PDBsum entry 2fym

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Lyase PDB id
Protein chains
431 a.a. *
15 a.a. *
_MG ×4
Waters ×1930
* Residue conservation analysis
PDB id:
Name: Lyase
Title: Crystal structure of e. Coli enolase complexed with the minimal binding segment of rnase e.
Structure: Enolase. Chain: a, c, d, f. Synonym: 2-phosphoglycerate dehydratase, 2-phospho-d- glycerate hydro-lyase. Engineered: yes. Ribonuclease e. Chain: b, e. Fragment: residues 833-850. Synonym: rnase e.
Source: Escherichia coli. Organism_taxid: 562. Gene: eno. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Other_details: the e. Coli rnase e peptide was synthesized.
Biol. unit: Trimer (from PQS)
1.60Å     R-factor:   0.167     R-free:   0.201
Authors: V.Chandran,B.F.Luisi
Key ref:
V.Chandran and B.F.Luisi (2006). Recognition of enolase in the Escherichia coli RNA degradosome. J Mol Biol, 358, 8-15. PubMed id: 16516921 DOI: 10.1016/j.jmb.2006.02.012
08-Feb-06     Release date:   28-Feb-06    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P0A6P9  (ENO_ECOLI) -  Enolase
432 a.a.
431 a.a.
Protein chains
Pfam   ArchSchema ?
P21513  (RNE_ECOLI) -  Ribonuclease E
1061 a.a.
15 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 2: Chains A, C, D, F: E.C.  - Phosphopyruvate hydratase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2-phospho-D-glycerate = phosphoenolpyruvate + H2O
= phosphoenolpyruvate
+ H(2)O
      Cofactor: Mg(2+)
   Enzyme class 3: Chains B, E: E.C.  - Ribonuclease E.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   7 terms 
  Biological process     glycolysis   1 term 
  Biochemical function     protein binding     6 terms  


    Added reference    
DOI no: 10.1016/j.jmb.2006.02.012 J Mol Biol 358:8-15 (2006)
PubMed id: 16516921  
Recognition of enolase in the Escherichia coli RNA degradosome.
V.Chandran, B.F.Luisi.
In Escherichia coli, the glycolytic enzyme enolase is a component of the RNA degradosome, which is an RNase E mediated assembly involved in RNA processing and transcript turnover. The recruitment of enolase by the RNA degradosome has been implicated in the turnover of certain transcripts, and it is mediated by a small segment of roughly a dozen residues that lie within a natively unstructured sub-domain of RNase E. Here, we present the crystal structure of enolase in complex with its recognition site from RNase E at 1.6A resolution. A single molecule of the RNase E peptide binds asymmetrically in a conserved cleft at the interface of the enolase dimer. The recognition site is well conserved in RNase E homologues in a subfamily of the gamma-proteobacteria, including enzymes from pathogens such as Yersinia pestis, Vibrio cholera and Salmonella sp. We suggest that enolase is recruited into putative RNA degradosome machinery in these bacilli, where it plays common regulatory functions.
  Selected figure(s)  
Figure 2.
Figure 2. Surface and electrostatic complementarity in the binding pocket. (a) View down the molecular dyad axis. (b) Electrostatic surface of the enolase dimer. The view is into the binding pocket for the peptide along an axis that is slightly inclined with respect to the dyad of the enolase dimer (red line). (c) Electrostatic surface for the peptide in the same orientation as in (a) and (b). (d) A schematic representation of the key contacts of the RNase E peptide with enolase. The Figure was prepared using LIGPLOT.^26
Figure 3.
Figure 3. The catalytic site of enolase, showing the details of the coordinated magnesium ion. The side-chains of the residues in the catalytic site are shown in stick representation.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 358, 8-15) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23241849 G.A.Mackie (2012).
RNase E: at the interface of bacterial RNA processing and decay.
  Nat Rev Microbiol, 11, 45-57.  
20952404 S.W.Hardwick, V.S.Chan, R.W.Broadhurst, and B.F.Luisi (2011).
An RNA degradosome assembly in Caulobacter crescentus.
  Nucleic Acids Res, 39, 1449-1459.  
21418661 V.R.Kaberdin, D.Singh, and S.Lin-Chao (2011).
Composition and conservation of the mRNA-degrading machinery in bacteria.
  J Biomed Sci, 18, 23.  
20169188 G.R.Mair, E.Lasonder, L.S.Garver, B.M.Franke-Fayard, C.K.Carret, J.C.Wiegant, R.W.Dirks, G.Dimopoulos, C.J.Janse, and A.P.Waters (2010).
Universal features of post-transcriptional gene regulation are critical for Plasmodium zygote development.
  PLoS Pathog, 6, e1000767.  
21126315 M.A.Erce, J.K.Low, and M.R.Wilkins (2010).
Analysis of the RNA degradosome complex in Vibrio angustum S14.
  FEBS J, 277, 5161-5173.  
20823555 S.Nurmohamed, A.R.McKay, C.V.Robinson, and B.F.Luisi (2010).
Molecular recognition between Escherichia coli enolase and ribonuclease E.
  Acta Crystallogr D Biol Crystallogr, 66, 1036-1040.
PDB code: 3h8a
19597536 B.He, K.Wang, Y.Liu, B.Xue, V.N.Uversky, and A.K.Dunker (2009).
Predicting intrinsic disorder in proteins: an overview.
  Cell Res, 19, 929-949.  
  19936110 K.L.Anderson, and P.M.Dunman (2009).
Messenger RNA Turnover Processes in Escherichia coli, Bacillus subtilis, and Emerging Studies in Staphylococcus aureus.
  Int J Microbiol, 2009, 525491.  
19327365 S.Nurmohamed, B.Vaidialingam, A.J.Callaghan, and B.F.Luisi (2009).
Crystal structure of Escherichia coli polynucleotide phosphorylase core bound to RNase E, RNA and manganese: implications for catalytic mechanism and RNA degradosome assembly.
  J Mol Biol, 389, 17-33.
PDB codes: 3gcm 3gll 3gme 3h1c
18366598 C.J.Oldfield, J.Meng, J.Y.Yang, M.Q.Yang, V.N.Uversky, and A.K.Dunker (2008).
Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners.
  BMC Genomics, 9, S1.  
18678873 L.Khidr, G.Wu, A.Davila, V.Procaccio, D.Wallace, and W.H.Lee (2008).
Role of SUV3 Helicase in Maintaining Mitochondrial Homeostasis in Human Cells.
  J Biol Chem, 283, 27064-27073.  
17447862 A.J.Carpousis (2007).
The RNA degradosome of Escherichia coli: an mRNA-degrading machine assembled on RNase E.
  Annu Rev Microbiol, 61, 71-87.  
17560162 C.Condon (2007).
Maturation and degradation of RNA in bacteria.
  Curr Opin Microbiol, 10, 271-278.  
17189683 J.A.Worrall, and B.F.Luisi (2007).
Information available at cut rates: structure and mechanism of ribonucleases.
  Curr Opin Struct Biol, 17, 128-137.  
17328674 M.Sharon, and C.V.Robinson (2007).
The role of mass spectrometry in structure elucidation of dynamic protein complexes.
  Annu Rev Biochem, 76, 167-193.  
17973494 Y.Cheng, C.J.Oldfield, J.Meng, P.Romero, V.N.Uversky, and A.K.Dunker (2007).
Mining alpha-helix-forming molecular recognition features with cross species sequence alignments.
  Biochemistry, 46, 13468-13477.  
16766188 M.J.Marcaida, M.A.DePristo, V.Chandran, A.J.Carpousis, and B.F.Luisi (2006).
The RNA degradosome: life in the fast lane of adaptive molecular evolution.
  Trends Biochem Sci, 31, 359-365.  
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.