spacer
spacer

PDBsum entry 1pfh
Go to PDB code: 
protein links
Transport protein PDB id
1pfh

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chain
85 a.a. *
* Residue conservation analysis
PDB id:
1pfh
Name: Transport protein
Title: The phosphorylated form of the histidine-containing phosphocarrier protein hpr
Structure: Phospho-hpr. Chain: a. Synonym: p-hpr. Other_details: ph 7.5, 20 degrees c, 50 mm kpi buffer
Source: Escherichia coli. Organism_taxid: 562. Strain: hb2154
NMR struc: 20 models
Authors: N.A.J.Van Nuland,R.M.Scheek,G.T.Robillard
Key ref: N.A.van Nuland et al. (1995). High-resolution structure of the phosphorylated form of the histidine-containing phosphocarrier protein HPr from Escherichia coli determined by restrained molecular dynamics from NMR-NOE data. J Mol Biol, 246, 180-193. PubMed id: 7853396
Date:
18-Aug-95     Release date:   14-Nov-95    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0AA04  (PTHP_ECOLI) -  Phosphocarrier protein HPr from Escherichia coli (strain K12)
Seq:
Struc: 		85 a.a.
85 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 

 
J Mol Biol 246:180-193 (1995)
PubMed id: 7853396  
 
 
High-resolution structure of the phosphorylated form of the histidine-containing phosphocarrier protein HPr from Escherichia coli determined by restrained molecular dynamics from NMR-NOE data.
N.A.van Nuland, R.Boelens, R.M.Scheek, G.T.Robillard.
 
  ABSTRACT  
 
The solution structure of the phosphorylated form of the histidine-containing phosphocarrier protein, HPr, from Escherichia coli has been determined by NMR in combination with restrained molecular dynamics simulations. The structure of phospho-HPr (P-HPr) results from a molecular dynamics simulation in water, using time-dependent distance restraints to attain agreement with the measured NOEs. Experimental restraints were identified from both three-dimensional 1H-1H-15N HSQC-NOESY and two-dimensional 1H-1HNOESY spectra, and compared with those of the unphosphorylated form. Structural changes upon phosphorylation of HPr are limited to the active site, as evidenced by changes in chemical shifts, in 3JNHH alpha-coupling constants and NOE patterns. Chemical shift changes were obtained mainly for protons that were positioned close to the phosphoryl group attached to the His15 imidazole ring. Differences could be detected in the intensity of the NOEs involving the side-chain protons of His15 and Pro18, resulting from a change in the relative position of the two rings. In addition, a small change could be detected in the three-bond J-coupling between the amide proton and the H alpha proton of Thr16 and Arg17 upon phosphorylation, in agreement with the changes of the phi torsion angle of these two residues obtained from time-averaged restrained molecular dynamics simulations in water. The proposed role of the torsion-angle strain at residue 16 in the mechanism of Streptococcus faecalis HPr is not supported by these results. In contrast, phosphorylation seems to introduce torsion angle strain at residue His15. This strain could facilitate the transfer of the phosphoryl group to the A-domain at enzyme II. The phospho-histidine is not stabilised by hydrogen bonds to the side-chain group of Arg17; instead stable hydrogen bonds are formed between the phosphate group and the backbone amide protons of Thr16 and Arg17, which show the largest changes in chemical shift upon phosphorylation, and a hydrogen bond involving the side-chain O gamma proton of Thr16. HPr accepts the phosphoryl group from enzyme I and donates it subsequently to the A domain of various enzyme II species. The binding site for EI on HPr resembles that of the A domain of the mannitol-specific enzyme II, as can be concluded from the changes on the amide proton and nitrogen chemical shifts observed via heteromolecular single-quantum coherence spectroscopy.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
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.  
18537106 K.Furihata, S.Shimotakahara, and M.Tashiro (2008).
An efficient use of the WATERGATE W5 sequence for observing a ligand binding with a protein receptor.
  Magn Reson Chem, 46, 799-802.  
18702519 S.Napper, L.Prasad, and L.T.Delbaere (2008).
Structural investigation of a phosphorylation-catalyzed, isoaspartate-free, protein succinimide: crystallographic structure of post-succinimide His15Asp histidine-containing protein.
  Biochemistry, 47, 9486-9496.
PDB code: 3ccd
17449611 B.Reichenbach, D.A.Breustedt, J.Stülke, B.Rak, and B.Görke (2007).
Genetic dissection of specificity determinants in the interaction of HPr with enzymes II of the bacterial phosphoenolpyruvate:sugar phosphotransferase system in Escherichia coli.
  J Bacteriol, 189, 4603-4613.  
16737961 J.S.Lott, B.Paget, J.M.Johnston, L.T.Delbaere, J.A.Sigrell-Simon, M.J.Banfield, and E.N.Baker (2006).
The structure of an ancient conserved domain establishes a structural basis for stable histidine phosphorylation and identifies a new family of adenosine-specific kinases.
  J Biol Chem, 281, 22131-22141.
PDB codes: 1wvq 2gl0
15476289 S.Shimotakahara, K.Furihata, and M.Tashiro (2005).
Application of NMR screening techniques for observing ligand binding with a protein receptor.
  Magn Reson Chem, 43, 69-72.  
15606769 A.Möglich, B.Koch, W.Gronwald, W.Hengstenberg, E.Brunner, and H.R.Kalbitzer (2004).
Solution structure of the active-centre mutant I14A of the histidine-containing phosphocarrier protein from Staphylococcus carnosus.
  Eur J Biochem, 271, 4815-4824.
PDB code: 1txe
15317796 T.Maurer, S.Meier, N.Kachel, C.E.Munte, S.Hasenbein, B.Koch, W.Hengstenberg, and H.R.Kalbitzer (2004).
High-resolution structure of the histidine-containing phosphocarrier protein (HPr) from Staphylococcus aureus and characterization of its interaction with the bifunctional HPr kinase/phosphorylase.
  J Bacteriol, 186, 5906-5918.
PDB code: 1ka5
14596413 H.Utsumi, H.Seki, K.Yamaguchi, and M.Tashiro (2003).
Segment identification of a ligand binding with a protein receptor using multidimensional T1rho-, diffusion-filtered and diffusion-ordered NOESY experiments.
  Anal Sci, 19, 1441-1443.  
12001233 J.G.Renisio, J.Pérez, M.Czisch, M.Guenneugues, O.Bornet, L.Frenken, C.Cambillau, and H.Darbon (2002).
Solution structure and backbone dynamics of an antigen-free heavy chain variable domain (VHH) from Llama.
  Proteins, 47, 546-555.
PDB code: 1g9e
11168402 T.Maurer, R.Döker, A.Görler, W.Hengstenberg, and H.R.Kalbitzer (2001).
Three-dimensional structure of the histidine-containing phosphocarrier protein (HPr) from Enterococcus faecalis in solution.
  Eur J Biochem, 268, 635-644.
PDB code: 1qfr
  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.  
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
  10794411 H.R.Kalbitzer, A.Görler, H.Li, P.V.Dubovskii, W.Hengstenberg, C.Kowolik, H.Yamada, and K.Akasaka (2000).
15N and 1H NMR study of histidine containing protein (HPr) from Staphylococcus carnosus at high pressure.
  Protein Sci, 9, 693-703.
PDB code: 1qr5
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.  
10668628 S.J.Brokx, S.Napper, G.Wong, A.Mirza, F.Georges, L.T.Delbaere, and E.B.Waygood (1999).
Identification of the Escherichia coli enzyme I binding site in histidine-containing protein, HPr, by the effects of mutagenesis.
  Biochem Cell Biol, 77, 507-513.  
10419492 S.Napper, L.T.Delbaere, and E.B.Waygood (1999).
The aspartyl replacement of the active site histidine in histidine-containing protein, HPr, of the Escherichia coli Phosphoenolpyruvate:Sugar phosphotransferase system can accept and donate a phosphoryl group. Spontaneous dephosphorylation of acyl-phosphate autocatalyzes an internal cyclization.
  J Biol Chem, 274, 21776-21782.
PDB codes: 1cm2 1cm3
  9541412 D.S.Garrett, Y.J.Seok, A.Peterkofsky, G.M.Clore, and A.M.Gronenborn (1998).
Tautomeric state and pKa of the phosphorylated active site histidine in the N-terminal domain of enzyme I of the Escherichia coli phosphoenolpyruvate:sugar phosphotransferase system.
  Protein Sci, 7, 789-793.  
9718298 P.P.Zhu, O.Herzberg, and A.Peterkofsky (1998).
Topography of the interaction of HPr(Ser) kinase with HPr.
  Biochemistry, 37, 11762-11770.  
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
9334231 B.E.Jones, V.Dossonnet, E.Küster, W.Hillen, J.Deutscher, and R.E.Klevit (1997).
Binding of the catabolite repressor protein CcpA to its DNA target is regulated by phosphorylation of its corepressor HPr.
  J Biol Chem, 272, 26530-26535.  
9329088 B.L.de Groot, D.M.van Aalten, R.M.Scheek, A.Amadei, G.Vriend, and H.J.Berendsen (1997).
Prediction of protein conformational freedom from distance constraints.
  Proteins, 29, 240-251.  
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
9434897 M.M.McEvoy, and F.W.Dahlquist (1997).
Phosphohistidines in bacterial signaling.
  Curr Opin Struct Biol, 7, 793-797.  
8953652 B.L.de Groot, A.Amadei, R.M.Scheek, N.A.van Nuland, and H.J.Berendsen (1996).
An extended sampling of the configurational space of HPr from E. coli.
  Proteins, 26, 314-322.  
8805571 D.I.Liao, E.Silverton, Y.J.Seok, B.R.Lee, A.Peterkofsky, and D.R.Davies (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.
PDB code: 1zym
8794735 J.E.Wedekind, P.A.Frey, and I.Rayment (1996).
The structure of nucleotidylated histidine-166 of galactose-1-phosphate uridylyltransferase provides insight into phosphoryl group transfer.
  Biochemistry, 35, 11560-11569.
PDB code: 1hxq
8784182 M.Eberstadt, S.G.Grdadolnik, G.Gemmecker, H.Kessler, A.Buhr, and B.Erni (1996).
Solution structure of the IIB domain of the glucose transporter of Escherichia coli.
  Biochemistry, 35, 11286-11292.
PDB code: 1iba
8784180 R.Thapar, E.M.Nicholson, P.Rajagopal, E.B.Waygood, J.M.Scholtz, and R.E.Klevit (1996).
Influence of N-cap mutations on the structure and stability of Escherichia coli HPr.
  Biochemistry, 35, 11268-11277.  
  8580838 K.Pullen, P.Rajagopal, B.R.Branchini, M.E.Huffine, J.Reizer, M.H.Saier, J.M.Scholtz, and R.E.Klevit (1995).
Phosphorylation of serine-46 in HPr, a key regulatory protein in bacteria, results in stabilization of its solution structure.
  Protein Sci, 4, 2478-2486.  
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 code is shown on the right.

 

spacer
spacer