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PDBsum entry 1iib

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Phosphotransferase PDB id
1iib
Jmol
Contents
Protein chains
103 a.a. *
Waters ×128
* Residue conservation analysis
PDB id:
1iib
Name: Phosphotransferase
Title: Crystal structure of iibcellobiose from escherichia coli
Structure: Enzyme iib of the cellobiose-specific phosphotran system. Chain: a, b. Fragment: enzyme iib. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 83333. Strain: k12. Cellular_location: cytoplasm. Gene: cela. Expressed in: escherichia coli str. K12 substr. W3110. Expression_system_taxid: 316407.
Resolution:
1.80Å     R-factor:   0.187     R-free:   0.241
Authors: R.L.M.Van Montfort,T.Pijning,K.H.Kalk,J.Reizer,M.H.Saier, M.M.G.M.Thunnissen,G.T.Robillard,B.W.Dijkstra
Key ref:
R.L.van Montfort et al. (1997). The structure of an energy-coupling protein from bacteria, IIBcellobiose, reveals similarity to eukaryotic protein tyrosine phosphatases. Structure, 5, 217-225. PubMed id: 9032081 DOI: 10.1016/S0969-2126(97)00180-9
Date:
23-Dec-96     Release date:   24-Dec-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P69795  (PTQB_ECOLI) -  N,N'-diacetylchitobiose-specific phosphotransferase enzyme IIB component
Seq:
Struc:
106 a.a.
103 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.2.7.1.69  - Protein-N(pi)-phosphohistidine--sugar phosphotransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Protein EIIB N(pi)-phospho-L-histidine/cysteine + sugar = protein EIIB + sugar phosphate

+
=
+
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     transport   5 terms 
  Biochemical function     transferase activity     3 terms  

 

 
    Key reference    
 
 
DOI no: 10.1016/S0969-2126(97)00180-9 Structure 5:217-225 (1997)
PubMed id: 9032081  
 
 
The structure of an energy-coupling protein from bacteria, IIBcellobiose, reveals similarity to eukaryotic protein tyrosine phosphatases.
R.L.van Montfort, T.Pijning, K.H.Kalk, J.Reizer, M.H.Saier, M.M.Thunnissen, G.T.Robillard, B.W.Dijkstra.
 
  ABSTRACT  
 
BACKGROUND:. The bacterial phosphoenolpyruvate-dependent phosphotransferase system (PTS) mediates the energy-driven uptake of carbohydrates and their concomitant phosphorylation. In addition, the PTS is intimately involved in the regulation of a variety of metabolic and transcriptional processes in the bacterium. The multiprotein PTS consists of a membrane channel and at least four cytoplasmic proteins or protein domains that sequentially transfer a phosphoryl group from phosphoenolpyruvate to the transported carbohydrate. Determination of the three-dimensional structure of the IIB enzymes within the multiprotein complex would provide insights into the mechanisms by which they promote efficient transport by the membrane channel IIC protein and phosphorylate the transported carbohydrate on the inside of the cell. RESULTS:. The crystal structure of the IIB enzyme specific for cellobiose, IIBcellobiose (molecular weight 11.4 kDa), has been determined to a resolution of 1.8 and refined to an R factor of 18.7% (Rfree of 24. 1%). The enzyme consists of a single four-stranded parallel beta sheet flanked by helices on both sides. The phosphorylation site (Cys 10) is located at the C-terminal end of the first beta strand. No positively charged residues, which could assist in phosphoryl-transfer, can be found in or near the active site. The fold of IIBcellobiose is remarkably similar to that of the mammalian low molecular weight protein tyrosine phosphatases. CONCLUSIONS:. A comparison between IIBcellobiose and the structurally similar low molecular weight protein tyrosine phosphatases provides insight into the mechanism of the phosphoryltransfer reactions in which IIBcellobiose is involved. The differences in tertiary structure and active-site composition between IIBcellobiose and the glucose-specific IIBglucose give a structural explanation why the carbo-hydrate-specific components of different families cannot complement each other.
 
  Selected figure(s)  
 
Figure 7.
Figure 7. Comparison of the structures of IIB^cel and the arabinose-binding protein (ABP; PDB entry code 8ABP. Strands of IIB^cel are shown in blue and helices in turquoise. Strands of ABP are shown in red and helices in gold. The galactose (Gal) in ABP is bound at the C-terminal end of the b strands. Superimposition of the N-terminal domain of ABP on IIB^cel would position the galactose close to the active site of IIB^cel, near Tyr84.
 
  The above figure is reprinted by permission from Cell Press: Structure (1997, 5, 217-225) copyright 1997.  
  Figure was selected by the author.  

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
19646450 D.E.Kim, B.Blum, P.Bradley, and D.Baker (2009).
Sampling bottlenecks in de novo protein structure prediction.
  J Mol Biol, 393, 249-260.  
18270202 J.Hu, K.Hu, D.C.Williams, M.E.Komlosh, M.Cai, and G.M.Clore (2008).
Solution NMR structures of productive and non-productive complexes between the A and B domains of the cytoplasmic subunit of the mannose transporter of the Escherichia coli phosphotransferase system.
  J Biol Chem, 283, 11024-11037.
PDB codes: 1vsq 2jzh 2jzn 2jzo
17612488 S.Watanabe, R.Matsumi, T.Arai, H.Atomi, T.Imanaka, and K.Miki (2007).
Crystal structures of [NiFe] hydrogenase maturation proteins HypC, HypD, and HypE: insights into cyanation reaction by thiol redox signaling.
  Mol Cell, 27, 29-40.
PDB codes: 2z1c 2z1d 2z1e 2z1f
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.  
16443929 J.Y.Suh, M.Cai, D.C.Williams, and G.M.Clore (2006).
Solution structure of a post-transition state analog of the phosphotransfer reaction between the A and B cytoplasmic domains of the mannitol transporter IIMannitol of the Escherichia coli phosphotransferase system.
  J Biol Chem, 281, 8939-8949.
PDB code: 2few
16963640 L.Volpon, C.R.Young, A.Matte, and K.Gehring (2006).
NMR structure of the enzyme GatB of the galactitol-specific phosphoenolpyruvate-dependent phosphotransferase system and its interaction with GatA.
  Protein Sci, 15, 2435-2441.
PDB code: 1tvm
15654077 C.Tang, D.C.Williams, R.Ghirlando, and G.M.Clore (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.
PDB code: 1wcr
15258141 P.M.Legler, M.Cai, A.Peterkofsky, and G.M.Clore (2004).
Three-dimensional solution structure of the cytoplasmic B domain of the mannitol transporter IImannitol of the Escherichia coli phosphotransferase system.
  J Biol Chem, 279, 39115-39121.
PDB code: 1vkr
12717033 B.M.Hespenheide, and L.A.Kuhn (2003).
Discovery of a significant, nontopological preference for antiparallel alignment of helices with parallel regions in sheets.
  Protein Sci, 12, 1119-1125.  
12624088 J.Benach, I.Lee, W.Edstrom, A.P.Kuzin, Y.Chiang, T.B.Acton, G.T.Montelione, and J.F.Hunt (2003).
The 2.3-A crystal structure of the shikimate 5-dehydrogenase orthologue YdiB from Escherichia coli suggests a novel catalytic environment for an NAD-dependent dehydrogenase.
  J Biol Chem, 278, 19176-19182.
PDB code: 1npd
12202490 G.Cornilescu, B.R.Lee, C.C.Cornilescu, G.Wang, A.Peterkofsky, and G.M.Clore (2002).
Solution structure of the phosphoryl transfer complex between the cytoplasmic A domain of the mannitol transporter IIMannitol and HPr of the Escherichia coli phosphotransferase system.
  J Biol Chem, 277, 42289-42298.
PDB code: 1j6t
11060015 G.Wang, J.M.Louis, M.Sondej, Y.J.Seok, A.Peterkofsky, and G.M.Clore (2000).
Solution structure of the phosphoryl transfer complex between the signal transducing proteins HPr and IIA(glucose) of the Escherichia coli phosphoenolpyruvate:sugar phosphotransferase system.
  EMBO J, 19, 5635-5649.
PDB code: 1ggr
10960084 M.H.Saier (2000).
Vectorial metabolism and the evolution of transport systems.
  J Bacteriol, 182, 5029-5035.  
10393270 G.T.Robillard, and J.Broos (1999).
Structure/function studies on the bacterial carbohydrate transporters, enzymes II, of the phosphoenolpyruvate-dependent phosphotransferase system.
  Biochim Biophys Acta, 1422, 73.  
10491176 H.Schüler, E.Korenbaum, C.E.Schutt, U.Lindberg, and R.Karlsson (1999).
Mutational analysis of Ser14 and Asp157 in the nucleotide-binding site of beta-actin.
  Eur J Biochem, 265, 210-220.  
  10595546 K.Volz (1999).
A test case for structure-based functional assignment: the 1.2 A crystal structure of the yjgF gene product from Escherichia coli.
  Protein Sci, 8, 2428-2437.
PDB code: 1qu9
10037691 R.Gutknecht, K.Flükiger, R.Lanz, and B.Erni (1999).
Mechanism of phosphoryl transfer in the dimeric IIABMan subunit of the Escherichia coli mannose transporter.
  J Biol Chem, 274, 6091-6096.  
9551558 R.L.van Montfort, T.Pijning, K.H.Kalk, I.Hangyi, M.L.Kouwijzer, G.T.Robillard, and B.W.Dijkstra (1998).
The structure of the Escherichia coli phosphotransferase IIAmannitol reveals a novel fold with two conformations of the active site.
  Structure, 6, 377-388.
PDB code: 1a3a
  9689219 J.Reizer, A.Reizer, M.Perego, and M.H.Saier (1997).
Characterization of a family of bacterial response regulator aspartyl-phosphate (RAP) phosphatases.
  Microb Comp Genomics, 2, 103-111.  
9261069 P.Sliz, R.Engelmann, W.Hengstenberg, and E.F.Pai (1997).
The structure of enzyme IIAlactose from Lactococcus lactis reveals a new fold and points to possible interactions of a multicomponent system.
  Structure, 5, 775-788.
PDB code: 1e2a
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.