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- PDB-2wy2: NMR structure of the IIAchitobiose-IIBchitobiose phosphoryl trans... -

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Basic information

Entry
Database: PDB / ID: 2wy2
TitleNMR structure of the IIAchitobiose-IIBchitobiose phosphoryl transition state complex of the N,N'-diacetylchitoboise brance of the E. coli phosphotransferase system.
Components
  • N\,N'-DIACETYLCHITOBIOSE-SPECIFIC PHOSPHOTRANSFERASE ENZYME IIA COMPONENT
  • N\,N'-DIACETYLCHITOBIOSE-SPECIFIC PHOSPHOTRANSFERASE ENZYME IIB COMPONENT
KeywordsTRANSFERASE / KINASE / PHOSPHOTRANSFERASE SYSTEM / CHITOBIOSE / SUGAR TRANSPORT
Function / homology
Function and homology information


protein-Npi-phosphohistidine-N,N'-diacetylchitobiose phosphotransferase / protein-phosphocysteine-N,N'-diacetylchitobiose phosphotransferase system transporter activity / N,N'-diacetylchitobiose import / protein-Npi-phosphohistidine-D-mannose phosphotransferase / protein-Npi-phosphohistidine-sugar phosphotransferase / D-glucosamine PTS permease activity / protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex ...protein-Npi-phosphohistidine-N,N'-diacetylchitobiose phosphotransferase / protein-phosphocysteine-N,N'-diacetylchitobiose phosphotransferase system transporter activity / N,N'-diacetylchitobiose import / protein-Npi-phosphohistidine-D-mannose phosphotransferase / protein-Npi-phosphohistidine-sugar phosphotransferase / D-glucosamine PTS permease activity / protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / kinase activity / phosphorylation / protein-containing complex / cytosol
Similarity search - Function
Phosphotransferase system, EIIB component, type 3 / PTS_EIIB type-3 domain profile. / 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, EIIB component, type 2/3 / PTS system IIB component-like superfamily / PTS system, Lactose/Cellobiose specific IIB subunit / Phosphotransferase system, lactose/cellobiose-type IIA subunit ...Phosphotransferase system, EIIB component, type 3 / PTS_EIIB type-3 domain profile. / 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, EIIB component, type 2/3 / PTS system IIB component-like superfamily / PTS system, Lactose/Cellobiose specific IIB subunit / Phosphotransferase system, lactose/cellobiose-type IIA subunit / Response regulator / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHITE ION / N,N'-diacetylchitobiose-specific enzyme IIB component of PTS / PTS system N,N'-diacetylchitobiose-specific EIIA component / PTS system N,N'-diacetylchitobiose-specific EIIB component
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodSOLUTION NMR
Model type detailsRESTRAINED MINIMIZED AVERAGE, MODEL 1
AuthorsSang, Y.S. / Cai, M. / Clore, G.M.
Citation
Journal: J.Biol.Chem. / Year: 2010
Title: Solution Structure of the Iiachitobose-Iibchitobiose Complex of the N,N'-Diacetylchitobiose Branch of the Escherichia Coli Phosphotransfer System
Authors: Jung, Y.S. / Cai, M. / Clore, G.M.
#1: Journal: J.Biol.Chem. / Year: 2005
Title: Solution Structure of Enzyme Iia(Chitobiose) from the N,N'-Diacetylchitobiose Branch of the Escherichia Coli Phosphotransferase System.
Authors: Tang, C. / Williams, D.C.J. / Ghirlando, R. / Clore, G.M.
#2: Journal: Structure / Year: 1997
Title: The Structure of an Energy-Coupling Protein from Bacteria, Iibcellobiose, Reveals Similarity to Eukaryotic Protein Tyrosine Phosphatases.
Authors: Van Montfort, R.L. / Pijning, T. / Kalk, K.H. / Reizer, J. / Saier, M.H.J. / Thunnissen, M.M. / Robillard, G.T. / Dijkstra, B.W.
#3: Journal: J.Mol.Biol. / Year: 2001
Title: NMR Structure of Cysteinyl-Phosphorylated Enzyme Iib of the N,N'-Diacetylchitobiose-Specific Phosphoenolpyruvate-Dependent Phosphotransferase System of Escherichia Coli.
Authors: Ab, E. / Schuurman-Wolters, G.K. / Nijlant, D. / Dijkstra, K. / Saier, M.H. / Robillard, G.T. / Scheek, R.M.
History
DepositionNov 11, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references / Other / Version format compliance
Revision 1.2Apr 19, 2017Group: Other
Revision 1.3Oct 16, 2019Group: Data collection / Other ...Data collection / Other / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_nmr_software
Item: _entity.src_method / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
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
D: N\,N'-DIACETYLCHITOBIOSE-SPECIFIC PHOSPHOTRANSFERASE ENZYME IIB COMPONENT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9135
Polymers44,8344
Non-polymers791
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint-54 kcal/mol
Surface area21200 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)64 / 64
RepresentativeModel #1

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Components

#1: Protein N\,N'-DIACETYLCHITOBIOSE-SPECIFIC PHOSPHOTRANSFERASE ENZYME IIA COMPONENT / IIACHB / PTS SYSTEM N\ / N'-DIACETYLCHITOBIOSE-SPECIFIC EIIA COMPONENT / EIIA-CHB / EIII-CHB


Mass: 11256.186 Da / Num. of mol.: 3 / Fragment: RESIDUES 14-116 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria)
References: UniProt: P69791, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Protein N\,N'-DIACETYLCHITOBIOSE-SPECIFIC PHOSPHOTRANSFERASE ENZYME IIB COMPONENT / IIBCHB / PTS SYSTEM N\ / N'-DIACETYLCHITOBIOSE-SPECIFIC EIIB COMPONENT


Mass: 11065.101 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria)
References: UniProt: C3T7F7, UniProt: P69795*PLUS, protein-Npi-phosphohistidine-sugar phosphotransferase
#3: Chemical ChemComp-PO3 / PHOSPHITE ION / Phosphite ester


Mass: 78.972 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO3
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 92 TO LEU ENGINEERED RESIDUE IN CHAIN B, ASP 92 TO LEU ...ENGINEERED RESIDUE IN CHAIN A, ASP 92 TO LEU ENGINEERED RESIDUE IN CHAIN B, ASP 92 TO LEU ENGINEERED RESIDUE IN CHAIN C, ASP 92 TO LEU
Nonpolymer detailsPHOSPHORYL GROUP (PO3): THIS IS A PLANAR PHOSPHORYL GROUP IN A PENTACOORDINATE TRANSITION STATE
Sequence detailsRESIDUE 1 IN CHAINS A, B AND C CORRESPONDS TO RESIDUE 14 OF WILD TYPE IIACHB, RESIDUE 76 IS A HIS. ...RESIDUE 1 IN CHAINS A, B AND C CORRESPONDS TO RESIDUE 14 OF WILD TYPE IIACHB, RESIDUE 76 IS A HIS. TO OBTAIN WILD TYPE NUMBERING ADD 14. IN THE CONSTRUCT EMPLOYED THE 1ST 13 RESIDUES OF THE WILD TYPE HAVE BEEN DELETED. CHAIN D SEQUENCE STARTS AT RESIDUE 3 CHAIN D BEST MATCH AGAINST UNIPROT SEQUENCE DATABASE WAS FOUND TO BE C3T7F7. CHAIN D IS CHEMICALLY SYNTHESIZED.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: NONE

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Sample preparation

Sample conditionsTemperature: 308.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DMXBrukerDMX6002
Bruker DRXBrukerDRX6003
Bruker DRXBrukerDRX8004
Bruker DRXBrukerDRX9005

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Processing

NMR softwareName: Xplor-NIH / Version: 2.23 / Developer: SCHWIETERS,KUSZEWSKI,CLORE / Classification: refinement
RefinementSoftware ordinal: 1
Details: THE STRUCTURE WAS SOLVED ON THE BASIS OF THE COORDINATES OF THE UNPHOSPHORYLATED COMPLEX 2WWV. TO SOLVE THE TRANSITION STATE COMPLEX, THE COORDINATES OF THE UNPHOSPHORYLATED COMPLEX 2WWV ARE ...Details: THE STRUCTURE WAS SOLVED ON THE BASIS OF THE COORDINATES OF THE UNPHOSPHORYLATED COMPLEX 2WWV. TO SOLVE THE TRANSITION STATE COMPLEX, THE COORDINATES OF THE UNPHOSPHORYLATED COMPLEX 2WWV ARE HELD FIXED WITH THE EXCEPTION OF THE ACTIVE SITE LOOP OF IIBCHB, THE ACTIVE SITE OF IIACHB, THE PHOSPHORYL GROUP, AND INTERFACIAL SIDE CHAINS IN THE IMMEDIATE VICINITY OF THE ACTIVE SITE AND THE PHOSPHORYL GROUP WHICH ARE GIVEN TORSION DEGREES OF FREEDOM. THE ACTIVE SITE LOOP OF IIBCHB COMPRISES RESIDUES 9-16 OF CHAIN D. THE ACTIVE SITE REGION OF IIACHB COMPRISES RESIDUES 74 TO 79 OF CHAINS A, B AND C. THE EXPERIMENTAL NMR RESTRAINTS ARE IDENTICAL TO THOSE USED TO CALCULATE 2WWV EXCEPT FOR THE DIPOLAR COUPLINGS WHICH WERE OBTAINED FROM FREE PHOSPHORYLATED IIBCHB. FOR FURTHER DETAILS SEE THE JNRL CITATION ABOVE.
NMR ensembleConformers calculated total number: 64 / Conformers submitted total number: 64

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