Helicase

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Line 79: Line 79:
**[[2q7t]], [[2q7u]] – EcHel I relaxase domain (mutant) <BR />
**[[2q7t]], [[2q7u]] – EcHel I relaxase domain (mutant) <BR />
**[[1p4d]] - EcHel I relaxase domain<BR />
**[[1p4d]] - EcHel I relaxase domain<BR />
 +
**[[4n8o]] - EcHel I + DNA<br />
**[[2a0i]] - EcHel I (mutant) + DNA<BR />
**[[2a0i]] - EcHel I (mutant) + DNA<BR />
**[[1q2z]], [[1rw2]] – hHel II KU86 C terminal – NMR<BR />
**[[1q2z]], [[1rw2]] – hHel II KU86 C terminal – NMR<BR />
Line 101: Line 102:
**[[2wjy]] - hRENT1 helicase CH domains<BR />
**[[2wjy]] - hRENT1 helicase CH domains<BR />
**[[2xzo]] – hRENT1 helicase domain + RNA<BR />
**[[2xzo]] – hRENT1 helicase domain + RNA<BR />
 +
 +
*ATP-dependent helicase Fun30
 +
 +
**[[5gn1]] – yFun C-terminal<br />
*ATP-dependent helicase Rho
*ATP-dependent helicase Rho
Line 145: Line 150:
**[[2dl6]] – hCHD8 BRK domain - NMR <br />
**[[2dl6]] – hCHD8 BRK domain - NMR <br />
**[[2cka]] – hCHD8 <br />
**[[2cka]] – hCHD8 <br />
 +
 +
*ATP-dependent DNA helicase PIF1
 +
 +
**[[5fhh]] – hPIF residues 200-641<br />
 +
 +
*ATP-dependent DNA helicase TA0057
 +
 +
**[[5h8w]] – TaTA0 + DNA – ''Thermoplasma acidophilum''<br />
*Dead box ATP-dependent RNA helicase
*Dead box ATP-dependent RNA helicase
Line 152: Line 165:
**[[2kbf]] - yDBP5 C terminal – NMR<BR />
**[[2kbf]] - yDBP5 C terminal – NMR<BR />
**[[3gfp]] - yDBP5 C-terminal<BR />
**[[3gfp]] - yDBP5 C-terminal<BR />
 +
**[[4xw3]] – hDDX1 SPRY domain<br />
**[[2i4i]] – hDDX3X residues 167-581<BR />
**[[2i4i]] – hDDX3X residues 167-581<BR />
**[[4px9]] - hDDX3X residues 135-407<br />
**[[4px9]] - hDDX3X residues 135-407<br />
**[[4pxa]] - hDDX3X residues 135-407 (mutant)<br />
**[[4pxa]] - hDDX3X residues 135-407 (mutant)<br />
 +
**[[5e7i]] - hDDX3X residues 133-584<br />
**[[2jgn]] – hDDX3X helicase domain residues 408-579<BR />
**[[2jgn]] – hDDX3X helicase domain residues 408-579<BR />
**[[3ly5]] – hDDX18 dead domain<BR />
**[[3ly5]] – hDDX18 dead domain<BR />
Line 170: Line 185:
**[[3i31]] - TtHera residues 431-517<br />
**[[3i31]] - TtHera residues 431-517<br />
**[[3i32]] - TtHera residues 218-517<br />
**[[3i32]] - TtHera residues 218-517<br />
-
**[[3nej]] - TtHera N terminal (mutant)
+
**[[3nej]] - TtHera N terminal (mutant)<br />
 +
**[[5ivl]] – GsDB CSHA - ''Geobacillus stearothermophilus''<br />
*''Dead box ATP-dependent RNA helicase complexes''
*''Dead box ATP-dependent RNA helicase complexes''
Line 176: Line 192:
**[[3rrm]] – yDBP5 residues 91-482 (mutant) + GLE1 + NUP159 + ADP + IP6 – yeast<BR />
**[[3rrm]] – yDBP5 residues 91-482 (mutant) + GLE1 + NUP159 + ADP + IP6 – yeast<BR />
**[[3rrn]] - yDBP5 residues 91-482 (mutant) + GLE1 + IP6<BR />
**[[3rrn]] - yDBP5 residues 91-482 (mutant) + GLE1 + IP6<BR />
 +
**[[5elx]] - yDBP5 residues 91-482 + RNA<br />
**[[3pew]], [[3pey]] - yDBP5 residues 91-482 (mutant) + ADP + BeF3 + RNA<BR />
**[[3pew]], [[3pey]] - yDBP5 residues 91-482 (mutant) + ADP + BeF3 + RNA<BR />
**[[3peu]], [[3pev]] - yDBP5 C-terminal (mutant) + GLE1 + IP6<BR />
**[[3peu]], [[3pev]] - yDBP5 C-terminal (mutant) + GLE1 + IP6<BR />
Line 183: Line 200:
**[[3i62]] - yMSS116 + ADP + AlF4 + RNA<BR />
**[[3i62]] - yMSS116 + ADP + AlF4 + RNA<BR />
**[[4tyn]] - yMSS116 + ADP + DNA<br />
**[[4tyn]] - yMSS116 + ADP + DNA<br />
-
**[[2xau]], [[3kx2]] – yPRP43 + ADP<BR />
+
**[[2xau]], [[3kx2]], [[5jpt]] – yPRP43 + nucleotide<BR />
 +
**[[5i8q]] - yPRP43 + ADPNP + RNA<br />
 +
**[[5ltk]], [[5ltj]], [[5ltk]], [[5d0u]] - CtPRP43 + ADP – ''Chaetomium thermophilum''<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 />
**[[3fmo]], [[3fhc]] – hDBP5 + Nup214<BR />
Line 190: Line 210:
**[[3g0h]] – hDDX19B residues 54-275 + ATP analog + RNA<BR />
**[[3g0h]] – hDDX19B residues 54-275 + ATP analog + RNA<BR />
**[[3ews]] - hDDX19B residues 54-275 + ADP<BR />
**[[3ews]] - hDDX19B residues 54-275 + ADP<BR />
 +
**[[5e7m]], [[5e7j]] – hDDX3X catalytic domain + nucleotide<br />
**[[3dkp]] – hDDX52 domain I + ADP<BR />
**[[3dkp]] – hDDX52 domain I + ADP<BR />
**[[5e3h]] - hDHX58 residues 232-925 + RNA<br />
**[[5e3h]] - hDHX58 residues 232-925 + RNA<br />
Line 205: Line 226:
**[[4u4c]] - yDOB1 residues 81-1073 + poly(A) RNA polymerase protein 2<br />
**[[4u4c]] - yDOB1 residues 81-1073 + poly(A) RNA polymerase protein 2<br />
**[[4qu4]] - yDOB1 <br />
**[[4qu4]] - yDOB1 <br />
 +
**[[5suq]] – ySUB2 + TEX1 + THO2 <br />
 +
**[[5sup]] – ySUB2 + YRA1 + RNA <br />
**[[2vso]], [[2vsx]] – yEIF4A + initiation factor 4F middle domain<BR />
**[[2vso]], [[2vsx]] – yEIF4A + initiation factor 4F middle domain<BR />
**[[2g9n]] - hEIF4A dead domain
**[[2g9n]] - hEIF4A dead domain
Line 216: Line 239:
**[[2v8o]], [[2wv9]] - Hel NS3 helicase domain – Murray valley encephalitis virus<BR />
**[[2v8o]], [[2wv9]] - Hel NS3 helicase domain – Murray valley encephalitis virus<BR />
**[[2qeq]] - Hel NS3 residues 1691-2124 – Kunjin virus<BR />
**[[2qeq]] - Hel NS3 residues 1691-2124 – Kunjin virus<BR />
 +
**[[5txg]], [[5jmt]] - ZvHel NS3 residues 1676-2119 – Zika virus<br />
 +
**[[5k8u]], [[5k8l]], [[5k8i]], [[5jwh]], [[5jrz]] - ZvHel NS3 residues 164-621<br />
**[[2v6i]] – KvHel helicase domain – Kokobera virus<BR />
**[[2v6i]] – KvHel helicase domain – Kokobera virus<BR />
**[[2v6j]] - KvHel helicase domain (mutant)
**[[2v6j]] - KvHel helicase domain (mutant)
Line 230: Line 255:
**[[2jlv]] - DvHel NS3 residues 1646-2092 + AMPPNP + RNA<BR />
**[[2jlv]] - DvHel NS3 residues 1646-2092 + AMPPNP + RNA<BR />
**[[2jlx]], [[2jly]], [[2jlz]] - DvHel NS3 residues 1646-2092 + ADP + RNA<BR />
**[[2jlx]], [[2jly]], [[2jlz]] - DvHel NS3 residues 1646-2092 + ADP + RNA<BR />
-
**[[2vbc]] - DvHel NS3 residues 1475-2092 + NS2A peptide
+
**[[2vbc]] - DvHel NS3 residues 1475-2092 + NS2A peptide<br />
 +
**[[5k8t]] - ZvHel NS3 residues 164-621 + GTP<br />
 +
**[[5gjc]] - ZvHel NS3 residues 1676-2119 + ATP<br />
 +
**[[5gjb]] - ZvHel NS3 residues 1676-2119 + RNA<br />
*ATP-dependent RNA helicase SUV3
*ATP-dependent RNA helicase SUV3
Line 275: Line 303:
**[[2v1x]] - hQ1 residues 49-616<BR />
**[[2v1x]] - hQ1 residues 49-616<BR />
**[[2wwy]], [[4u7d]] – hQ1 residues 49-616 + DNA<br />
**[[2wwy]], [[4u7d]] – hQ1 residues 49-616 + DNA<br />
-
**[[2kmu]] – hQ4 N terminal - NMR
+
**[[2kmu]] – hQ4 N terminal - NMR<br />
 +
**[[5lb8]] – hQ5 <br />
 +
**[[5lb5]], [[5lb3]] – hQ5 + ADP<br />
 +
**[[5lba]] – hQ5 + urea derivative<br />
*ATP-dependent DNA helicase RecG
*ATP-dependent DNA helicase RecG
Line 286: Line 317:
**[[2rhf]] – DrRecQ HRDC domain 3 – ''Deinococcus radiodurans''<BR />
**[[2rhf]] – DrRecQ HRDC domain 3 – ''Deinococcus radiodurans''<BR />
**[[2ma1]] - DrRecQ HRDC domain – NMR <br />
**[[2ma1]] - DrRecQ HRDC domain – NMR <br />
 +
**[[4q48]] - DrRecQ catalytic domain <br />
 +
**[[4q47]] - DrRecQ catalytic domain + ADP <br />
**[[1wud]] - EcRecQ HRDC domain<BR />
**[[1wud]] - EcRecQ HRDC domain<BR />
**[[1oyw]] - EcRecQ catalytic domain<BR />
**[[1oyw]] - EcRecQ catalytic domain<BR />
Line 314: Line 347:
**[[3upu]] – T4DDA + DNA<br />
**[[3upu]] – T4DDA + DNA<br />
- 
-
*ATP-dependent DNA helicase UVRD
 
- 
-
**[[2is1]] - EcUVRD + DNA
 
*ATP-dependent DNA helicase PriA
*ATP-dependent DNA helicase PriA
Line 326: Line 355:
*ATP-dependent DNA helicase PcrA
*ATP-dependent DNA helicase PcrA
-
**[[1qhg]] – GsPcrA (mutant) + ADPNP – ''Geobacillus stearothermophilus''<BR />
+
**[[1qhg]] – GsPcrA (mutant) + ADPNP <BR />
**[[1qhh]] - GsPcrA + ADPNP<br />
**[[1qhh]] - GsPcrA + ADPNP<br />
**[[2pjr]], [[3pjr]] - GsPcrA + DNA<br />
**[[2pjr]], [[3pjr]] - GsPcrA + DNA<br />
-
**[[1pjr]] - GsPcrA
+
**[[1pjr]] - GsPcrA<br />
 +
**[[5dma]] – GsPcrA C-terminal tudor domain<br />
*DnaB helicase
*DnaB helicase
Line 352: Line 382:
**[[3ec2]] – AaDnaC – ''Aquifex aeolicus''<br />
**[[3ec2]] – AaDnaC – ''Aquifex aeolicus''<br />
**[[3ecc]] – AaDnaC + ADP<br />
**[[3ecc]] – AaDnaC + ADP<br />
 +
 +
*Helicase BLM
 +
 +
**[[5lut]] – BLM DHBN domain - chicken<br />
 +
**[[5lus]] – BLM DHBN domain - pelican<br />
 +
**[[5lup]] – hBLM DHBN domain <br />
*Helicase NSP2
*Helicase NSP2
**[[2hwk]] – NSP2 – Venzuelan equine encephalitis virus
**[[2hwk]] – NSP2 – Venzuelan equine encephalitis virus
 +
 +
*Helicase SEN1
 +
 +
**[[5mzn]] – ySEN1<br />
*Helicase SNF2
*Helicase SNF2
Line 368: Line 408:
**[[4a4k]] – ySKI2 insertion domain<br />
**[[4a4k]] – ySKI2 insertion domain<br />
**[[4a4z]] – ySKI2 + AMPPNP
**[[4a4z]] – ySKI2 + AMPPNP
 +
 +
*Helicase SWR1
 +
 +
**[[5i9e]] – ySWR1 + actin + actin-related protein<br />
*Helicase XPD
*Helicase XPD
**[[3crv]], [[3crw]], [[5h8c]] – XPD – ''Sulfolobus acidocaldarius''<br />
**[[3crv]], [[3crw]], [[5h8c]] – XPD – ''Sulfolobus acidocaldarius''<br />
-
**[[4a15]] - TaXPD + DNA – ''Thermoplasma acidophilum''<br />
+
**[[4a15]] - TaXPD + DNA <br />
**[[2vsf]] - TaXPD<br />
**[[2vsf]] - TaXPD<br />
**[[2vl7]] - XPD - ''Sulfolobus tokodaii''<br />
**[[2vl7]] - XPD - ''Sulfolobus tokodaii''<br />
Line 380: Line 424:
**[[3hib]], [[3im1]], [[3im2]] – yBrr2 2nd SEC63 domain<br />
**[[3hib]], [[3im1]], [[3im2]] – yBrr2 2nd SEC63 domain<br />
-
**[[4bgd]] – yBrr2 + pre-mRNA-splicing factor 8<br />
+
**[[4bgd]], [[5m5p]], [[5m52]], [[5dca]] – yBrr2 + pre-mRNA-splicing factor 8<br />
**[[4w7s]] – yCa8<br />
**[[4w7s]] – yCa8<br />
Line 390: Line 434:
**[[4qqy]] – TfCas3 + ADP + HD nuclease<br />
**[[4qqy]] – TfCas3 + ADP + HD nuclease<br />
**[[4qqz]] – TfCas3 + AMPPNP <br />
**[[4qqz]] – TfCas3 + AMPPNP <br />
 +
**[[5gqh]] – PaCas3 + anti-crispr protein 3 – ''Pseudomonas aeruginosa''<br />
 +
**[[5b7i]] – PaCas3 + ACRF3<br />
}}
}}

Revision as of 09:59, 8 June 2017

DNA-dependent helicase PcrA (PDB code 1pjr)

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3D structures of helicase

Updated on 08-June-2017

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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