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PDBsum entry 2p81

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protein links
Transcription PDB id
2p81
Jmol
Contents
Protein chain
44 a.a. *
* Residue conservation analysis
PDB id:
2p81
Name: Transcription
Title: Engrailed homeodomain helix-turn-helix motif
Structure: Segmentation polarity homeobox protein engrailed. Chain: a. Fragment: helix-turn-helix motif. Engineered: yes. Mutation: yes
Source: Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Gene: en. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 25 models
Authors: T.L.Religa
Key ref:
T.L.Religa et al. (2007). The helix-turn-helix motif as an ultrafast independently folding domain: The pathway of folding of Engrailed homeodomain. Proc Natl Acad Sci U S A, 104, 9272-9277. PubMed id: 17517666 DOI: 10.1073/pnas.0703434104
Date:
21-Mar-07     Release date:   12-Jun-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P02836  (HMEN_DROME) -  Segmentation polarity homeobox protein engrailed
Seq:
Struc:
 
Seq:
Struc:
552 a.a.
44 a.a.*
Key:    PfamA domain  PfamB 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     nucleus   1 term 
  Biological process     regulation of transcription, DNA-dependent   1 term 
  Biochemical function     transcription regulatory region sequence-specific DNA binding     4 terms  

 

 
DOI no: 10.1073/pnas.0703434104 Proc Natl Acad Sci U S A 104:9272-9277 (2007)
PubMed id: 17517666  
 
 
The helix-turn-helix motif as an ultrafast independently folding domain: The pathway of folding of Engrailed homeodomain.
T.L.Religa, C.M.Johnson, D.M.Vu, S.H.Brewer, R.B.Dyer, A.R.Fersht.
 
  ABSTRACT  
 
Helices 2 and 3 of Engrailed homeodomain (EnHD) form a helix-turn-helix (HTH) motif. This common motif is believed not to fold independently, which is the characteristic feature of a motif rather than a domain. But we found that the EnHD HTH motif is monomeric and folded in solution, having essentially the same structure as in full-length protein. It had a sigmoidal thermal denaturation transition. Both native backbone and local tertiary interactions were formed concurrently at 4 x 10(5) s(-1) at 25 degrees C, monitored by IR and fluorescence T-jump kinetics, respectively, the same rate constant as for the fast phase in the folding of EnHD. The HTH motif, thus, is an ultrafast-folding, natural protein domain. Its independent stability and appropriate folding kinetics account for the stepwise folding of EnHD, satisfy fully the criteria for an on-pathway intermediate, and explain the changes in mechanism of folding across the homeodomain family. Experiments on mutated and engineered fragments of the parent protein with different probes allowed the assignment of the observed kinetic phases to specific events to show that EnHD is not an example of one-state downhill folding.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Comparison of chemical shifts between EnHD L16A and its 16–59 fragment. (a) The ^1H-^15N HSQC spectra of EnHD residues 16–59 (red) overlayed with that of L16A (blue). Peaks for L16A residues up to 15 are shown as black contours. (b) The natural abundance ^1H-^13C HSQC spectra of EnHD residues 16–59 (red) overlayed with that of L16A (blue). The methyl groups in the fragment were not stereospecifically assigned.
Figure 4.
Fig. 4. Relaxation kinetics of EnHD residues 16–59 monitored by fluorescence (a, b, and f) and IR (c and d) and equilibrium properties (e). (a) Kinetic time course for EnHD residues 16–59 at 25°C, 2 M [NaCl]. The raw data (red) were fitted after subtracting from the NATA trace (blue), giving the rate constant of 206,000 s^–1 (4.8 µs). (b) Kinetic time course for EnHD L16A at 25°C, 2 M [NaCl]. As for the fragment, the raw data were subtracted from the NATA trace and fitted to both single (gray) and double (brown) exponentials. The single-exponential fit gave a rate of 44,000 s^–1, and the double-exponential fit produced rates of 34,000 s^–1 and 205,000 s^–1. (c) Folding of EnHD L16A (red) and 16–59 fragment (blue), monitored by IR at 25°C, 100 mM [NaCl]. (d) As in c, but measured at 500 mM [NaCl]. Two kinetic phases were observed in the folding of L16A and 16–59 fragment at low salt concentrations when monitored by IR: the fast phase and the (previously unidentified) ultrafast phase. In addition to these phases, a slow phase was observed in the folding kinetics of L16A at 500 mM. No slow phase was observed in the folding kinetics of the fragment at high salt, as shown in Table 1. (e) Thermal denaturation of the fragment at increasing salt concentrations, followed by CD at 222 nm. (f) Rates extracted from independent traces at multiple temperatures for the fragment (red) and the L16A mutant (blue/gray) at 2 M [NaCl]. The spread in the data shows the inaccuracy of the measurement and/or data fitting. The L16A data were fitted to a single and a double exponential. At higher temperatures, it was not possible to fit the L16A data to a double exponential.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21051320 R.D.Schaeffer, and V.Daggett (2011).
Protein folds and protein folding.
  Protein Eng Des Sel, 24, 11-19.  
21187427 W.Banachewicz, C.M.Johnson, and A.R.Fersht (2011).
Folding of the Pit1 homeodomain near the speed limit.
  Proc Natl Acad Sci U S A, 108, 569-573.  
21422286 W.Banachewicz, T.L.Religa, R.D.Schaeffer, V.Daggett, and A.R.Fersht (2011).
Malleability of folding intermediates in the homeodomain superfamily.
  Proc Natl Acad Sci U S A, 108, 5596-5601.  
20829478 D.M.Korzhnev, T.L.Religa, W.Banachewicz, A.R.Fersht, and L.E.Kay (2010).
A transient and low-populated protein-folding intermediate at atomic resolution.
  Science, 329, 1312-1316.
PDB code: 2kzg
20662005 E.Arbely, H.Neuweiler, T.D.Sharpe, C.M.Johnson, and A.R.Fersht (2010).
The human peripheral subunit-binding domain folds rapidly while overcoming repulsive Coulomb forces.
  Protein Sci, 19, 1704-1713.  
21135210 H.Neuweiler, W.Banachewicz, and A.R.Fersht (2010).
Kinetics of chain motions within a protein-folding intermediate.
  Proc Natl Acad Sci U S A, 107, 22106-22110.  
19594171 A.J.Lee, R.W.Clark, H.Youn, S.Ponter, and J.N.Burstyn (2009).
Guanidine hydrochloride-induced unfolding of the three heme coordination states of the CO-sensing transcription factor, CooA.
  Biochemistry, 48, 6585-6597.  
19445951 B.G.Wensley, M.Gärtner, W.X.Choo, S.Batey, and J.Clarke (2009).
Different members of a simple three-helix bundle protein family have very different folding rate constants and fold by different mechanisms.
  J Mol Biol, 390, 1074-1085.  
19157852 C.Travaglini-Allocatelli, Y.Ivarsson, P.Jemth, and S.Gianni (2009).
Folding and stability of globular proteins and implications for function.
  Curr Opin Struct Biol, 19, 3-7.  
19624233 M.Zamparo, and A.Pelizzola (2009).
Nearly symmetrical proteins: folding pathways and transition states.
  J Chem Phys, 131, 035101.  
19452555 Z.Liu, J.Zhang, X.Wang, Y.Ding, J.Wu, and Y.Shi (2009).
Temperature-induced partially unfolded state of hUBF HMG Box-5: conformational and dynamic investigations of the Box-5 thermal intermediate ensemble.
  Proteins, 77, 432-447.  
18808671 B.Dasgupta, and P.Chakrabarti (2008).
pi-Turns: types, systematics and the context of their occurrence in protein structures.
  BMC Struct Biol, 8, 39.  
18498109 B.Nölting, and D.A.Agard (2008).
How general is the nucleation-condensation mechanism?
  Proteins, 73, 754-764.  
18242977 R.D.Schaeffer, A.Fersht, and V.Daggett (2008).
Combining experiment and simulation in protein folding: closing the gap for small model systems.
  Curr Opin Struct Biol, 18, 4-9.  
18502978 T.R.Sosnick (2008).
Kinetic barriers and the role of topology in protein and RNA folding.
  Protein Sci, 17, 1308-1318.  
18185928 Y.Ivarsson, C.Travaglini-Allocatelli, M.Brunori, and S.Gianni (2008).
Mechanisms of protein folding.
  Eur Biophys J, 37, 721-728.  
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.