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PDBsum entry 1goj

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protein ligands metals links
Motor protein PDB id
1goj
Jmol
Contents
Protein chain
354 a.a. *
Ligands
ADP
Metals
_MG
Waters ×114
* Residue conservation analysis
PDB id:
1goj
Name: Motor protein
Title: Structure of a fast kinesin: implications for atpase mechanism and interactions with microtubules
Structure: Kinesin heavy chain. Chain: a. Fragment: motor domain, residues 1-355. Synonym: kinesin. Engineered: yes
Source: Neurospora crassa. Organism_taxid: 5141. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Resolution:
2.3Å     R-factor:   0.223     R-free:   0.264
Authors: Y.-H.Song,A.Marx,J.Muller,G.Woehlke,M.Schliwa,A.Krebs, A.Hoenger,E.Mandelkow
Key ref:
Y.H.Song et al. (2001). Structure of a fast kinesin: implications for ATPase mechanism and interactions with microtubules. EMBO J, 20, 6213-6225. PubMed id: 11707393 DOI: 10.1093/emboj/20.22.6213
Date:
21-Oct-01     Release date:   30-Nov-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P48467  (KINH_NEUCR) -  Kinesin heavy chain
Seq:
Struc:
 
Seq:
Struc:
928 a.a.
354 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     kinesin complex   1 term 
  Biological process     microtubule-based movement   1 term 
  Biochemical function     microtubule binding     3 terms  

 

 
DOI no: 10.1093/emboj/20.22.6213 EMBO J 20:6213-6225 (2001)
PubMed id: 11707393  
 
 
Structure of a fast kinesin: implications for ATPase mechanism and interactions with microtubules.
Y.H.Song, A.Marx, J.Müller, G.Woehlke, M.Schliwa, A.Krebs, A.Hoenger, E.Mandelkow.
 
  ABSTRACT  
 
We determined the crystal structure of the motor domain of the fast fungal kinesin from Neurospora crassa (NcKin). The structure has several unique features. (i) Loop 11 in the switch 2 region is ordered and enables one to describe the complete nucleotide-binding pocket, including three inter-switch salt bridges between switch 1 and 2. (ii) Loop 9 in the switch 1 region bends outwards, making the nucleotide-binding pocket very wide. The displacement in switch 1 resembles that of the G-protein ras complexed with its guanosine nucleotide exchange factor. (iii) Loop 5 in the entrance to the nucleotide-binding pocket is remarkably long and interacts with the ribose of ATP. (iv) The linker and neck region is not well defined, indicating that it is mobile. (v) Image reconstructions of ice-embedded microtubules decorated with NcKin show that it interacts with several tubulin subunits, including a central beta-tubulin monomer and the two flanking alpha-tubulin monomers within the microtubule protofilament. Comparison of NcKin with other kinesins, myosin and G-proteins suggests that the rate-limiting step of ADP release is accelerated in the fungal kinesin and accounts for the unusually high velocity and ATPase activity.
 
  Selected figure(s)  
 
Figure 2.
Figure 2 Comparisons between the Sw2 structures of NcKin (black) and Ncd (grey) in ribbon representations. The orientation of the view is the same as in Figure 1. The switch 2 helix 4 and the strand are somewhat extended into the L11 region.
Figure 6.
Figure 6 Comparisons of salt bridges at the -phosphate-sensing region. (A) Stereo view of the superposition of NcKin (dark colour) and RnKin (pale colour). In NcKin, there are three inter-switch salt bridges and in RnKin there is only one. The salt bridge E97 -K188 of RnKin cannot be formed in NcKin because at the corresponding positions there are no charged residues, which are Met99 and Gly191, respectively. (B) Summary of all known salt bridges of known kinesin structures.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2001, 20, 6213-6225) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21277856 N.Naber, A.Larson, S.Rice, R.Cooke, and E.Pate (2011).
Multiple conformations of the nucleotide site of Kinesin family motors in the triphosphate state.
  J Mol Biol, 408, 628-642.  
21278385 N.Umezu, N.Hanzawa, M.D.Yamada, K.Kondo, T.Mitsui, and S.Maruta (2011).
Biochemical characterization of the novel rice kinesin K23 and its kinetic study using fluorescence resonance energy transfer between an intrinsic tryptophan residue and a fluorescent ATP analogue.
  J Biochem, 149, 539-550.  
19530174 A.Marx, A.Hoenger, and E.Mandelkow (2009).
Structures of kinesin motor proteins.
  Cell Motil Cytoskeleton, 66, 958-966.  
19037104 N.Zekert, and R.Fischer (2009).
The Aspergillus nidulans kinesin-3 UncA motor moves vesicles along a subpopulation of microtubules.
  Mol Biol Cell, 20, 673-684.  
21544223 V.Hariharan, and W.O.Hancock (2009).
Insights into the Mechanical Properties of the Kinesin Neck Linker Domain from Sequence Analysis and Molecular Dynamics Simulations.
  Cell Mol Bioeng, 2, 177-189.  
18280159 M.Kikkawa (2008).
The role of microtubules in processive kinesin movement.
  Trends Cell Biol, 18, 128-135.  
17382884 J.S.Allingham, L.R.Sproul, I.Rayment, and S.P.Gilbert (2007).
Vik1 modulates microtubule-Kar3 interactions through a motor domain that lacks an active site.
  Cell, 128, 1161-1172.
PDB code: 2o0a
16362723 A.Marx, J.Müller, E.M.Mandelkow, A.Hoenger, and E.Mandelkow (2006).
Interaction of kinesin motors, microtubules, and MAPs.
  J Muscle Res Cell Motil, 27, 125-137.  
16682419 K.Hahlen, B.Ebbing, J.Reinders, J.Mergler, A.Sickmann, and G.Woehlke (2006).
Feedback of the kinesin-1 neck-linker position on the catalytic site.
  J Biol Chem, 281, 18868-18877.  
16794924 P.J.Atzberger, and C.S.Peskin (2006).
A Brownian Dynamics model of kinesin in three dimensions incorporating the force-extension profile of the coiled-coil cargo tether.
  Bull Math Biol, 68, 131-160.  
16450053 S.Adio, J.Reth, F.Bathe, and G.Woehlke (2006).
Review: regulation mechanisms of Kinesin-1.
  J Muscle Res Cell Motil, 27, 153-160.  
16402342 S.Brier, D.Lemaire, S.DeBonis, F.Kozielski, and E.Forest (2006).
Use of hydrogen/deuterium exchange mass spectrometry and mutagenesis as a tool to identify the binding region of inhibitors targeting the human mitotic kinesin Eg5.
  Rapid Commun Mass Spectrom, 20, 456-462.  
16453157 S.Lakämper, and E.Meyhöfer (2006).
Back on track - on the role of the microtubule for kinesin motility and cellular function.
  J Muscle Res Cell Motil, 27, 161-171.  
16118217 S.D.Auerbach, and K.A.Johnson (2005).
Kinetic effects of kinesin switch I and switch II mutations.
  J Biol Chem, 280, 37061-37068.  
15879477 W.Zheng, and B.R.Brooks (2005).
Probing the local dynamics of nucleotide-binding pocket coupled to the global dynamics: myosin versus kinesin.
  Biophys J, 89, 167-178.  
14973135 E.P.Sablin, and R.J.Fletterick (2004).
Coordination between motor domains in processive kinesins.
  J Biol Chem, 279, 15707-15710.  
15005614 L.M.Klumpp, K.M.Brendza, J.E.Gatial, A.Hoenger, W.M.Saxton, and S.P.Gilbert (2004).
Microtubule-kinesin interface mutants reveal a site critical for communication.
  Biochemistry, 43, 2792-2803.  
12660159 G.Skiniotis, T.Surrey, S.Altmann, H.Gross, Y.H.Song, E.Mandelkow, and A.Hoenger (2003).
Nucleotide-induced conformations in the neck region of dimeric kinesin.
  EMBO J, 22, 1518-1528.  
12860992 L.M.Klumpp, A.T.Mackey, C.M.Farrell, J.M.Rosenberg, and S.P.Gilbert (2003).
A kinesin switch I arginine to lysine mutation rescues microtubule function.
  J Biol Chem, 278, 39059-39067.  
12730601 N.Naber, T.J.Minehardt, S.Rice, X.Chen, J.Grammer, M.Matuska, R.D.Vale, P.A.Kollman, R.Car, R.G.Yount, R.Cooke, and E.Pate (2003).
Closing of the nucleotide pocket of kinesin-family motors upon binding to microtubules.
  Science, 300, 798-801.
PDB codes: 1ozx 1syj 1syp 1sz4 1sz5
12609885 S.Lakämper, A.Kallipolitou, G.Woehlke, M.Schliwa, and E.Meyhöfer (2003).
Single fungal kinesin motor molecules move processively along microtubules.
  Biophys J, 84, 1833-1843.  
12609886 S.Rice, Y.Cui, C.Sindelar, N.Naber, M.Matuska, R.Vale, and R.Cooke (2003).
Thermodynamic properties of the kinesin neck-region docking to the catalytic core.
  Biophys J, 84, 1844-1854.  
14662360 X.Xiang, and M.Plamann (2003).
Cytoskeleton and motor proteins in filamentous fungi.
  Curr Opin Microbiol, 6, 628-633.  
12234929 A.Seitz, H.Kojima, K.Oiwa, E.M.Mandelkow, Y.H.Song, and E.Mandelkow (2002).
Single-molecule investigation of the interference between kinesin, tau and MAP2c.
  EMBO J, 21, 4896-4905.  
11864969 C.M.Farrell, A.T.Mackey, L.M.Klumpp, and S.P.Gilbert (2002).
The role of ATP hydrolysis for kinesin processivity.
  J Biol Chem, 277, 17079-17087.  
12368902 C.V.Sindelar, M.J.Budny, S.Rice, N.Naber, R.Fletterick, and R.Cooke (2002).
Two conformations in the human kinesin power stroke defined by X-ray crystallography and EPR spectroscopy.
  Nat Struct Biol, 9, 844-848.
PDB code: 1mkj
12355402 E.Reid, M.Kloos, A.Ashley-Koch, L.Hughes, S.Bevan, I.K.Svenson, F.L.Graham, P.C.Gaskell, A.Dearlove, M.A.Pericak-Vance, D.C.Rubinsztein, and D.A.Marchuk (2002).
A kinesin heavy chain (KIF5A) mutation in hereditary spastic paraplegia (SPG10).
  Am J Hum Genet, 71, 1189-1194.  
12209147 P.Chène (2002).
ATPases as drug targets: learning from their structure.
  Nat Rev Drug Discov, 1, 665-673.  
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.