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Transferase PDB id
1w4h
Jmol
Contents
Protein chain
45 a.a. *
* Residue conservation analysis
PDB id:
1w4h
Name: Transferase
Title: Peripheral-subunit from mesophilic, thermophilic and hyperthermophilic bacteria fold by ultrafast, apparently two-state transitions
Structure: Dihydrolipoyllysine-residue acetyltransferase. Chain: a. Fragment: residues 108-152. Synonym: dihydrolipoamide acetyltransferase. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 469008.
NMR struc: 20 models
Authors: N.Ferguson,T.D.Sharpe,P.J.Schartau,M.D.Allen,C.M.Johnson, A.R.Fersht
Key ref:
N.Ferguson et al. (2005). Ultra-fast barrier-limited folding in the peripheral subunit-binding domain family. J Mol Biol, 353, 427-446. PubMed id: 16168437 DOI: 10.1016/j.jmb.2005.08.031
Date:
23-Jul-04     Release date:   20-Jul-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0AFG6  (ODO2_ECOLI) -  Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex
Seq:
Struc: 		405 a.a.
45 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.3.1.61  - Dihydrolipoyllysine-residue succinyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway: 		Citric acid cycle
      Reaction: Succinyl-CoA + enzyme N6-(dihydrolipoyl)lysine = CoA + enzyme N6- (S-succinyldihydrolipoyl)lysine
Succinyl-CoA
 + enzyme N(6)-(dihydrolipoyl)lysine
 = CoA
 + enzyme N(6)- (S-succinyldihydrolipoyl)lysine
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   1 term 
  Biochemical function     transferase activity, transferring acyl groups     1 term  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2005.08.031 J Mol Biol 353:427-446 (2005)
PubMed id: 16168437  
 
 
Ultra-fast barrier-limited folding in the peripheral subunit-binding domain family.
N.Ferguson, T.D.Sharpe, P.J.Schartau, S.Sato, M.D.Allen, C.M.Johnson, T.J.Rutherford, A.R.Fersht.
 
  ABSTRACT  
 
We have determined the solution structures, equilibrium properties and ultra-fast folding kinetics for three bacterial homologues of the peripheral subunit-binding domain (PSBD) family. The mesophilic homologue, BBL, was less stable than the thermophilic and hyper-thermophilic variants (E3BD and POB, respectively). The broad unfolding transitions of each PSBD, when probed by different techniques, were essentially superimposable, consistent with co-operative denaturation. Temperature-jump and continuous-flow fluorescence methods were used to measure the folding kinetics for E3BD, POB and BBL. E3BD folded fairly rapidly at 298K (folding half-time approximately 25 micros) and BBL and POB folded even faster (folding half-times approximately 3-5 micros). The variations in equilibrium and kinetic behaviour observed for the PSBD family resembles that of the homeodomain family, where the folding pattern changes from apparent two-state transitions to multi-state kinetics as the denatured state becomes more structured. The faster folding of POB may be a consequence of its higher propensity to form helical structure in the region corresponding to the folding nucleus of E3BD. The ultra-fast folding of BBL appears to be a consequence of residual structure in the denatured ensemble, as with engrailed homeodomain. We discuss issues concerning "one-state", downhill folding, and find no evidence for, and strong evidence against, it occurring in these PSBDs. The shorter construct used previously for BBL was destabilized significantly and the stability further perturbed by the introduction of fluorescent probes. Thermal titrations for 11 side-chains scattered around the protein, when probed by (13)C-NMR experiments, could be fit globally to a common co-operative transition.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. PSBD solution structures. The ensemble determined for each PSBD is shown. Each domain is shown in the same orientation. For clarity, the N and C termini are shown only for E3BD Y138W. For similar reasons, we have not shown all of the highly flexible regions at the N and C termini.
Figure 6.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 353, 427-446) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21453060 H.S.Chan, Z.Zhang, S.Wallin, and Z.Liu (2011).
Cooperativity, local-nonlocal coupling, and nonnative interactions: principles of protein folding from coarse-grained models.
  Annu Rev Phys Chem, 62, 301-326.  
20570731 A.A.Nickson, and J.Clarke (2010).
What lessons can be learned from studying the folding of homologous proteins?
  Methods, 52, 38-50.  
20130106 C.A.Dodson, N.Ferguson, T.J.Rutherford, C.M.Johnson, and A.R.Fersht (2010).
Engineering a two-helix bundle protein for folding studies.
  Protein Eng Des Sel, 23, 357-364.
PDB code: 2wqg
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.  
20028088 J.H.Cho, N.O'Connell, D.P.Raleigh, and A.G.Palmer (2010).
Phi-value analysis for ultrafast folding proteins by NMR relaxation dispersion.
  J Am Chem Soc, 132, 450-451.  
20338854 Y.Qi, Y.Huang, H.Liang, Z.Liu, and L.Lai (2010).
Folding simulations of a de novo designed protein with a betaalphabeta fold.
  Biophys J, 98, 321-329.  
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.  
19805287 F.Huang, L.Ying, and A.R.Fersht (2009).
Direct observation of barrier-limited folding of BBL by single-molecule fluorescence resonance energy transfer.
  Proc Natl Acad Sci U S A, 106, 16239-16244.  
19841261 H.Neuweiler, C.M.Johnson, and A.R.Fersht (2009).
Direct observation of ultrafast folding and denatured state dynamics in single protein molecules.
  Proc Natl Acad Sci U S A, 106, 18569-18574.  
19472192 J.Zhang, W.Li, J.Wang, M.Qin, L.Wu, Z.Yan, W.Xu, G.Zuo, and W.Wang (2009).
Protein folding simulations: from coarse-grained model to all-atom model.
  IUBMB Life, 61, 627-643.  
19368477 K.Itoh, and M.Sasai (2009).
Multidimensional theory of protein folding.
  J Chem Phys, 130, 145104.  
19317567 L.Prieto, and A.Rey (2009).
Topology-based potentials and the study of the competition between protein folding and aggregation.
  J Chem Phys, 130, 115101.  
19691415 L.Wu, W.F.Li, F.Liu, J.Zhang, J.Wang, and W.Wang (2009).
Understanding protein folding cooperativity based on topological consideration.
  J Chem Phys, 131, 065105.  
19118204 P.Li, F.Y.Oliva, A.N.Naganathan, and V.Muñoz (2009).
Dynamics of one-state downhill protein folding.
  Proc Natl Acad Sci U S A, 106, 103-108.  
19598233 W.Meng, B.Shan, Y.Tang, and D.P.Raleigh (2009).
Native like structure in the unfolded state of the villin headpiece helical subdomain, an ultrafast folding protein.
  Protein Sci, 18, 1692-1701.  
18498109 B.Nölting, and D.A.Agard (2008).
How general is the nucleation-condensation mechanism?
  Proteins, 73, 754-764.  
18326644 J.W.Pitera, W.C.Swope, and F.F.Abraham (2008).
Observation of noncooperative folding thermodynamics in simulations of 1BBL.
  Biophys J, 94, 4837-4846.  
18320591 J.Zhang, W.Li, J.Wang, M.Qin, and W.Wang (2008).
All-atom replica exchange molecular simulation of protein BBL.
  Proteins, 72, 1038-1047.  
18573083 K.A.Dill, S.B.Ozkan, M.S.Shell, and T.R.Weikl (2008).
The protein folding problem.
  Annu Rev Biophys, 37, 289-316.  
17847092 S.Muff, and A.Caflisch (2008).
Kinetic analysis of molecular dynamics simulations reveals changes in the denatured state and switch of folding pathways upon single-point mutation of a beta-sheet miniprotein.
  Proteins, 70, 1185-1195.  
18172203 S.S.Cho, P.Weinkam, and P.G.Wolynes (2008).
Origins of barriers and barrierless folding in BBL.
  Proc Natl Acad Sci U S A, 105, 118-123.  
19436488 V.Muñoz, M.Sadqi, A.N.Naganathan, and D.de Sancho (2008).
Exploiting the downhill folding regime via experiment.
  HFSP J, 2, 342-353.  
18272497 W.Yu, K.Chung, M.Cheon, M.Heo, K.H.Han, S.Ham, and I.Chang (2008).
Cooperative folding kinetics of BBL protein and peripheral subunit-binding domain homologues.
  Proc Natl Acad Sci U S A, 105, 2397-2402.  
17289578 A.L.Watters, P.Deka, C.Corrent, D.Callender, G.Varani, T.Sosnick, and D.Baker (2007).
The highly cooperative folding of small naturally occurring proteins is likely the result of natural selection.
  Cell, 128, 613-624.  
17419630 A.N.Naganathan, U.Doshi, and V.Muñoz (2007).
Protein folding kinetics: barrier effects in chemical and thermal denaturation experiments.
  J Am Chem Soc, 129, 5673-5682.  
17239580 D.J.Brockwell, and S.E.Radford (2007).
Intermediates: ubiquitous species on folding energy landscapes?
  Curr Opin Struct Biol, 17, 30-37.  
17200301 F.Huang, S.Sato, T.D.Sharpe, L.Ying, and A.R.Fersht (2007).
Distinguishing between cooperative and unimodal downhill protein folding.
  Proc Natl Acad Sci U S A, 104, 123-127.  
17994851 L.Prieto, and A.Rey (2007).
Influence of the native topology on the folding barrier for small proteins.
  J Chem Phys, 127, 175101.  
17301742 N.Ferguson, T.D.Sharpe, C.M.Johnson, P.J.Schartau, and A.R.Fersht (2007).
Structural biology: analysis of 'downhill' protein folding.
  Nature, 445, E14.  
17567220 P.Bruscolini, A.Pelizzola, and M.Zamparo (2007).
Downhill versus two-state protein folding in a statistical mechanical model.
  J Chem Phys, 126, 215103.  
17223539 R.B.Dyer (2007).
Ultrafast and downhill protein folding.
  Curr Opin Struct Biol, 17, 38-47.  
17179212 T.Kimura, J.C.Lee, H.B.Gray, and J.R.Winkler (2007).
Site-specific collapse dynamics guide the formation of the cytochrome c' four-helix bundle.
  Proc Natl Acad Sci U S A, 104, 117-122.  
16909416 M.Knott, and H.S.Chan (2006).
Criteria for downhill protein folding: calorimetry, chevron plot, kinetic relaxation, and single-molecule radius of gyration in chain models with subdued degrees of cooperativity.
  Proteins, 65, 373-391.  
17060612 N.Ferguson, J.Becker, H.Tidow, S.Tremmel, T.D.Sharpe, G.Krause, J.Flinders, M.Petrovich, J.Berriman, H.Oschkinat, and A.R.Fersht (2006).
General structural motifs of amyloid protofilaments.
  Proc Natl Acad Sci U S A, 103, 16248-16253.
PDB code: 2nnt
17301744 , (0).
  , 0, 0.  
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.