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PDBsum entry 1ebb
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Hydrolase PDB id
1ebb

 

 

 

 

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Contents
Protein chain
202 a.a. *
Ligands
SO4 ×5
GOL ×3
Waters ×33
* Residue conservation analysis
PDB id:
1ebb
Name: Hydrolase
Title: Bacillus stearothermophilus yhfr
Structure: Phosphatase. Chain: a. Synonym: yhfr. Engineered: yes
Source: Bacillus stearothermophilus. Organism_taxid: 1422. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Biol. unit: Monomer (from PDB file)
Resolution:
2.30Å     R-factor:   0.230     R-free:   0.263
Authors: D.J.Rigden,M.J.Jedrzejas
Key ref:
D.J.Rigden et al. (2002). Structure and mechanism of action of a cofactor-dependent phosphoglycerate mutase homolog from Bacillus stearothermophilus with broad specificity phosphatase activity. J Mol Biol, 315, 1129-1143. PubMed id: 11827481 DOI: 10.1006/jmbi.2001.5290
Date:
24-Jul-01     Release date:   11-Feb-02    
PROCHECK
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 Headers
 References

Protein chain
Q9ALU0  (Q9ALU0_GEOSE) -  Phosphoglycerate mutase (Fragment) from Geobacillus stearothermophilus
Seq:
Struc: 		195 a.a.
202 a.a.*
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 

 
DOI no: 10.1006/jmbi.2001.5290 J Mol Biol 315:1129-1143 (2002)
PubMed id: 11827481  
 
 
Structure and mechanism of action of a cofactor-dependent phosphoglycerate mutase homolog from Bacillus stearothermophilus with broad specificity phosphatase activity.
D.J.Rigden, L.V.Mello, P.Setlow, M.J.Jedrzejas.
 
  ABSTRACT  
 
The crystal structure of Bacillus stearothermophilus PhoE (originally termed YhfR), a broad specificity monomeric phosphatase with a molecular mass of approximately 24 kDa, has been solved at 2.3 A resolution in order to investigate its structure and function. PhoE, already identified as a homolog of a cofactor-dependent phosphoglycerate mutase, shares with the latter an alpha/beta/alpha sandwich structure spanning, as a structural excursion, a smaller subdomain composed of two alpha-helices and one short beta-strand. The active site contains residues from both the alpha/beta/alpha sandwich and the sub-domain. With the exception of the hydrophilic catalytic machinery conserved throughout the cofactor-dependent phosphoglycerate mutase family, the active-site cleft is strikingly hydrophobic. Docking studies with two diverse, favored substrates show that 3-phosphoglycerate may bind to the catalytic core, while alpha-napthylphosphate binding also involves the hydrophobic portion of the active-site cleft. Combining a highly favorable phospho group binding site common to these substrate binding modes and data from related enzymes, a catalytic mechanism can be proposed that involves formation of a phosphohistidine intermediate on His10 and likely acid-base behavior of Glu83. Other structural factors contributing to the broad substrate specificity of PhoE can be identified. The dynamic independence of the subdomain may enable the active-site cleft to accommodate substrates of different sizes, although similar motions are present in simulations of cofactor-dependent phosphoglycerate mutases, perhaps favoring a more general functional role. A significant number of entries in protein sequence databases, particularly from unfinished microbial genomes, are more similar to PhoE than to cofactor-dependent phosphoglycerate mutases or to fructose-2,6-bisphosphatases. This PhoE structure will therefore serve as a valuable basis for inference of structural and functional characteristics of these proteins.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Neighbor-joining tree representation of structural relationships in the dPGM superfamily. Distances between structures were based on their structural similarities. The PDB codes were as follows: rat 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, 1bif; E. coli dPGM, 1e58; S. cerevisiae dPGM, 1qhf; Sch. pombe dPGM, 1fzt; human prostatic acid phosphatase, 1cvi; E. coli phytase, 1dkl; Aspergillus ficuum phytase, 1ihp; A. niger acid phosphatase, 1qfx. 		Figure 6.
Figure 6. Modeled binding conformations for modeled substrates 3-phosphoglycerate and a-napthylphosphate. The same protein residues coloring scheme as that used in Figure 4 and Figure 5 is applied but only side-chain and C^a atoms of residues predicted to bind either substrate are shown. Asn16 was omitted for clarity from (a), since it lies in front of the 3-phosphoglycerate moiety. Hydrogen bonds are shown with dotted lines. (a) 3-Phosphoglycerate and (b) a-napthylphosphate.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 315, 1129-1143) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20363939 H.A.Watkins, and E.N.Baker (2010).
Structural and functional characterization of an RNase HI domain from the bifunctional protein Rv2228c from Mycobacterium tuberculosis.
  J Bacteriol, 192, 2878-2886.
PDB code: 3hst
19015259 H.Li, and G.Jogl (2009).
Structural and Biochemical Studies of TIGAR (TP53-induced Glycolysis and Apoptosis Regulator).
  J Biol Chem, 284, 1748-1754.  
19836403 H.Singh, R.L.Felts, J.P.Schuermann, T.J.Reilly, and J.J.Tanner (2009).
Crystal Structures of the histidine acid phosphatase from Francisella tularensis provide insight into substrate recognition.
  J Mol Biol, 394, 893-904.
PDB codes: 3it0 3it1 3it2 3it3
17024352 A.Djikeng, S.Raverdy, J.Foster, D.Bartholomeu, Y.Zhang, N.M.El-Sayed, and C.Carlow (2007).
Cofactor-independent phosphoglycerate mutase is an essential gene in procyclic form Trypanosoma brucei.
  Parasitol Res, 100, 887-892.  
17348005 L.Davies, I.P.Anderson, P.C.Turner, A.D.Shirras, H.H.Rees, and D.J.Rigden (2007).
An unsuspected ecdysteroid/steroid phosphatase activity in the key T-cell regulator, Sts-1: surprising relationship to insect ecdysteroid phosphate phosphatase.
  Proteins, 67, 720-731.  
17468884 L.Song, Z.Xu, and X.Yu (2007).
Molecular cloning and characterization of a phosphoglycerate mutase gene from Clonorchis sinensis.
  Parasitol Res, 101, 709-714.  
17085493 M.Nukui, L.V.Mello, J.E.Littlejohn, B.Setlow, P.Setlow, K.Kim, T.Leighton, and M.J.Jedrzejas (2007).
Structure and molecular mechanism of Bacillus anthracis cofactor-independent phosphoglycerate mutase: a crucial enzyme for spores and growing cells of Bacillus species.
  Biophys J, 92, 977-988.
PDB code: 2ify
16672613 H.A.Watkins, and E.N.Baker (2006).
Structural and functional analysis of Rv3214 from Mycobacterium tuberculosis, a protein with conflicting functional annotations, leads to its characterization as a phosphatase.
  J Bacteriol, 188, 3589-3599.
PDB code: 2a6p
17052986 Y.Wang, L.Liu, Z.Wei, Z.Cheng, Y.Lin, and W.Gong (2006).
Seeing the process of histidine phosphorylation in human bisphosphoglycerate mutase.
  J Biol Chem, 281, 39642-39648.
PDB codes: 2a9j 2f90 2h4x 2h4z 2h52 2hhj
15388943 Y.Wang, Z.Cheng, L.Liu, Z.Wei, M.Wan, and W.Gong (2004).
Cloning, purification, crystallization and preliminary crystallographic analysis of human phosphoglycerate mutase.
  Acta Crystallogr D Biol Crystallogr, 60, 1893-1894.  
15258155 Y.Wang, Z.Wei, Q.Bian, Z.Cheng, M.Wan, L.Liu, and W.Gong (2004).
Crystal structure of human bisphosphoglycerate mutase.
  J Biol Chem, 279, 39132-39138.
PDB code: 1t8p
15234973 Y.Zhang, J.M.Foster, S.Kumar, M.Fougere, and C.K.Carlow (2004).
Cofactor-independent phosphoglycerate mutase has an essential role in Caenorhabditis elegans and is conserved in parasitic nematodes.
  J Biol Chem, 279, 37185-37190.  
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.

 

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