Helicase

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Line 85: Line 85:
*DNA helicase II or UvrD
*DNA helicase II or UvrD
 +
**[[1q2z]], [[1rw2]] – hHel II KU86 C terminal – human - NMR<BR />
 +
**[[5y58]] – yHel II + DNA – yeast<br />
 +
**[[5y59]] – yHel II subunit 2 + Sir4P peptide<br />
**[[3lfu]] – EcHel II <BR />
**[[3lfu]] – EcHel II <BR />
**[[2is1]], [[2is2]] - EcHel II (mutant) + DNA<BR />
**[[2is1]], [[2is2]] - EcHel II (mutant) + DNA<BR />
**[[2is4]], [[2is6]] - EcHel II (mutant) + ADP + DNA<BR />
**[[2is4]], [[2is6]] - EcHel II (mutant) + ADP + DNA<BR />
**[[4c2t]], [[4c2u]], [[4c30]] – DrHel II + DNA - ''Deinococcus radiodurans''<br />
**[[4c2t]], [[4c2u]], [[4c30]] – DrHel II + DNA - ''Deinococcus radiodurans''<br />
-
**[[1q2z]], [[1rw2]] – hHel II KU86 C terminal – NMR<BR />
 
-
**[[5y58]] – yHel II + DNA – yeast<br />
 
-
**[[5y59]] – yHel II subunit 2 + Sir4P peptide<br />
 
*ATP-dependent helicase ATRX
*ATP-dependent helicase ATRX
Line 137: Line 137:
*ATP-dependent helicase CHD
*ATP-dependent helicase CHD
-
**[[2h1e]], [[2xb0]], [[3mwy]] – yCHD1 chromodomain<BR />
 
-
**[[2dy7]] - yCHD1 chromodomain 1 – NMR<BR />
 
-
**[[2dy8]] - yCHD1 chromodomain 2 – NMR<BR />
 
-
**[[3ted]] - yCHD1 chromodomain 1 + DNA<br />
 
**[[2b2y]] – hCHD1 <br />
**[[2b2y]] – hCHD1 <br />
**[[4b4c]] – hCHD1 DNA-binding domain<br />
**[[4b4c]] – hCHD1 DNA-binding domain<br />
Line 152: Line 148:
**[[2dl6]] – hCHD8 BRK domain - NMR <br />
**[[2dl6]] – hCHD8 BRK domain - NMR <br />
**[[2cka]] – hCHD8 <br />
**[[2cka]] – hCHD8 <br />
 +
**[[2h1e]], [[2xb0]], [[3mwy]] – yCHD1 chromodomain<BR />
 +
**[[2dy7]] - yCHD1 chromodomain 1 – NMR<BR />
 +
**[[2dy8]] - yCHD1 chromodomain 2 – NMR<BR />
 +
**[[3ted]] - yCHD1 chromodomain 1 + DNA<br />
*ATP-dependent DNA helicase PIF1
*ATP-dependent DNA helicase PIF1
Line 169: Line 169:
*Dead box ATP-dependent RNA helicase
*Dead box ATP-dependent RNA helicase
-
**[[3fho]] – DBP5 – fission yeast<BR />
 
-
**[[2kbe]] – yDBP5 N terminal – NMR<BR />
 
-
**[[2kbf]] - yDBP5 C terminal – NMR<BR />
 
-
**[[3gfp]] - yDBP5 C-terminal<BR />
 
**[[4xw3]] – hDDX1 SPRY domain<br />
**[[4xw3]] – hDDX1 SPRY domain<br />
**[[2i4i]] – hDDX3X residues 167-581<BR />
**[[2i4i]] – hDDX3X residues 167-581<BR />
Line 184: Line 180:
**[[2e29]], [[2m3d]] - hDDX50 GUCT domain - NMR<BR />
**[[2e29]], [[2m3d]] - hDDX50 GUCT domain - NMR<BR />
**[[1vec]] – hP54 N terminal<BR />
**[[1vec]] – hP54 N terminal<BR />
 +
**[[3fho]] – DBP5 – fission yeast<BR />
 +
**[[2kbe]] – yDBP5 N terminal – NMR<BR />
 +
**[[2kbf]] - yDBP5 C terminal – NMR<BR />
 +
**[[3gfp]] - yDBP5 C-terminal<BR />
**[[2hjv]] – BsDBPA domain 2 – ''Bacillus subtilis''<BR />
**[[2hjv]] – BsDBPA domain 2 – ''Bacillus subtilis''<BR />
**[[2g0c]] - BsDBPA RNA-binding domain<br />
**[[2g0c]] - BsDBPA RNA-binding domain<br />
Line 197: Line 197:
*''Dead box ATP-dependent RNA helicase complexes''
*''Dead box ATP-dependent RNA helicase complexes''
 +
**[[3fmo]], [[3fhc]] – hDBP5 + Nup214<BR />
 +
**[[3fht]] – hDBP5 + AMPPNP + RNA<BR />
 +
**[[3fmp]] – hDDX19B + Nup214<br />
 +
**[[3g0h]] – hDDX19B residues 54-275 + ATP analog + RNA<BR />
 +
**[[3ews]] - hDDX19B residues 54-275 + ADP<BR />
 +
**[[5e7m]], [[5e7j]] – hDDX3X catalytic domain + nucleotide<br />
 +
**[[3dkp]] – hDDX52 domain I + ADP<BR />
 +
**[[2wax]], [[2way]] – hDDX6 C terminal + EDC3-FDF peptide<BR />
 +
**[[2j0s]], [[2j0q]], [[2hyi]] – hDDX48 + protein mago nashi homolog + RNA-binding protein 8A + protein CASC3 + RNA<BR />
 +
**[[2j0u]] - hDDX48 + protein CASC3<BR />
 +
**[[2db3]] – DmVASA residues 200-623 + RNA – ''Drosophila melanogaster''<br />
 +
**[[5nt7]] – DmVASA RecA-like domain + maternal effect protein<br />
**[[3rrm]] – yDBP5 residues 91-482 (mutant) + GLE1 + NUP159 + ADP + IP6<BR />
**[[3rrm]] – yDBP5 residues 91-482 (mutant) + GLE1 + NUP159 + ADP + IP6<BR />
**[[3rrn]] - yDBP5 residues 91-482 (mutant) + GLE1 + IP6<BR />
**[[3rrn]] - yDBP5 residues 91-482 (mutant) + GLE1 + IP6<BR />
Line 212: Line 224:
**[[5lta]] - CtPrp43 + ADP + RNA<br />
**[[5lta]] - CtPrp43 + ADP + RNA<br />
**[[3jrv]] – DDX3X + protein K7 – Vaccinia virus<BR />
**[[3jrv]] – DDX3X + protein K7 – Vaccinia virus<BR />
-
**[[3fmo]], [[3fhc]] – hDBP5 + Nup214<BR />
 
-
**[[3fht]] – hDBP5 + AMPPNP + RNA<BR />
 
-
**[[3fmp]] – hDDX19B + Nup214<br />
 
-
**[[3g0h]] – hDDX19B residues 54-275 + ATP analog + RNA<BR />
 
-
**[[3ews]] - hDDX19B residues 54-275 + ADP<BR />
 
-
**[[5e7m]], [[5e7j]] – hDDX3X catalytic domain + nucleotide<br />
 
-
**[[3dkp]] – hDDX52 domain I + ADP<BR />
 
-
**[[2wax]], [[2way]] – hDDX6 C terminal + EDC3-FDF peptide<BR />
 
-
**[[2j0s]], [[2j0q]], [[2hyi]] – hDDX48 + protein mago nashi homolog + RNA-binding protein 8A + protein CASC3 + RNA<BR />
 
-
**[[2j0u]] - hDDX48 + protein CASC3<BR />
 
-
**[[2db3]] – DmVASA residues 200-623 + RNA – ''Drosophila melanogaster''<br />
 
-
**[[5nt7]] – DmVASA RecA-like domain + maternal effect protein<br />
 
**[[3nbf]] - TtHera N terminal (mutant) + 8-oxo-ADP<br />
**[[3nbf]] - TtHera N terminal (mutant) + 8-oxo-ADP<br />
**[[3moj]] - BsDBPA RNA-binding domain + RNA
**[[3moj]] - BsDBPA RNA-binding domain + RNA
Line 229: Line 229:
* DEAH box RNA helicase
* DEAH box RNA helicase
-
**[[2eqs]] – hDHX8 S1 domain<br />
+
**[[2eqs]] – hDHX8 S1 domain residues 260-355<br />
**[[3i4u]] – hDHX8 residues 950-1183<br />
**[[3i4u]] – hDHX8 residues 950-1183<br />
**[[3llm]] – hDHX9<br />
**[[3llm]] – hDHX9<br />
-
**[[2rs6]], [[2rs7]] – DHX9 RNA-binding domain – mouse – NMR<br />
 
**[[5xdr]] – hDHX15 residues 110-795 (mutant)<br />
**[[5xdr]] – hDHX15 residues 110-795 (mutant)<br />
**[[2n16]] – hDHX36 G-quadruplex domain - NMR<br />
**[[2n16]] – hDHX36 G-quadruplex domain - NMR<br />
Line 243: Line 242:
**[[5vhc]], [[5vhd]] – bDHX36 residues 150-1010 + ADP<br />
**[[5vhc]], [[5vhd]] – bDHX36 residues 150-1010 + ADP<br />
**[[5vhe]] – bDHX36 residues 56-1010 + DNA<br />
**[[5vhe]] – bDHX36 residues 56-1010 + DNA<br />
 +
**[[2rs6]], [[2rs7]] – mDHX9 RNA-binding domain – NMR<br />
*ATP-dependent RNA helicase
*ATP-dependent RNA helicase
 +
**[[2g9n]] - hEIF4A dead domain<br />
 +
**[[6ro1]] - hDOB1 residues 70-1042 + NVL<br />
**[[2xzl]] – yNAM7 CH and helicase domains + RNA<BR />
**[[2xzl]] – yNAM7 CH and helicase domains + RNA<BR />
**[[2xgj]] – yDOB1 residues 81-1073 + RNA<BR />
**[[2xgj]] – yDOB1 residues 81-1073 + RNA<BR />
Line 327: Line 329:
**[[2fbv]], [[2fbx]], [[2fby]], [[2fc0]] - hWRN exonuclease domain + metal ion
**[[2fbv]], [[2fbx]], [[2fby]], [[2fc0]] - hWRN exonuclease domain + metal ion
**[[3aaf]] – hWRN C terminal + DNA<br />
**[[3aaf]] – hWRN C terminal + DNA<br />
-
**[[2e6l]], [[2e6m]]- WRN exonuclease domain - mouse
+
**[[2e6l]], [[2e6m]]- mWRN exonuclease domain
*ATP-dependent DNA helicase Q
*ATP-dependent DNA helicase Q
Line 345: Line 347:
*ATP-dependent DNA helicase RecQ (Bloom Syndrome helicase)
*ATP-dependent DNA helicase RecQ (Bloom Syndrome helicase)
 +
**[[4cgz]], [[4o3m]] - hRecQ catalytic domain + DNA<br />
 +
**[[4cdg]] - hRecQ catalytic domain + nanobody<br />
 +
**[[1d8b]] - yRecQ HRDC domain - NMR<BR />
**[[3iuo]] – RecQ residues 604-725 – ''Porphyromonas gingivalis''<BR />
**[[3iuo]] – RecQ residues 604-725 – ''Porphyromonas gingivalis''<BR />
**[[2rhf]] – DrRecQ HRDC domain 3 – ''Deinococcus radiodurans''<BR />
**[[2rhf]] – DrRecQ HRDC domain 3 – ''Deinococcus radiodurans''<BR />
Line 353: Line 358:
**[[1oyw]] - EcRecQ catalytic domain<BR />
**[[1oyw]] - EcRecQ catalytic domain<BR />
**[[1oyy]] - EcRecQ catalytic domain + ATP<BR />
**[[1oyy]] - EcRecQ catalytic domain + ATP<BR />
-
**[[1d8b]] - yRecQ HRDC domain - NMR<BR />
 
-
**[[4cgz]], [[4o3m]] - hRecQ catalytic domain + DNA<br />
 
-
**[[4cdg]] - hRecQ catalytic domain + nanobody<br />
 
*ATP-dependent DNA helicase RuvA, RuvB
*ATP-dependent DNA helicase RuvA, RuvB
Line 417: Line 419:
*Helicase BLM
*Helicase BLM
 +
**[[5lup]] – hBLM DHBN domain <br />
**[[5lut]] – BLM DHBN domain - chicken<br />
**[[5lut]] – BLM DHBN domain - chicken<br />
**[[5lus]] – BLM DHBN domain - pelican<br />
**[[5lus]] – BLM DHBN domain - pelican<br />
-
**[[5lup]] – hBLM DHBN domain <br />
 
*Helicase CA8 or Prp28
*Helicase CA8 or Prp28
Line 441: Line 443:
*Helicase SKI2
*Helicase SKI2
-
**[[2va8]] – SsSKI2<br />
 
**[[4a4k]] – ySKI2 insertion domain<br />
**[[4a4k]] – ySKI2 insertion domain<br />
-
**[[4a4z]] – ySKI2 + AMPPNP
+
**[[4a4z]] – ySKI2 + AMPPNP<br />
 +
**[[2va8]] – SsSKI2<br />
*Helicase SWR1
*Helicase SWR1

Revision as of 08:10, 23 July 2019

DNA-dependent helicase PcrA (PDB code 1pjr)

Drag the structure with the mouse to rotate

3D structures of helicase

Updated on 23-July-2019

References

Crystal structure of a DExx box DNA helicase., Subramanya HS, Bird LE, Brannigan JA, Wigley DB, Nature. 1996 Nov 28;384(6607):379-83. PMID:8934527
^ Johnson DS, Bai L, Smith BY, Patel SS, Wang MD (2007). "Single-molecule studies reveal dynamics of DNA unwinding by the ring-shaped t7 helicase". Cell 129 (7): 1299–309. doi:10.1016/j.cell.2007.04.038. PMID 17604719.
^ a b "Researchers solve mystery of how DNA strands separate" (2007-07-03). Retrieved on 2007-07-05.
^ Dumont S, Cheng W, Serebrov V, Beran RK, Tinoco Jr I, Pylr AM, Bustamante C, "RNA Translocation and Unwinding Mechanism of HCV NS3 Helicase and its Coordination by ATP", Nature. 2006 Jan 5; 439: 105-108. Anand SP, Zheng H, Bianco PR, Leuba SH, Khan SA. DNA helicase activity of PcrA is not required for displacement of RecA protein from DNA or inhibition of RecA-mediated DNA strand exchange. Journal of Bacteriology (2007) 189 (12):4502-4509.
Bird L, Subramanya HS, Wigley DB, "Helicases: a unifying structural theme?", Current Opinion in Structural Biology. 1998 Feb; 8 (1): 14-18.
Betterton MD, Julicher F, "Opening of nucleic-acid double strands by helicases: active versus passive opening.", Physical Review E. 2005 Jan; 71 (1): 011904.

  • Sengoku T, Nureki O, Nakamura A, Kobayashi S, Yokoyama S. Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa. Cell. 2006 Apr 21;125(2):287-300. PMID:16630817 doi:10.1016/j.cell.2006.01.054
  • Sengoku T, Nureki O, Dohmae N, Nakamura A, Yokoyama S. Crystallization and preliminary X-ray analysis of the helicase domains of Vasa complexed with RNA and an ATP analogue. Acta Crystallogr D Biol Crystallogr. 2004 Feb;60(Pt 2):320-2. Epub 2004, Jan 23. PMID:14747711 doi:10.1107/S0907444903025897

Content Donators

Created with the participation of Luis E Ramirez-Tapia, Wayne Decatur.

Proteopedia Page Contributors and Editors (what is this?)

Michal Harel, Alexander Berchansky, Wayne Decatur, Joel L. Sussman

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