rna helicase structure n.
Download
Skip this Video
Loading SlideShow in 5 Seconds..
RNA Helicase Structure PowerPoint Presentation
Download Presentation
RNA Helicase Structure

Loading in 2 Seconds...

play fullscreen
1 / 24

RNA Helicase Structure - PowerPoint PPT Presentation


  • 382 Views
  • Uploaded on

RNA Helicase Structure. Christie Carter Protein Structure and Function Fall 2006. Image: UAP56 helicase from helicase.net. Helicase Background. Use energy generated by NTP hydrolysis to break hydrogen bonds holding strands of DNA/RNA together. (DNA/RNA + Protein)

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

PowerPoint Slideshow about 'RNA Helicase Structure' - rhett


An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript
rna helicase structure

RNA Helicase Structure

Christie Carter

Protein Structure and Function

Fall 2006

Image: UAP56 helicase from helicase.net

helicase background
Helicase Background
  • Use energy generated by NTP hydrolysis to break hydrogen bonds holding strands of DNA/RNA together. (DNA/RNA + Protein)
  • Eukaryotes, Prokaryotes, Viruses
  • Involved in repair, recombination, transcription, translation, etc.
  • There are 4 superfamilies (SF) of Helicases.
  • The RNA helicases belong to SF1 and SF2 (and SF3).
  • DNA helicases also belong to both families.
superfamilies
Superfamilies
  • The superfamilies are segregated based on motifs (not activity, substrate, source or direction of unwinding).
  • All have Walker A and B motifs in common.
  • Superfamilies 1 & 2 are the largest groups. These families contain most of the RNA Helicases.
  • Superfamily 3 contains helicases typically found in Viruses. This family contains mostly DNA helicases but does contain a few RNA helicases.
  • Superfamily 4 members come from bacterial systems. All DNA helicases.
  • Other families
superfamilies 1 2
Superfamilies 1 & 2
  • Homologous in 7 motifs
  • Walker A (P-loop or Phosphate binding loop)
  • Ia. Oligonucleotide interaction motif
  • Walker B (ATP binding motif, DExx)
  • Unknown :“Sensor I” motif/helicase activity
  • Oligonucleotide interaction motif
  • Unknown/may participate in helicase activity
  • Arginine interacts with ATP

Helicase Structure and Mechanism Cur Opin Struc Bio, 2002, 12:123-133

dead h box rna helicases
DEAD/H-box RNA Helicases
  • Superfamily 2
  • Largest family of RNA helicases.
  • Share 9 conserved motifs including: Asp-Glu-Ala-Asp (DEAD/H): Walker B motif

The DEAD-box protein family of RNA helicases, Cordin, Gene 2006, 367:17-37

basic structure of dead box proteins
Basic Structure of DEAD-Box Proteins

Two covalently linked globular domains create a “Dumbell shape”

dead box protein bound to ssrna
DEAD-box protein bound to ssRNA

Q

VI

I

III

V

II

Ia

IV

Ib

The DEAD-box protein family of RNA helicases, Cordin, Gene 2006, 367:17-37

motifs
Motifs
  • Many have poorly understood functions because of very few crystal structures.
  • So far, only 2 DEAD-box proteins have been cocrystallized with a bound nucleotide.
  • NO DEAD-box proteins have been cocrystallized with an RNA substrate.
  • Structural interactions and other information is based on information obtained with other (non-DEAD-box helicases).
q motif
Q-motif
  • An additional B-strand and 2 a-helices upstream of motif I
  • Forms a “cap” on top of domain I.
  • Potential ATP binding motif.

The DEAD-box protein family of RNA helicases, Cordin, Gene 2006, 367:17-37

motif i
Motif I
  • AxTGoGKT
  • Walker A motif (P-loop, phosphate binding).
  • Common to all helicases.
  • Required for ATPase and helicase activity.
  • In crystal structures, this loop was shown to have 2 conformations (OPEN and CLOSED).
  • Open in nucleotide bound forms, closed in absence of nucleotide ligand.
  • In the closed state, ATP cannot be bound because of steric hindrance.
motif i1
Motif I

CLOSED

OPEN

The DEAD-box protein family of RNA helicases, Cordin, Gene 2006, 367:17-37

motifs ia and ib
Motifs Ia and Ib
  • Ia – PTRELA, Ib – TPGR
  • Poorly studied.
  • May be necessary for RNA binding and structural rearrangements that occur through ATP binding.
  • Alanine substitutions in Ia of DEAD-box proteins alter ATPase and helicase activities; however, minor effect seen in DEAH-box proteins.
  • Structurally similar to IV and V, proposed to have similar function but not yet demonstrated

The DEAD-box protein family of RNA helicases, Cordin, Gene 2006, 367:17-37

gg doublet
GG Doublet
  • Present in some but not all DEAD-box proteins.
  • Found in a loop between Ia and Ib.
  • Facilitate formation of a sharp turn.
  • Mutations in yeast eIF4a helicase affect growth.

The DEAD-box protein family of RNA helicases, Cordin, Gene 2006, 367:17-37

eIF4A

MjDEAD

motif ii
Motif II
  • Walker B motif – DEAD (Also DExD/H)
  • ATP binding domain.
  • Mutations in this motif alter ATPase and helicase activity, but do not affect RNA binding.
motif iii
Motif III
  • SAT
  • Mutations in this motif lead to loss of helicase activity, while only minor effects on RNA binding, ATP binding/hydrolysis are seen.
  • SF1 motif III was shown to bind phosphates of ATP to serve to transduce information to motifs IV and V.
  • No evidence has shown this to be the case in DEAD-box proteins, although, it is thought that the function of motif III in DEAD-box proteins could be simlilar.
  • Possibly shifts into the inter-domain cleft during ATP binding
motif iii1
Motif III

CLOSED

OPEN

Receptive to ATP

motif iv
Motif IV
  • Minimal sequence: (L/V)IF
  • Poorly studied in DEAD-box proteins.
  • Potential RNA binding motif.
motif v
Motif V
  • TDVuARGID
  • RNA binding motif.
  • May play role in ATPase activity or helicase activity.
  • This motif interacts with motif VI.
  • Mutations in this motif affect growth.
motif vi
Motif VI
  • HRIGRTGR
  • ATPase activity and RNA binding.
  • May interact with motif III.
  • The 2nd R may function as an “asparagine finger” which stabilizes water-Mg2+-phosphate intermediate in ATP hydrolysis.
dead box protein bound to ssrna1
DEAD-box protein bound to ssRNA

Q

VI

I

III

V

II

Ia

IV

Ib

The DEAD-box protein family of RNA helicases, Cordin, Gene 2006, 367:17-37

dead box protein bound to ssrna with adp mg 2 present
DEAD-box protein bound to ssRNA with ADP + Mg2+ present

ADP decreases affinity for RNA substrate

Q

VI

I

III

V

II

Ia

IV

Ib

The DEAD-box protein family of RNA helicases, Cordin, Gene 2006, 367:17-37

cool websites and references
Cool Websites and References
  • www.helicase.net
  • Cordin, O., et. al. 2006. The DEAD-box protein family of RNA helicases. Gene 367:17-37
  • Linder, P, et. al. 2006. Bent out of shape: RNA unwinding by the DEAD-box helicase Vasa. Cell 125:219-221
  • Sengoku, T., et. al. 2006. Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa. Cell 125:287-300
  • Caruthers, J., et. al. 2002. Helicase structure and mechanism. Current Opinion in Structural Biology 12:123-133
structural similarity
Structural Similarity

Structural Basis for RNA Unwinding…Cell 2006, 125:287-300