass: 14755.821 Da / Num. of mol.: 2 / Fragment: EIIA DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: manX, gptB, ptsL / Production host: Escherichia coli (E. coli)
References: UniProt: P69797, protein-Npi-phosphohistidine-sugar phosphotransferase
#2: Protein Phosphocarrier protein HPr / Histidine-containing protein


Mass: 9129.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ptsH, hpr / Production host: Escherichia coli (E. coli) / References: UniProt: P0AA04
#3: Chemical ChemComp-PO3 / PHOSPHITE ION / Phosphite ester


Mass: 78.972 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO3

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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
121(2) QUANTITATIVE J CORRELATION FOR COUPLING CONSTANTS
131(3) 3D,4D HETERONUCLEAR SEPARATED, FILTERED NOE EXPTS'
161(4) TRSOE-BASED 2D, 3D EXPERIMENTS FOR DIPOLAR COUPLINGS. DIPOLAR COUPLINGS WERE MEASURED IN A NEMATIC PHASE OF A 5% PEG/HEXANOL (SURFACTANT TO ALCOHOL RATION OF 0.96)

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Sample preparation

Sample conditionsIonic strength: 40 mM SODIUM PHOSPHATE / pH: 6.5 / Temperature: 308.00 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE DMXBrukerAVANCE DMX5001
Bruker AVANCE DMXBrukerAVANCE DMX6002
Bruker AVANCE DRXBrukerAVANCE DRX7503
Bruker AVANCE DRXBrukerAVANCE DRX8004
Bruker AVANCE DRXBrukerAVANCE DRX8005

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH(HTTP://NMR.CIT.NIH.GOV/XPLOR_NIH)CLORE, KUSZEWSKI, SCHWIETERS, TJANDRArefinement
X-PLOR NIHCLORE, KUSZEWSKI, SCHWIETERS, TJANDRAstructure solution
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 NOE RESTRAINTS, ...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 NOE RESTRAINTS, SIDECHAIN TORSION ANGLE RESTRAINTS, RESIDUAL DIPOLAR COUPLING RESTRAINTS (CLORE ET AL. J.MAGN.RESON. 131, 159-162 (1998); J.MAGN.RESON.133, 216-221(1998)), A RADIUS OF GYRATION TERM (KUSZEWSKI ET AL.(1999), A QUARTIC VAN DER WAALS REPULSION TERM (NILGES ET AL. (1988) FEBS LETT. 229, 129- 136), AND A TORSION ANGLE CONFORMATIONAL DATABASE POTENTIAL OF MEAN FORCE (CLORE AND KUSZEWSKI 2002) J.AM.CHEM.SOC 124, 2866-2867). THE STARTING COORDINATE COME FROM THE X-RAY STRUCTURES (WITH PROTONS ADDED) OF E. COLI HPR (1POH, JIA ET AL. (1993) J.BIOL.CHEM. 268, 22940-22501, RESOLUTION 2.0 A); AND IIAMAN (1PDO, NUNN ET AL. (1996) J.MOL.BI J.MOL.BIOL. 259, 502-511; RESOLUTION 1.7A). THE BACKBONE COORDINATES AND NON-INTERFACIAL SIDECHAINS ARE TREATED AS RIGID BODIES THROUGHOUT WITH THE IIAMAN DIMER HELD FIXED, THE TWO HPR MOLECULES ALLOWED TO ROTATE AND TRANSLATE, AND THE AXIS OF THE SINGLE DIPOLAR COUPLING ALIGNMENT TENSOR FREE TO ROTATE. THE INTERFACIAL SIDECHAINS ARE GIVEN FULL TORSIONAL DEGREES OF FREEDOM.
NMR ensembleConformer selection criteria: REGULARIZED MEAN STRUCTURES / Conformers calculated total number: 100 / Conformers submitted total number: 2

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