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- PDB-2lrk: Solution Structures of the IIA(Chitobiose)-HPr complex of the N,N... -

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Basic information

Entry
Database: PDB / ID: 2lrk
TitleSolution Structures of the IIA(Chitobiose)-HPr complex of the N,N'-Diacetylchitobiose
Components
  • N,N'-diacetylchitobiose-specific phosphotransferase enzyme IIA component
  • Phosphocarrier protein HPr
KeywordsTRANSFERASE / protein-protein complex
Function / homology
Function and homology information


protein-phosphocysteine-N,N'-diacetylchitobiose phosphotransferase system transporter activity / N,N'-diacetylchitobiose import / phosphotransferase activity, nitrogenous group as acceptor / regulation of carbon utilization / antisigma factor binding / positive regulation of glycogen catabolic process / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / enzyme inhibitor activity / enzyme activator activity ...protein-phosphocysteine-N,N'-diacetylchitobiose phosphotransferase system transporter activity / N,N'-diacetylchitobiose import / phosphotransferase activity, nitrogenous group as acceptor / regulation of carbon utilization / antisigma factor binding / positive regulation of glycogen catabolic process / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / enzyme inhibitor activity / enzyme activator activity / enzyme regulator activity / protein-containing complex / cytosol
Similarity search - Function
Phosphotransferase system, lactose/cellobiose-type IIA subunit / Phosphotransferase system, lactose/cellobiose-type IIA subunit superfamily / PTS system, Lactose/Cellobiose specific IIA subunit / PTS_EIIA type-3 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 / Phosphotransferase system, lactose/cellobiose-type IIA subunit ...Phosphotransferase system, lactose/cellobiose-type IIA subunit / Phosphotransferase system, lactose/cellobiose-type IIA subunit superfamily / PTS system, Lactose/Cellobiose specific IIA subunit / PTS_EIIA type-3 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 / Phosphotransferase system, lactose/cellobiose-type IIA subunit / Histidine-containing Protein; Chain: A; / Phosphocarrier protein HPr-like / HPr-like superfamily / PTS HPr component phosphorylation site / PTS HPR domain profile. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Phosphocarrier protein HPr / PTS system N,N'-diacetylchitobiose-specific EIIA component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsCai, M. / Jung, Y. / Clore, M.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Solution Structure of the IIAChitobiose-HPr Complex of the N,N'-Diacetylchitobiose Branch of the Escherichia coli Phosphotransferase System.
Authors: Jung, Y.S. / Cai, M. / Clore, G.M.
History
DepositionApr 6, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2012Group: Database references
Revision 1.2Jul 25, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Phosphocarrier protein HPr
A: N,N'-diacetylchitobiose-specific phosphotransferase enzyme IIA component
B: N,N'-diacetylchitobiose-specific phosphotransferase enzyme IIA component
C: N,N'-diacetylchitobiose-specific phosphotransferase enzyme IIA component


Theoretical massNumber of molelcules
Total (without water)42,8714
Polymers42,8714
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Phosphocarrier protein HPr / Histidine-containing protein


Mass: 9129.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ptsH, hpr, b2415, JW2408 / Production host: Escherichia coli (E. coli)
References: UniProt: P0AA04, Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases
#2: Protein N,N'-diacetylchitobiose-specific phosphotransferase enzyme IIA component / EIIA-Chb / EIII-Chb / PTS system N / N'-diacetylchitobiose-specific EIIA component


Mass: 11247.152 Da / Num. of mol.: 3 / Fragment: PTS EIIA type-3 residues 14-116 / Mutation: H76E, D79L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: chbA, celC, b1736, JW1725 / Production host: Escherichia coli (E. coli)
References: UniProt: P69791, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(COCA)CB
1413D HNCA
151c13-c12 edited/filted NOESY
1622D 1H-15N HSQC
1723D CBCA(CO)NH
1823D HN(COCA)CB
1923D HNCA
1102c13-c12 edited/filted NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-100% 15N] HPr/IIAChb complex, 1.0 mM [U-100% 13C; U-100% 15N] HPR/IIAChb complex, 1.0 mM [U-100% 13C; U-100% 15N] HPR/IIAChb complex, 90% H2O/10% D2O90% H2O/10% D2O
21.0 mM [U-100% 15N] HPr/IIAChb complex, 1.0 mM [U-100% 13C; U-100% 15N] HPR/IIAChb complex, 1.0 mM [U-100% 13C; U-100% 15N] HPR/IIAChb complex, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMHPr/IIAChb complex-1[U-100% 15N]1
1.0 mMHPR/IIAChb complex-2[U-100% 13C; U-100% 15N]1
1.0 mMHPR/IIAChb complex-3[U-100% 13C; U-100% 15N]1
1.0 mMHPr/IIAChb complex-4[U-100% 15N]2
1.0 mMHPR/IIAChb complex-5[U-100% 13C; U-100% 15N]2
1.0 mMHPR/IIAChb complex-6[U-100% 13C; U-100% 15N]2
Sample conditionsIonic strength: 0.02 / pH: 7.4 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 900 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR_NIHSchwieters, Kuszewski, Tjandra and Cloredata analysis
X-PLOR_NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: conjoined rigid body/torsion angle simulated annealing
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 21

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