Summary information

PDB id
8xak
Class
hydrolase-DNA
Method
X-ray (3.5 Å)
Summary
Structure of pif1-g4 complex
Reference
Hong Z, Byrd AK, Gao J, Das P, Tan VQ, Malone EG, Osei B, Marecki JC, Protacio RU, Wahls WP, Raney KD, Song H (2024): "Eukaryotic Pif1 helicase unwinds G-quadruplex and dsDNA using a conserved wedge." Nat Commun, 15, 6104. doi: 10.1038/s41467-024-50575-8.
Abstract
G-quadruplexes (G4s) formed by guanine-rich nucleic acids induce genome instability through impeding DNA replication fork progression. G4s are stable DNA structures, the unfolding of which require the functions of DNA helicases. Pif1 helicase binds preferentially to G4 DNA and plays multiple roles in maintaining genome stability, but the mechanism by which Pif1 unfolds G4s is poorly understood. Here we report the co-crystal structure of Saccharomyces cerevisiae Pif1 (ScPif1) bound to a G4 DNA with a 5' single-stranded DNA (ssDNA) segment. Unlike the Thermus oshimai Pif1-G4 structure, in which the 1B and 2B domains confer G4 recognition, ScPif1 recognizes G4 mainly through the wedge region in the 1A domain that contacts the 5' most G-tetrad directly. A conserved Arg residue in the wedge is required for Okazaki fragment processing but not for mitochondrial function or for suppression of gross chromosomal rearrangements. Multiple substitutions at this position have similar effects on resolution of DNA duplexes and G4s, suggesting that ScPif1 may use the same wedge to unwind G4 and dsDNA. Our results reveal the mechanism governing dsDNA unwinding and G4 unfolding by ScPif1 helicase that can potentially be generalized to other eukaryotic Pif1 helicases and beyond.
G4 notes
8 G-tetrads, 2 G4 helices, 4 G4 stems, 2 G4 coaxial stacks, 2(-P-P-P), parallel(4+0), UUUU, coaxial interfaces: 3'/5'

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 8 G-tetrads

 1 glyco-bond=---- sugar=---- groove=---- planarity=0.168 type=other  nts=4 GGGG D.DG9,D.DG12,D.DG15,D.DG19
 2 glyco-bond=---- sugar=3--- groove=---- planarity=0.231 type=other  nts=4 GGGG D.DG10,D.DG13,D.DG16,D.DG22
 3 glyco-bond=---- sugar=-..- groove=---- planarity=0.213 type=other  nts=4 GGGG D.DG24,D.DG27,D.DG30,D.DG33
 4 glyco-bond=---- sugar=---. groove=---- planarity=0.229 type=other  nts=4 GGGG D.DG25,D.DG28,D.DG31,D.DG34
 5 glyco-bond=---- sugar=---- groove=---- planarity=0.204 type=other  nts=4 GGGG B.DG9,B.DG12,B.DG15,B.DG19
 6 glyco-bond=---- sugar=.--- groove=---- planarity=0.263 type=other  nts=4 GGGG B.DG10,B.DG13,B.DG16,B.DG22
 7 glyco-bond=---- sugar=---- groove=---- planarity=0.208 type=other  nts=4 GGGG B.DG24,B.DG27,B.DG30,B.DG33
 8 glyco-bond=---- sugar=---- groove=---- planarity=0.218 type=other  nts=4 GGGG B.DG25,B.DG28,B.DG31,B.DG34

List of 2 G4-helices

In DSSR, a G4-helix is defined by stacking interactions of G-tetrads, regardless of backbone connectivity, and may contain more than one G4-stem.

Helix#1, 4 G-tetrad layers, INTRA-molecular, with 2 stems

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG D.DG9,D.DG12,D.DG15,D.DG19
 2* glyco-bond=---- sugar=3--- groove=---- WC-->Major nts=4 GGGG D.DG10,D.DG13,D.DG16,D.DG22
 3  glyco-bond=---- sugar=..-- groove=---- WC-->Major nts=4 GGGG D.DG27,D.DG30,D.DG33,D.DG24
 4  glyco-bond=---- sugar=--.- groove=---- WC-->Major nts=4 GGGG D.DG28,D.DG31,D.DG34,D.DG25
  step#1  pm(>>,forward)  area=8.45  rise=3.33 twist=36.2
  step#2  pm(>>,forward)  area=23.35 rise=3.41 twist=17.8
  step#3  pm(>>,forward)  area=12.07 rise=3.36 twist=31.8
  strand#1 DNA glyco-bond=---- sugar=-3.- nts=4 GGGG D.DG9,D.DG10,D.DG27,D.DG28
  strand#2 DNA glyco-bond=---- sugar=--.- nts=4 GGGG D.DG12,D.DG13,D.DG30,D.DG31
  strand#3 DNA glyco-bond=---- sugar=---. nts=4 GGGG D.DG15,D.DG16,D.DG33,D.DG34
  strand#4 DNA glyco-bond=---- sugar=---- nts=4 GGGG D.DG19,D.DG22,D.DG24,D.DG25

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3 stacking diagrams 
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG D.DG9,D.DG12,D.DG15,D.DG19
 2* glyco-bond=---- sugar=3--- groove=---- WC-->Major nts=4 GGGG D.DG10,D.DG13,D.DG16,D.DG22
  step#1  pm(>>,forward)  area=8.45  rise=3.33 twist=36.2

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 2* glyco-bond=---- sugar=3--- groove=---- WC-->Major nts=4 GGGG D.DG10,D.DG13,D.DG16,D.DG22
 3  glyco-bond=---- sugar=..-- groove=---- WC-->Major nts=4 GGGG D.DG27,D.DG30,D.DG33,D.DG24
  step#2  pm(>>,forward)  area=23.35 rise=3.41 twist=17.8

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 3  glyco-bond=---- sugar=..-- groove=---- WC-->Major nts=4 GGGG D.DG27,D.DG30,D.DG33,D.DG24
 4  glyco-bond=---- sugar=--.- groove=---- WC-->Major nts=4 GGGG D.DG28,D.DG31,D.DG34,D.DG25
  step#3  pm(>>,forward)  area=12.07 rise=3.36 twist=31.8

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Helix#2, 4 G-tetrad layers, INTRA-molecular, with 2 stems

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG9,B.DG12,B.DG15,B.DG19
 2* glyco-bond=---- sugar=.--- groove=---- WC-->Major nts=4 GGGG B.DG10,B.DG13,B.DG16,B.DG22
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG27,B.DG30,B.DG33,B.DG24
 4  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG28,B.DG31,B.DG34,B.DG25
  step#1  pm(>>,forward)  area=9.31  rise=3.32 twist=35.3
  step#2  pm(>>,forward)  area=19.39 rise=3.45 twist=18.3
  step#3  pm(>>,forward)  area=9.53  rise=3.23 twist=34.3
  strand#1 DNA glyco-bond=---- sugar=-.-- nts=4 GGGG B.DG9,B.DG10,B.DG27,B.DG28
  strand#2 DNA glyco-bond=---- sugar=---- nts=4 GGGG B.DG12,B.DG13,B.DG30,B.DG31
  strand#3 DNA glyco-bond=---- sugar=---- nts=4 GGGG B.DG15,B.DG16,B.DG33,B.DG34
  strand#4 DNA glyco-bond=---- sugar=---- nts=4 GGGG B.DG19,B.DG22,B.DG24,B.DG25

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3 stacking diagrams 
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG9,B.DG12,B.DG15,B.DG19
 2* glyco-bond=---- sugar=.--- groove=---- WC-->Major nts=4 GGGG B.DG10,B.DG13,B.DG16,B.DG22
  step#1  pm(>>,forward)  area=9.31  rise=3.32 twist=35.3

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 2* glyco-bond=---- sugar=.--- groove=---- WC-->Major nts=4 GGGG B.DG10,B.DG13,B.DG16,B.DG22
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG27,B.DG30,B.DG33,B.DG24
  step#2  pm(>>,forward)  area=19.39 rise=3.45 twist=18.3

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 3  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG27,B.DG30,B.DG33,B.DG24
 4  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG28,B.DG31,B.DG34,B.DG25
  step#3  pm(>>,forward)  area=9.53  rise=3.23 twist=34.3

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List of 4 G4-stems

In DSSR, a G4-stem is defined as a G4-helix with backbone connectivity. Bulges are also allowed along each of the four strands.

Stem#1, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 2(-P-P-P), parallel(4+0)

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG D.DG9,D.DG12,D.DG15,D.DG19
 2  glyco-bond=---- sugar=3--- groove=---- WC-->Major nts=4 GGGG D.DG10,D.DG13,D.DG16,D.DG22
  step#1  pm(>>,forward)  area=8.45  rise=3.33 twist=36.2
  strand#1  U DNA glyco-bond=-- sugar=-3 nts=2 GG D.DG9,D.DG10
  strand#2  U DNA glyco-bond=-- sugar=-- nts=2 GG D.DG12,D.DG13
  strand#3  U DNA glyco-bond=-- sugar=-- nts=2 GG D.DG15,D.DG16
  strand#4* U DNA glyco-bond=-- sugar=-- nts=2 GG D.DG19,D.DG22 bulged-nts=2 TT D.DT20,D.DT21
  loop#1 type=propeller strands=[#1,#2] nts=1 T D.DT11
  loop#2 type=propeller strands=[#2,#3] nts=1 T D.DT14
  loop#3 type=propeller strands=[#3,#4] nts=2 TT D.DT17,D.DT18

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Stem#2, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 2(-P-P-P), parallel(4+0)

 1  glyco-bond=---- sugar=-..- groove=---- WC-->Major nts=4 GGGG D.DG24,D.DG27,D.DG30,D.DG33
 2  glyco-bond=---- sugar=---. groove=---- WC-->Major nts=4 GGGG D.DG25,D.DG28,D.DG31,D.DG34
  step#1  pm(>>,forward)  area=12.07 rise=3.36 twist=31.8
  strand#1  U DNA glyco-bond=-- sugar=-- nts=2 GG D.DG24,D.DG25
  strand#2  U DNA glyco-bond=-- sugar=.- nts=2 GG D.DG27,D.DG28
  strand#3  U DNA glyco-bond=-- sugar=.- nts=2 GG D.DG30,D.DG31
  strand#4  U DNA glyco-bond=-- sugar=-. nts=2 GG D.DG33,D.DG34
  loop#1 type=propeller strands=[#1,#2] nts=1 T D.DT26
  loop#2 type=propeller strands=[#2,#3] nts=1 T D.DT29
  loop#3 type=propeller strands=[#3,#4] nts=1 T D.DT32

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Stem#3, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 2(-P-P-P), parallel(4+0)

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG9,B.DG12,B.DG15,B.DG19
 2  glyco-bond=---- sugar=.--- groove=---- WC-->Major nts=4 GGGG B.DG10,B.DG13,B.DG16,B.DG22
  step#1  pm(>>,forward)  area=9.31  rise=3.32 twist=35.3
  strand#1  U DNA glyco-bond=-- sugar=-. nts=2 GG B.DG9,B.DG10
  strand#2  U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG12,B.DG13
  strand#3  U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG15,B.DG16
  strand#4* U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG19,B.DG22 bulged-nts=2 TT B.DT20,B.DT21
  loop#1 type=propeller strands=[#1,#2] nts=1 T B.DT11
  loop#2 type=propeller strands=[#2,#3] nts=1 T B.DT14
  loop#3 type=propeller strands=[#3,#4] nts=2 TT B.DT17,B.DT18

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Stem#4, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 2(-P-P-P), parallel(4+0)

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG24,B.DG27,B.DG30,B.DG33
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG25,B.DG28,B.DG31,B.DG34
  step#1  pm(>>,forward)  area=9.53  rise=3.23 twist=34.3
  strand#1  U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG24,B.DG25
  strand#2  U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG27,B.DG28
  strand#3  U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG30,B.DG31
  strand#4  U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG33,B.DG34
  loop#1 type=propeller strands=[#1,#2] nts=1 T B.DT26
  loop#2 type=propeller strands=[#2,#3] nts=1 T B.DT29
  loop#3 type=propeller strands=[#3,#4] nts=1 T B.DT32

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List of 2 G4 coaxial stacks

 1 G4 helix#1 contains 2 G4 stems: [#1,#2]  [3'/5']
 2 G4 helix#2 contains 2 G4 stems: [#3,#4]  [3'/5']