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PDBsum entry 2k39
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Signaling protein PDB id
2k39

 

 

 

 

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Contents
Protein chain
76 a.a. *
* Residue conservation analysis
PDB id:
2k39
Name: Signaling protein
Title: Recognition dynamics up to microseconds revealed from rdc derived ubiquitin ensemble in solution
Structure: Ubiquitin. Chain: a. Engineered: yes
Source: Xenopus laevis. African clawed frog. Organism_taxid: 8355. Expressed in: escherichia coli. Expression_system_taxid: 562
NMR struc: 116 models
Authors: O.F.Lange,N.A.Lakomek,C.Fares,G.Schroder,K.Walter,S.Becker,J.Meiler, H.Grubmuller,C.Griesinger,B.L.De Groot
Key ref: O.F.Lange et al. (2008). Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution. Science, 320, 1471-1475. PubMed id: 18556554
Date:
25-Apr-08     Release date:   24-Jun-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P62972  (UBIQP_XENLA) -  Polyubiquitin (Fragment) from Xenopus laevis
Seq:
Struc: 		167 a.a.
76 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
Science 320:1471-1475 (2008)
PubMed id: 18556554  
 
 
Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution.
O.F.Lange, N.A.Lakomek, C.Farès, G.F.Schröder, K.F.Walter, S.Becker, J.Meiler, H.Grubmüller, C.Griesinger, B.L.de Groot.
 
  ABSTRACT  
 
Protein dynamics are essential for protein function, and yet it has been challenging to access the underlying atomic motions in solution on nanosecond-to-microsecond time scales. We present a structural ensemble of ubiquitin, refined against residual dipolar couplings (RDCs), comprising solution dynamics up to microseconds. The ensemble covers the complete structural heterogeneity observed in 46 ubiquitin crystal structures, most of which are complexes with other proteins. Conformational selection, rather than induced-fit motion, thus suffices to explain the molecular recognition dynamics of ubiquitin. Marked correlations are seen between the flexibility of the ensemble and contacts formed in ubiquitin complexes. A large part of the solution dynamics is concentrated in one concerted mode, which accounts for most of ubiquitin's molecular recognition heterogeneity and ensures a low entropic complex formation cost.
 

Literature references that cite this PDB file's key reference

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PDB codes: 3h7b 3h9h 3h9s 3ixa
19919148 P.R.Markwick, G.Bouvignies, L.Salmon, J.A.McCammon, M.Nilges, and M.Blackledge (2009).
Toward a unified representation of protein structural dynamics in solution.
  J Am Chem Soc, 131, 16968-16975.  
19475638 S.Doose, H.Neuweiler, and M.Sauer (2009).
Fluorescence quenching by photoinduced electron transfer: a reporter for conformational dynamics of macromolecules.
  Chemphyschem, 10, 1389-1398.  
19477632 S.Koide (2009).
Engineering of recombinant crystallization chaperones.
  Curr Opin Struct Biol, 19, 449-457.  
  20948662 S.R.Van Doren (2009).
Nuclear magnetic resonance captures the elusive.
  F1000 Biol Rep, 1, 0.  
19591434 T.M.Sabo, and M.C.Maurer (2009).
Biophysical investigation of GpIbalpha binding to thrombin anion binding exosite II.
  Biochemistry, 48, 7110-7122.  
19887638 T.Wlodarski, and B.Zagrovic (2009).
Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin.
  Proc Natl Acad Sci U S A, 106, 19346-19351.  
19751682 V.Borsi, C.Luchinat, and G.Parigi (2009).
Global and local mobility of apocalmodulin monitored through fast-field cycling relaxometry.
  Biophys J, 97, 1765-1771.  
19629713 V.Chevelkov, U.Fink, and B.Reif (2009).
Quantitative analysis of backbone motion in proteins using MAS solid-state NMR spectroscopy.
  J Biomol NMR, 45, 197-206.  
19918063 W.K.Erbil, M.S.Price, D.E.Wemmer, and M.A.Marletta (2009).
A structural basis for H-NOX signaling in Shewanella oneidensis by trapping a histidine kinase inhibitory conformation.
  Proc Natl Acad Sci U S A, 106, 19753-19760.
PDB codes: 2kii 2kil
19274444 X.Xu, P.H.Keizers, W.Reinle, F.Hannemann, R.Bernhardt, and M.Ubbink (2009).
Intermolecular dynamics studied by paramagnetic tagging.
  J Biomol NMR, 43, 247-254.  
19888307 Y.Pan, C.J.Tsai, B.Ma, and R.Nussinov (2009).
How do transcription factors select specific binding sites in the genome?
  Nat Struct Mol Biol, 16, 1118-1120.  
19629163 Y.Pan, and R.Nussinov (2009).
Cooperativity dominates the genomic organization of p53-response elements: a mechanistic view.
  PLoS Comput Biol, 5, e1000448.  
20064442 Y.Yin, and R.A.Mariuzza (2009).
The multiple mechanisms of T cell receptor cross-reactivity.
  Immunity, 31, 849-851.  
19381265 Z.Yang, P.Májek, and I.Bahar (2009).
Allosteric transitions of supramolecular systems explored by network models: application to chaperonin GroEL.
  PLoS Comput Biol, 5, e1000360.  
18931260 F.Pontiggia, A.Zen, and C.Micheletti (2008).
Small- and large-scale conformational changes of adenylate kinase: a molecular dynamics study of the subdomain motion and mechanics.
  Biophys J, 95, 5901-5912.  
19015511 J.Völker, H.H.Klump, and K.J.Breslauer (2008).
DNA energy landscapes via calorimetric detection of microstate ensembles of metastable macrostates and triplet repeat diseases.
  Proc Natl Acad Sci U S A, 105, 18326-18330.  
19049453 L.Yao, B.Vögeli, J.Ying, and A.Bax (2008).
NMR determination of amide N-H equilibrium bond length from concerted dipolar coupling measurements.
  J Am Chem Soc, 130, 16518-16520.  
19016297 S.Doose (2008).
Importance of backbone and solvent properties for conformational dynamics in polypeptides.
  Chemphyschem, 9, 2687-2689.  
18682221 V.Z.Miloushev, F.Bahna, C.Ciatto, G.Ahlsen, B.Honig, L.Shapiro, and A.G.Palmer (2008).
Dynamic properties of a type II cadherin adhesive domain: implications for the mechanism of strand-swapping of classical cadherins.
  Structure, 16, 1195-1205.  
18644446 W.Kelly, and M.Stumpf (2008).
Protein-protein interactions: from global to local analyses.
  Curr Opin Biotechnol, 19, 396-403.  
19000814 X.Luo, and H.Yu (2008).
Protein metamorphosis: the two-state behavior of Mad2.
  Structure, 16, 1616-1625.  
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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