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PDBsum entry 1cm3

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Transferase PDB id
1cm3
Jmol
Contents
Protein chain
85 a.a. *
Waters ×243
* Residue conservation analysis
PDB id:
1cm3
Name: Transferase
Title: His15asp hpr from e. Coli
Structure: Histidine-containing protein. Chain: a. Synonym: phosphocarrier protein hpr. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: ptsh. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.60Å     R-factor:   0.191    
Authors: S.Napper,E.B.Waygood,L.T.J.Delbaere
Key ref:
S.Napper et al. (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. PubMed id: 10419492 DOI: 10.1074/jbc.274.31.21776
Date:
13-May-99     Release date:   17-May-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0AA04  (PTHP_ECOLI) -  Phosphocarrier protein HPr
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)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   2 terms 
  Biological process     transport   8 terms 
  Biochemical function     protein binding     7 terms  

 

 
DOI no: 10.1074/jbc.274.31.21776 J Biol Chem 274:21776-21782 (1999)
PubMed id: 10419492  
 
 
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.
S.Napper, L.T.Delbaere, E.B.Waygood.
 
  ABSTRACT  
 
The active site residue, His(15), in histidine-containing protein, HPr, can be replaced by aspartate and still act as a phosphoacceptor and phosphodonor with enzyme I and enzyme IIA(glucose), respectively. Other substitutions, including cysteine, glutamate, serine, threonine, and tyrosine, failed to show any activity. Enzyme I K(m) for His(15) --> Asp HPr is increased 10-fold and V(max) is decreased 1000-fold compared with wild type HPr. The phosphorylation of Asp(15) led to a spontaneous internal rearrangement involving the loss of the phosphoryl group and a water molecule, which was confirmed by mass spectrometry. The protein species formed had a higher pI than His(15) --> Asp HPr, which could arise from the formation of a succinimide or an isoimide. Hydrolysis of the isolated high pI form gave only aspartic acid at residue 15, and no isoaspartic acid was detected. This indicates that an isoimide rather than a succinimide is formed. In the absence of phosphorylation, no formation of the high pI form could be found, indicating that phosphorylation catalyzed the formation of the cyclization. The possible involvement of Asn(12) in an internal cyclization with Asp(15) was eliminated by the Asn(12) --> Ala mutation in His(15) --> AspHPr. Asn(12) substitutions of alanine, aspartate, serine, and threonine in wild type HPr indicated a general requirement for residues capable of forming a hydrogen bond with the Nepsilon(2) atom of His(15), but elimination of the hydrogen bond has only a 4-fold decrease in k(cat)/K(m).
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Mechanisms of formation of succinimide and isoimide rings. A, mechanism of succinimide formation according to Geiger and Clarke (21). Not shown is the formation of small amounts of D-aspartyl and D-isoaspartyl that also occurs. B, mechanism of isoimide formation (23). C, proposed mechanism for isoimide formation by P-Asp^15 in HPr involving hydrogen bonding with the amide nitrogen of residue 16.
Figure 6.
Fig. 6. Active site of His^15 Asp HPr. A, the active site residue Asp^15 and the electron density. The electron density map is from the 1.8 Å resolution structure of His^15 Asp HPr isolated high pI form in which the putative cyclization reverts to Asp^15. B and C, comparison of the active sites of HPr. B, the active sites of wild type HPr structure (11) with His^15 and His^15 Asp HPr structure (1.6 Å resolution structure) are compared by superimposition of the whole HPr structures. C, similarly normal His^15 Asp HPr and the putative cyclized form are compared.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (1999, 274, 21776-21782) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19544580 S.Sinha, L.Zhang, S.Duan, T.D.Williams, J.Vlasak, R.Ionescu, and E.M.Topp (2009).
Effect of protein structure on deamidation rate in the Fc fragment of an IgG1 monoclonal antibody.
  Protein Sci, 18, 1573-1584.  
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
17142294 G.van den Bogaart, V.Krasnikov, and B.Poolman (2007).
Dual-color fluorescence-burst analysis to probe protein efflux through the mechanosensitive channel MscL.
  Biophys J, 92, 1233-1240.  
17558470 J.A.Vila, M.E.Villegas, H.A.Baldoni, and H.A.Scheraga (2007).
Predicting 13Calpha chemical shifts for validation of protein structures.
  J Biomol NMR, 38, 221-235.  
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.