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Yorodumi- PDB-2wy2: NMR structure of the IIAchitobiose-IIBchitobiose phosphoryl trans... -
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-Basic information
Entry | Database: PDB / ID: 2wy2 | ||||||
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Title | NMR structure of the IIAchitobiose-IIBchitobiose phosphoryl transition state complex of the N,N'-diacetylchitoboise brance of the E. coli phosphotransferase system. | ||||||
Components |
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Keywords | TRANSFERASE / 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 | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | SOLUTION NMR | ||||||
Model type details | RESTRAINED MINIMIZED AVERAGE, MODEL 1 | ||||||
Authors | Sang, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wy2.cif.gz | 7.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2wy2.ent.gz | 6.7 MB | Display | PDB format |
PDBx/mmJSON format | 2wy2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wy/2wy2 ftp://data.pdbj.org/pub/pdb/validation_reports/wy/2wy2 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | 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 | | 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 / | Compound details | ENGINEERED RESIDUE IN CHAIN A, ASP 92 TO LEU ENGINEERED RESIDUE IN CHAIN B, ASP 92 TO LEU ...ENGINEERED | Nonpolymer details | PHOSPHORYL | Sequence details | RESIDUE 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 CORRESPOND | |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR details | Text: NONE |
-Sample preparation
Sample conditions | Temperature: 308.0 K |
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-NMR measurement
NMR spectrometer |
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-Processing
NMR software | Name: Xplor-NIH / Version: 2.23 / Developer: SCHWIETERS,KUSZEWSKI,CLORE / Classification: refinement |
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Refinement | Software 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 ensemble | Conformers calculated total number: 64 / Conformers submitted total number: 64 |