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PDBsum entry 1zym

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protein Protein-protein interface(s) links
Phosphotransferase PDB id
1zym
Jmol
Contents
Protein chains
247 a.a. *
Waters ×64
* Residue conservation analysis
PDB id:
1zym
Name: Phosphotransferase
Title: Amino terminal domain of enzyme i from escherichia coli
Structure: Enzyme i. Chain: a, b. Fragment: amino-terminal domain residues 1 - 258. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Strain: gi698. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.50Å     R-factor:   0.205     R-free:   0.306
Authors: D.-I.Liao,D.R.Davies
Key ref:
D.I.Liao et al. (1996). The first step in sugar transport: crystal structure of the amino terminal domain of enzyme I of the E. coli PEP: sugar phosphotransferase system and a model of the phosphotransfer complex with HPr. Structure, 4, 861-872. PubMed id: 8805571
Date:
21-May-96     Release date:   07-Dec-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P08839  (PT1_ECOLI) -  Phosphoenolpyruvate-protein phosphotransferase
Seq:
Struc:
 
Seq:
Struc:
575 a.a.
247 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.3.9  - Phosphoenolpyruvate--protein phosphotransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Phosphoenolpyruvate + protein L-histidine = pyruvate + protein N(pi)- phospho-L-histidine
Phosphoenolpyruvate
+ protein L-histidine
= pyruvate
+ protein N(pi)- phospho-L-histidine
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     phosphoenolpyruvate-dependent sugar phosphotransferase system   2 terms 
  Biochemical function     transferase activity, transferring phosphorus-containing groups     1 term  

 

 
    reference    
 
 
Structure 4:861-872 (1996)
PubMed id: 8805571  
 
 
The first step in sugar transport: crystal structure of the amino terminal domain of enzyme I of the E. coli PEP: sugar phosphotransferase system and a model of the phosphotransfer complex with HPr.
D.I.Liao, E.Silverton, Y.J.Seok, B.R.Lee, A.Peterkofsky, D.R.Davies.
 
  ABSTRACT  
 
BACKGROUND: The bacterial phosphoenolpyruvate (PEP): sugar phosphotransferase system (PTS) transports exogenous hexose sugars through the membrane and tightly couples transport with phosphoryl transfer from PEP to the sugar via several phosphoprotein intermediates. The phosphate group is first transferred to enzyme I, second to the histidine-containing phosphocarrier protein HPr, and then to one of a number of sugar-specific enzymes II. The structures of several HPrs and enzymes IIA are known. Here we report the structure of the N-terminal half of enzyme I from Escherichia coli (EIN). RESULTS: The crystal structure of EIN (MW approximately 30 kDa) has been determined and refined at 2.5 A resolution. It has two distinct structural subdomains; one contains four alpha helices arranged as two hairpins in a claw-like conformation. The other consists of a beta sandwich containing a three-stranded antiparallel beta sheet and a four-stranded parallel beta sheet, together with three short alpha helices. Plausible models of complexes between EIN and HPr can be made without assuming major structural changes in either protein. CONCLUSIONS: The alpha/beta subdomain of EIN is topologically similar to the phosphohistidine domain of the enzyme pyruvate phosphate dikinase, which is phosphorylated by PEP on a histidyl residue but does not interact with HPr. It is therefore likely that features of this subdomain are important in the autophosphorylation of enzyme I. The helical subdomain of EIN is not found in pyruvate phosphate dikinase; this subdomain is therefore more likely to be involved in phosphoryl transfer to HPr.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21455271 N.M.Burton, and L.J.Bruce (2011).
Modelling the structure of the red cell membrane.
  Biochem Cell Biol, 89, 200-215.  
20024602 D.Stratmann, E.Guittet, and C.van Heijenoort (2010).
Robust structure-based resonance assignment for functional protein studies by NMR.
  J Biomol NMR, 46, 157-173.  
20392103 Y.Ryabov, G.M.Clore, and C.D.Schwieters (2010).
Direct use of 15N relaxation rates as experimental restraints on molecular shape and orientation for docking of protein-protein complexes.
  J Am Chem Soc, 132, 5987-5989.  
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
19801641 A.E.Oberholzer, P.Schneider, C.Siebold, U.Baumann, and B.Erni (2009).
Crystal structure of enzyme I of the phosphoenolpyruvate sugar phosphotransferase system in the dephosphorylated state.
  J Biol Chem, 284, 33169-33176.
PDB code: 2wqd
19074506 D.Stratmann, C.van Heijenoort, and E.Guittet (2009).
NOEnet--use of NOE networks for NMR resonance assignment of proteins with known 3D structure.
  Bioinformatics, 25, 474-481.  
19537713 Y.Ryabov, J.Y.Suh, A.Grishaev, G.M.Clore, and C.D.Schwieters (2009).
Using the experimentally determined components of the overall rotational diffusion tensor to restrain molecular shape and size in NMR structure determination of globular proteins and protein-protein complexes.
  J Am Chem Soc, 131, 9522-9531.  
18931781 G.M.Clore (2008).
Visualizing lowly-populated regions of the free energy landscape of macromolecular complexes by paramagnetic relaxation enhancement.
  Mol Biosyst, 4, 1058-1069.  
18445588 J.Y.Suh, M.Cai, and G.M.Clore (2008).
Impact of phosphorylation on structure and thermodynamics of the interaction between the N-terminal domain of enzyme I and the histidine phosphocarrier protein of the bacterial phosphotransferase system.
  J Biol Chem, 283, 18980-18989.  
16967193 C.Tang, and G.M.Clore (2006).
A simple and reliable approach to docking protein-protein complexes from very sparse NOE-derived intermolecular distance restraints.
  J Biomol NMR, 36, 37-44.  
16581832 E.Hurtado-Gómez, G.Fernández-Ballester, H.Nothaft, J.Gómez, F.Titgemeyer, and J.L.Neira (2006).
Biophysical characterization of the enzyme I of the Streptomyces coelicolor phosphoenolpyruvate:sugar phosphotransferase system.
  Biophys J, 90, 4592-4604.  
16547354 H.V.Patel, K.A.Vyas, R.L.Mattoo, M.Southworth, F.B.Perler, D.Comb, and S.Roseman (2006).
Properties of the C-terminal domain of enzyme I of the Escherichia coli phosphotransferase system.
  J Biol Chem, 281, 17579-17587.  
16547355 H.V.Patel, K.A.Vyas, R.Savtchenko, and S.Roseman (2006).
The monomer/dimer transition of enzyme I of the Escherichia coli phosphotransferase system.
  J Biol Chem, 281, 17570-17578.  
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.  
16867985 J.Márquez, S.Reinelt, B.Koch, R.Engelmann, W.Hengstenberg, and K.Scheffzek (2006).
Structure of the full-length enzyme I of the phosphoenolpyruvate-dependent sugar phosphotransferase system.
  J Biol Chem, 281, 32508-32515.
PDB code: 2hro
17008723 P.Zhang, J.Zhao, B.Wang, J.Du, Y.Lu, J.Chen, and J.Ding (2006).
The MRG domain of human MRG15 uses a shallow hydrophobic pocket to interact with the N-terminal region of PAM14.
  Protein Sci, 15, 2423-2434.
PDB code: 2f5j
15647264 A.Gorrell, S.H.Lawrence, and J.G.Ferry (2005).
Structural and kinetic analyses of arginine residues in the active site of the acetate kinase from Methanosarcina thermophila.
  J Biol Chem, 280, 10731-10742.
PDB codes: 1tuu 1tuy
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
15869381 D.Davies, and D.Davies (2005).
A quiet life with proteins.
  Annu Rev Biophys Biomol Struct, 34, 1.  
16195557 N.Leulliot, S.Quevillon-Cheruel, M.Graille, M.Schiltz, K.Blondeau, J.Janin, and H.Van Tilbeurgh (2005).
Crystal structure of yeast YER010Cp, a knotable member of the RraA protein family.
  Protein Sci, 14, 2751-2758.
PDB code: 2c5q
16339738 R.D.Barabote, and M.H.Saier (2005).
Comparative genomic analyses of the bacterial phosphotransferase system.
  Microbiol Mol Biol Rev, 69, 608-634.  
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
12945046 A.Dobrodumov, and A.M.Gronenborn (2003).
Filtering and selection of structural models: combining docking and NMR.
  Proteins, 53, 18-32.  
12966101 C.Siebold, I.Arnold, L.F.Garcia-Alles, U.Baumann, and B.Erni (2003).
Crystal structure of the Citrobacter freundii dihydroxyacetone kinase reveals an eight-stranded alpha-helical barrel ATP-binding domain.
  J Biol Chem, 278, 48236-48244.
PDB codes: 1un8 1un9
12517345 D.I.Liao, L.Reiss, I.Turner, and G.Dotson (2003).
Structure of glycerol dehydratase reactivase: a new type of molecular chaperone.
  Structure, 11, 109-119.
PDB code: 1nbw
12837779 J.M.Johnston, V.L.Arcus, C.J.Morton, M.W.Parker, and E.N.Baker (2003).
Crystal structure of a putative methyltransferase from Mycobacterium tuberculosis: misannotation of a genome clarified by protein structural analysis.
  J Bacteriol, 185, 4057-4065.
PDB code: 1nxj
11904409 J.A.Márquez, S.Hasenbein, B.Koch, S.Fieulaine, S.Nessler, R.B.Russell, W.Hengstenberg, and K.Scheffzek (2002).
Structure of the full-length HPr kinase/phosphatase from Staphylococcus xylosus at 1.95 A resolution: Mimicking the product/substrate of the phospho transfer reactions.
  Proc Natl Acad Sci U S A, 99, 3458-3463.
PDB code: 1ko7
11741915 L.F.Garcia-Alles, K.Flükiger, J.Hewel, R.Gutknecht, C.Siebold, S.Schürch, and B.Erni (2002).
Mechanism-based inhibition of enzyme I of the Escherichia coli phosphotransferase system. Cysteine 502 is an essential residue.
  J Biol Chem, 277, 6934-6942.  
11350937 R.Gutknecht, R.Beutler, L.F.Garcia-Alles, U.Baumann, and B.Erni (2001).
The dihydroxyacetone kinase of Escherichia coli utilizes a phosphoprotein instead of ATP as phosphoryl donor.
  EMBO J, 20, 2480-2486.  
11551914 S.Napper, S.J.Brokx, E.Pally, J.Kindrachuk, L.T.Delbaere, and E.B.Waygood (2001).
Substitution of aspartate and glutamate for active center histidines in the Escherichia coli phosphoenolpyruvate:sugar phosphotransferase system maintain phosphotransfer potential.
  J Biol Chem, 276, 41588-41593.  
11567104 X.J.Morelli, P.N.Palma, F.Guerlesquin, and A.C.Rigby (2001).
A novel approach for assessing macromolecular complexes combining soft-docking calculations with NMR data.
  Protein Sci, 10, 2131-2137.  
  10892802 A.Ginsburg, R.H.Szczepanowski, S.B.Ruvinov, N.J.Nosworthy, M.Sondej, T.C.Umland, and A.Peterkofsky (2000).
Conformational stability changes of the amino terminal domain of enzyme I of the Escherichia coli phosphoenolpyruvate: sugar phosphotransferase system produced by substituting alanine or glutamate for the active-site histidine 189: implications for phosphorylation effects.
  Protein Sci, 9, 1085-1094.  
10922057 G.M.Clore (2000).
Accurate and rapid docking of protein-protein complexes on the basis of intermolecular nuclear overhauser enhancement data and dipolar couplings by rigid body minimization.
  Proc Natl Acad Sci U S A, 97, 9021-9025.  
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
10801478 M.W.Vetting, and D.H.Ohlendorf (2000).
The 1.8 A crystal structure of catechol 1,2-dioxygenase reveals a novel hydrophobic helical zipper as a subunit linker.
  Structure, 8, 429-440.
PDB codes: 1dlm 1dlq 1dlt 1dmh
10736161 S.J.Brokx, J.Talbot, F.Georges, and E.B.Waygood (2000).
Enzyme I of the phosphoenolpyruvate:sugar phosphotransferase system. In vitro intragenic complementation: the roles of Arg126 in phosphoryl transfer and the C-terminal domain in dimerization.
  Biochemistry, 39, 3624-3635.  
10569929 P.P.Zhu, R.H.Szczepanowski, N.J.Nosworthy, A.Ginsburg, and A.Peterkofsky (1999).
Reconstitution studies using the helical and carboxy-terminal domains of enzyme I of the phosphoenolpyruvate:sugar phosphotransferase system.
  Biochemistry, 38, 15470-15479.  
10368305 V.L.Robinson, and A.M.Stock (1999).
High energy exchange: proteins that make or break phosphoramidate bonds.
  Structure, 7, R47-R53.  
9671705 A.Fomenkov, A.Valiakhmetov, L.Brand, and S.Roseman (1998).
In vivo and in vitro complementation of the N-terminal domain of enzyme I of the Escherichia coli phosphotransferase system by the cloned C-terminal domain.
  Proc Natl Acad Sci U S A, 95, 8491-8495.  
9578555 N.J.Nosworthy, A.Peterkofsky, S.König, Y.J.Seok, R.H.Szczepanowski, and A.Ginsburg (1998).
Phosphorylation destabilizes the amino-terminal domain of enzyme I of the Escherichia coli phosphoenolpyruvate:sugar phosphotransferase system.
  Biochemistry, 37, 6718-6726.  
9575172 R.Gutknecht, R.Lanz, and B.Erni (1998).
Mutational analysis of invariant arginines in the IIAB(Man) subunit of the Escherichia coli phosphotransferase system.
  J Biol Chem, 273, 12234-12238.  
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
  9336834 B.E.Jones, P.Rajagopal, and R.E.Klevit (1997).
Phosphorylation on histidine is accompanied by localized structural changes in the phosphocarrier protein, HPr from Bacillus subtilis.
  Protein Sci, 6, 2107-2119.
PDB codes: 1jem 2hid
9109646 D.S.Garrett, Y.J.Seok, A.Peterkofsky, G.M.Clore, and A.M.Gronenborn (1997).
Identification by NMR of the binding surface for the histidine-containing phosphocarrier protein HPr on the N-terminal domain of enzyme I of the Escherichia coli phosphotransferase system.
  Biochemistry, 36, 4393-4398.  
9054557 D.S.Garrett, Y.J.Seok, D.I.Liao, A.Peterkofsky, A.M.Gronenborn, and G.M.Clore (1997).
Solution structure of the 30 kDa N-terminal domain of enzyme I of the Escherichia coli phosphoenolpyruvate:sugar phosphotransferase system by multidimensional NMR.
  Biochemistry, 36, 2517-2530.
PDB codes: 1eza 1ezb 1ezc 1ezd
9204284 J.Reizer, and M.H.Saier (1997).
Modular multidomain phosphoryl transfer proteins of bacteria.
  Curr Opin Struct Biol, 7, 407-415.  
9434897 M.M.McEvoy, and F.W.Dahlquist (1997).
Phosphohistidines in bacterial signaling.
  Curr Opin Struct Biol, 7, 793-797.  
9187651 N.Tjandra, D.S.Garrett, A.M.Gronenborn, A.Bax, and G.M.Clore (1997).
Defining long range order in NMR structure determination from the dependence of heteronuclear relaxation times on rotational diffusion anisotropy.
  Nat Struct Biol, 4, 443-449.
PDB codes: 2eza 2ezb 2ezc
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
9032081 R.L.van Montfort, T.Pijning, K.H.Kalk, J.Reizer, M.H.Saier, M.M.Thunnissen, G.T.Robillard, and B.W.Dijkstra (1997).
The structure of an energy-coupling protein from bacteria, IIBcellobiose, reveals similarity to eukaryotic protein tyrosine phosphatases.
  Structure, 5, 217-225.
PDB code: 1iib
9030753 S.Seip, R.Lanz, R.Gutknecht, K.Flükiger, and B.Erni (1997).
The fructose transporter of Bacillus subtilis encoded by the lev operon: backbone assignment and secondary structure of the IIB(Lev) subunit.
  Eur J Biochem, 243, 306-314.  
8994876 L.N.Johnson, and M.O'Reilly (1996).
Control by phosphorylation.
  Curr Opin Struct Biol, 6, 762-769.  
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.