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PDBsum entry 3dco

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protein ligands metals Protein-protein interface(s) links
Motor protein PDB id
3dco
Jmol
Contents
Protein chains
291 a.a. *
412 a.a. *
426 a.a. *
Ligands
GTP
GDP
ADP
TA1
Metals
_MG ×2
_ZN
* Residue conservation analysis
PDB id:
3dco
Name: Motor protein
Title: Drosophila nod (3dc4) and bovine tubulin (1jff) docked into the 11-angstrom cryo-em map of nucleotide-free nod complexed to the microtubule
Structure: Kinesin-like protein nod. Chain: n. Fragment: catalytic core domain (residues 1-318). Engineered: yes. Bovine alpha tubulin. Chain: a. Fragment: alpha tubulin subunit. Bovine beta tubulin. Chain: b.
Source: Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Gene: cg1763, nod, noda. Expressed in: escherichia coli. Expression_system_taxid: 562. Bos taurus. Organism_taxid: 9913. Organism_taxid: 9913
Authors: C.V.Sindelar,J.C.Cochran,F.J.Kull
Key ref:
J.C.Cochran et al. (2009). ATPase cycle of the nonmotile kinesin NOD allows microtubule end tracking and drives chromosome movement. Cell, 136, 110-122. PubMed id: 19135893 DOI: 10.1016/j.cell.2008.11.048
Date:
04-Jun-08     Release date:   10-Feb-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P18105  (NOD_DROME) -  Kinesin-like protein Nod
Seq:
Struc:
 
Seq:
Struc:
666 a.a.
291 a.a.*
Protein chain
Pfam   ArchSchema ?
P81947  (TBA1B_BOVIN) -  Tubulin alpha-1B chain
Seq:
Struc:
451 a.a.
412 a.a.*
Protein chain
Pfam   ArchSchema ?
Q6B856  (TBB2B_BOVIN) -  Tubulin beta-2B chain
Seq:
Struc:
445 a.a.
426 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 14 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     protein complex   8 terms 
  Biological process     cellular response to interleukin-4   7 terms 
  Biochemical function     nucleotide binding     8 terms  

 

 
DOI no: 10.1016/j.cell.2008.11.048 Cell 136:110-122 (2009)
PubMed id: 19135893  
 
 
ATPase cycle of the nonmotile kinesin NOD allows microtubule end tracking and drives chromosome movement.
J.C.Cochran, C.V.Sindelar, N.K.Mulko, K.A.Collins, S.E.Kong, R.S.Hawley, F.J.Kull.
 
  ABSTRACT  
 
Segregation of nonexchange chromosomes during Drosophila melanogaster meiosis requires the proper function of NOD, a nonmotile kinesin-10. We have determined the X-ray crystal structure of the NOD catalytic domain in the ADP- and AMPPNP-bound states. These structures reveal an alternate conformation of the microtubule binding region as well as a nucleotide-sensitive relay of hydrogen bonds at the active site. Additionally, a cryo-electron microscopy reconstruction of the nucleotide-free microtubule-NOD complex shows an atypical binding orientation. Thermodynamic studies show that NOD binds tightly to microtubules in the nucleotide-free state, yet other nucleotide states, including AMPPNP, are weakened. Our pre-steady-state kinetic analysis demonstrates that NOD interaction with microtubules occurs slowly with weak activation of ADP product release. Upon rapid substrate binding, NOD detaches from the microtubule prior to the rate-limiting step of ATP hydrolysis, which is also atypical for a kinesin. We propose a model for NOD's microtubule plus-end tracking that drives chromosome movement.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. X-Ray Crystal Structure of NOD•ADP and NOD•AMPPNP
(A) Structure of NOD•ADP is shown. ADP is displayed as a ball-and-stick model.
(B) NOD•AMPPNP is shown as in (A).
(C and D) Superposition of NOD•ADP (blue) and NOD•AMPPNP (orange) through alignment of the P loop (G87-S94) as viewed from the top (C) and from the side (D). Arrows highlight the differences between the two states in Sw1, Sw2, α3, and L11.
(E) Configuration of hydrogen bonds between Sw1/Sw2 residues in NOD•ADP. Hydrogen bonds with measured distances are highlighted with magenta dashed lines. The water molecules that coordinate Mg^2+ are shown as red spheres.
(F) Active site configuration of hydrogen bonds for NOD•AMPPNP in a similar orientation as (E).
Figure 2.
Figure 2. L5 and MT Binding Region in NOD Show Unique Conformation Compared to Other Kinesins
(A) Comparison of L5 in different kinesin families (gray) after P loop superposition. The N-terminal half of L5 in NOD (blue) packs against α3.
(B) Detailed view of L5 in NOD (blue) compared to L5 in kinesin-5 (orange) bound to monastrol (Mon). The pocket formed by P101 and P102 on L5 and L180, H181, and L184 on α3 is shown.
(C) NOD•ADP (blue) was superposed with KHC•ADP (gold) and oriented to show the β5-L8 lobe.
(D–F) NOD's “Sw2 cluster” (blue) is compared to the “ADP-like” conformation in kinesin-1 ([D], 1bg2, magenta), the “ATP-like” conformation in kinesin-1 ([E], 1mkj, gold), and KIF2C ([F], 1v8j, red). View is from the MT binding surface. Clockwise rotation of NOD's α4 relative to kinesin-1's α4 is highlighted in (D) and (E).
 
  The above figures are reprinted from an Open Access publication published by Cell Press: Cell (2009, 136, 110-122) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22198464 J.C.Cochran, Y.C.Zhao, D.E.Wilcox, and F.J.Kull (2012).
A metal switch for controlling the activity of molecular motor proteins.
  Nat Struct Mol Biol, 19, 122-127.
PDB code: 3pxn
21795813 C.J.Tsai, and R.Nussinov (2011).
A unified convention for biological assemblies with helical symmetry.
  Acta Crystallogr D Biol Crystallogr, 67, 716-728.  
20817499 K.Jiang, and A.Akhmanova (2011).
Microtubule tip-interacting proteins: a view from both ends.
  Curr Opin Cell Biol, 23, 94.  
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.  
20018897 C.L.Parke, E.J.Wojcik, S.Kim, and D.K.Worthylake (2010).
ATP hydrolysis in Eg5 kinesin involves a catalytic two-water mechanism.
  J Biol Chem, 285, 5859-5867.
PDB code: 3hqd
20221784 G.Civelekoglu-Scholey, and J.M.Scholey (2010).
Mitotic force generators and chromosome segregation.
  Cell Mol Life Sci, 67, 2231-2250.  
20109570 L.Wordeman (2010).
How kinesin motor proteins drive mitotic spindle function: Lessons from molecular assays.
  Semin Cell Dev Biol, 21, 260-268.  
19935670 N.Hirokawa, R.Nitta, and Y.Okada (2009).
The mechanisms of kinesin motor motility: lessons from the monomeric motor KIF1A.
  Nat Rev Mol Cell Biol, 10, 877-884.  
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.