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PDBsum entry 1wcr

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protein Protein-protein interface(s) links
Transferase PDB id
1wcr
Jmol
Contents
Protein chains
103 a.a. *
* Residue conservation analysis
PDB id:
1wcr
Name: Transferase
Title: Trimeric structure of the enzyme iia from escherichia coli phosphotransferase system specific for n,n'- diacetylchitobiose
Structure: Pts system, n, n'-diacetylchitobiose-specific iia component. Chain: a, b, c. Fragment: residues 14-116. Synonym: eiia-chb, n, n'-diacetylchitobiose-permease iia component, phosphotransferase enzyme ii a component, eiii-chb. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 469008.
NMR struc: 1 models
Authors: C.Tang,G.M.Clore
Key ref:
C.Tang et al. (2005). Solution structure of enzyme IIA(Chitobiose) from the N,N'-diacetylchitobiose branch of the Escherichia coli phosphotransferase system. J Biol Chem, 280, 11770-11780. PubMed id: 15654077 DOI: 10.1074/jbc.M414300200
Date:
19-Nov-04     Release date:   19-Jan-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P69791  (PTQA_ECOLI) -  N,N'-diacetylchitobiose-specific phosphotransferase enzyme IIA component
Seq:
Struc:
116 a.a.
103 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     phosphoenolpyruvate-dependent sugar phosphotransferase system   1 term 

 

 
DOI no: 10.1074/jbc.M414300200 J Biol Chem 280:11770-11780 (2005)
PubMed id: 15654077  
 
 
Solution structure of enzyme IIA(Chitobiose) from the N,N'-diacetylchitobiose branch of the Escherichia coli phosphotransferase system.
C.Tang, D.C.Williams, R.Ghirlando, G.M.Clore.
 
  ABSTRACT  
 
The solution structure of trimeric Escherichia coli enzyme IIA(Chb) (34 kDa), a component of the N,N'-diacetylchitobiose/lactose branch of the phosphotransferase signal transduction system, has been determined by NMR spectroscopy. Backbone residual dipolar couplings were used to provide long range orientational restraints, and long range (|i - j| > or = 5 residues) nuclear Overhauser enhancement restraints were derived exclusively from samples in which at least one subunit was 15N/13C/2H/(Val-Leu-Ile)-methyl-protonated. Each subunit consists of a three-helix bundle. Hydrophobic residues lining helix 3 of each subunit are largely responsible for the formation of a parallel coiled-coil trimer. The active site histidines (His-89 from each subunit) are located in three symmetrically placed deep crevices located at the interface of two adjacent subunits (A and C, C and B, and B and A). Partially shielded from bulk solvent, structural modeling suggests that phosphorylated His-89 is stabilized by electrostatic interactions with the side chains of His-93 from the same subunit and Gln-91 from the adjacent subunit. Comparison with the x-ray structure of Lactobacillus lactis IIA(Lac) reveals some substantial structural differences, particularly in regard to helix 3, which exhibits a 40 degrees kink in IIA(Lac) versus a 7 degrees bend in IIA(Chb). This is associated with the presence of an unusually large (230-angstroms3) buried hydrophobic cavity at the trimer interface in IIA(Lac) that is reduced to only 45 angstroms3) in IIA(Chb).
 
  Selected figure(s)  
 
Figure 1.
FIG. 1. Sequence alignment of E. coli IIA^Chb and L. lactis IIA^Lac. The residue shown at position 92 of IIA^Chb is that of the IIA^Chb-N 13D92L double mutant (IIA^Chb*) used for structural studies; both wild-type IIA^Chb and L. lactis IIA^Lac have an Asp residue at this position. The N-terminal 13 residues that were deleted from wild-type IIA^Chb are colored in green; residue 92, the site of the engineered Asp to Leu mutation, is colored in bold red. Identical residues between IIA^Chb and IIA^Lac are shaded in yellow, closely similar ones are in magenta, and remotely similar ones are in cyan.
Figure 7.
FIG. 7. Comparison of the NMR structure of E. coli IIA^Chb* and the crystal structure of L. lactis IIA^Lac. A and B, ribbon diagrams showing best fit superpositions of the restrained regularized mean structure of IIA^Chb* (blue) and L. lactis IIA^Lac (red). Two views, orthogonal and parallel to the long axes of the helices, are shown in A and B, respectively, with the trimer displayed in A and an individual subunit in B. Best fitting was carried out with respect to the backbone atoms of helices 1 (residues 17-43) and 2 (residues 47-73) of all three subunits in A and with respect to helix 1 (residues 17-43) and the N-terminal half of helix 2 (residues 47-63) in B. For clarity, only the helices are shown in A, and the disordered N- and C-terminal residues are omitted in B. The side chains of Leu-92 of IIA^Chb* and the equivalent Asp of IIA^Lac are represented as bonds in A, and their C atom positions are 1.02, 0.92, and 0.92 Å apart for subunits A, B, and C, respectively. The three subunits are indicated in A, and the three helices of a single subunit are labeled in B. Note that the distance between the C-terminal end of helix 2 and the N-terminal end of helix 3 is significantly longer in IIA^Lac ( 21 Å) than in IIA^Chb ( 15 Å), yet the number of residues in the loop connecting helices 2 and 3 is 3 residues fewer in IIA^Lac. This may account for the observation that this loop is ordered in IIA^Lac but disordered in IIA^Chb. C, buried hydrophobic cavity (green) in IIA^Chb* (left-hand panel) and the crystal structure of L. lactis IIA^Lac (right-hand panel). The backbone atoms of residues 95-111 of the three subunits are depicted as tubes (blue), and the side chains of residues 99, 100, 103, and 107 are displayed in red as bonds (numbering scheme of IIA^Chb*). The cavity was calculated and displayed as a surface (green) using the program GRASP (32). The volume of the cavity in IIA^Chb* is 45 Å3 and lined by the side chains of Leu-103 and Leu-107; the volume of the cavity of IIA^Lac is 230 Å3 and lined by the side chains of Leu-99, Leu-100, Val-103, and Leu-107. D, comparison of the intersubunit interactions between helix 1 (subunit A) and helix 3 (subunit C) at the site of the kink in helix 3 (Glu-102) observed in the NMR structure of IIA^Chb* and the x-ray structure of IIA^Lac. The backbone (blue for IIA^Chb* and red for IIA^Lac) is displayed as a tube, and the side chains (cyan for IIA^Chb* and purple for IIA^Lac) are displayed as bonds. The coordinates for the crystal structure of L. lactis IIA^Lac are taken from Ref. 18 (Protein Data Bank code 1E2A [PDB] ).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 11770-11780) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19959833 Y.S.Jung, M.Cai, and G.M.Clore (2010).
Solution structure of the IIAChitobiose-IIBChitobiose complex of the N,N'-diacetylchitobiose branch of the Escherichia coli phosphotransferase system.
  J Biol Chem, 285, 4173-4184.
PDB codes: 2wwv 2wy2
17328009 M.Fischer, K.Kloiber, J.Häusler, K.Ledolter, R.Konrat, and W.Schmid (2007).
Synthesis of a 13C-methyl-group-labeled methionine precursor as a useful tool for simplifying protein structural analysis by NMR spectroscopy.
  Chembiochem, 8, 610-612.  
17158705 J.Deutscher, C.Francke, and P.W.Postma (2006).
How phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria.
  Microbiol Mol Biol Rev, 70, 939.  
16140525 A.Bax, and A.Grishaev (2005).
Weak alignment NMR: a hawk-eyed view of biomolecular structure.
  Curr Opin Struct Biol, 15, 563-570.  
16258829 C.Tang, J.Iwahara, and G.M.Clore (2005).
Accurate determination of leucine and valine side-chain conformations using U-[15N/13C/2H]/[1H-(methine/methyl)-Leu/Val] isotope labeling, NOE pattern recognition, and methine Cgamma-Hgamma/Cbeta-Hbeta residual dipolar couplings: application to the 34-kDa enzyme IIA(chitobiose).
  J Biomol NMR, 33, 105-121.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.