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Structural and Functional insights into the human Upf1 helicase core

Source organism: Homo sapiens
Biochemical function: hydrolase activity
Biological process: not assigned
Cellular component: not assigned

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EC 3.6.4.13: RNA helicase

Reaction catalysed:
ATP + H(2)O = ADP + phosphate
Systematic name:
ATP phosphohydrolase (RNA helix unwinding)
Alternative Name(s):
  • CSFV NS3 helicase
  • DBP2
  • DDX17
  • DDX25
  • DDX3
  • DDX3X
  • DDX3Y
  • DDX4
  • DDX5
  • DEAD-box RNA helicase
  • DEAD-box protein DED1
  • DEAH-box RNA helicase
  • DEAH-box protein 2
  • DED1
  • DbpA
  • Dex(H/D) RNA helicase
  • EIF4A helicase
  • EhDEAD1
  • EhDEAD1 RNA helicase
  • GRTH/DDX25
  • KOKV helicase
  • Mtr4p
  • NPH-II
  • Nonstructural protein 3 helicase
  • RHA
  • RNA helicase A
  • RNA helicase DDX3
  • RNA helicase Hera
  • RNA-dependent ATPase
  • TGBp1 NTPase/helicase domain
  • VRH1

EC 3.6.4.12: DNA helicase

Reaction catalysed:
ATP + H(2)O = ADP + phosphate
Systematic name:
ATP phosphohydrolase (DNA helix unwinding)
Alternative Name(s):
  • 3' to 5' DNA helicase
  • 3'-5' DNA helicase
  • 3'-5' PfDH
  • 5' to 3' DNA helicase
  • AvDH1
  • BACH1 helicase
  • BLM protein
  • BRCA1-associated C-terminal helicase
  • BcMCM
  • CeWRN-1
  • DNA helicase 120
  • DNA helicase A
  • DNA helicase E
  • DNA helicase II
  • DNA helicase III
  • DNA helicase RECQL5'
  • DNA helicase VI
  • Dbp9p
  • DmRECQ5
  • DnaB
  • DnaB helicase E1
  • HHcsA
  • HPif1
  • Hel E
  • Helicase DnaB
  • Helicase HDH IV
  • Helicase domain of bacteriophage T7 gene 4 protein helicase
  • Hmi1p
  • MCM helicase
  • MCM protein
  • MER3 helicase
  • MER3 protein
  • MPH1
  • PDH120
  • PIF1
  • PcrA
  • PcrA helicase
  • PfDH A
  • Pfh1p
  • UvrD

GO terms

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned

Sequence families

Pfam Protein families (Pfam)
PF13086
Domain description: AAA domain
Occurring in:
  1. Regulator of nonsense transcripts 1
The deposited structure of PDB entry 2gk6 contains 4 copies of Pfam domain PF13086 (AAA domain) in Regulator of nonsense transcripts 1. Showing 2 copies in chain A.

PF13087
Domain description: AAA domain
Occurring in:
  1. Regulator of nonsense transcripts 1
The deposited structure of PDB entry 2gk6 contains 2 copies of Pfam domain PF13087 (AAA domain) in Regulator of nonsense transcripts 1. Showing 1 copy in chain A.

PF18141
Domain description: RNA helicase UPF1, 1B domain
Occurring in:
  1. Regulator of nonsense transcripts 1
The deposited structure of PDB entry 2gk6 contains 2 copies of Pfam domain PF18141 (RNA helicase UPF1, 1B domain) in Regulator of nonsense transcripts 1. Showing 1 copy in chain A.

InterPro InterPro annotations
IPR027417
Domain description: P-loop containing nucleoside triphosphate hydrolase
Occurring in:
  1. Regulator of nonsense transcripts 1
IPR040812
Domain description: RNA helicase UPF1, 1B domain
Occurring in:
  1. Regulator of nonsense transcripts 1
IPR047187
Domain description: Upf1-like, C-terminal helicase domain
Occurring in:
  1. Regulator of nonsense transcripts 1
IPR041679
Domain description: DNA2/NAM7 helicase-like, C-terminal
Occurring in:
  1. Regulator of nonsense transcripts 1
IPR041677
Domain description: DNA2/NAM7 helicase, helicase domain
Occurring in:
  1. Regulator of nonsense transcripts 1
IPR006935
Domain description: Helicase/UvrB, N-terminal
Occurring in:
  1. Regulator of nonsense transcripts 1
IPR045055
Domain description: DNA2/NAM7-like helicase
Occurring in:
  1. Regulator of nonsense transcripts 1

Structure domains

CATH CATH domains
3.40.50.300
Class: Alpha Beta
Architecture: 3-Layer(aba) Sandwich
Topology: Rossmann fold
Homology: P-loop containing nucleotide triphosphate hydrolases
Occurring in:
  1. Regulator of nonsense transcripts 1
The deposited structure of PDB entry 2gk6 contains 4 copies of CATH domain 3.40.50.300 (Rossmann fold) in Regulator of nonsense transcripts 1. Showing 2 copies in chain A.
6.10.140.1240
Class: Special
Architecture: Helix non-globular
Topology: Helix Hairpins
Homology: Helix Hairpins
Occurring in:
  1. Regulator of nonsense transcripts 1
The deposited structure of PDB entry 2gk6 contains 2 copies of CATH domain 6.10.140.1240 (Helix Hairpins) in Regulator of nonsense transcripts 1. Showing 1 copy in chain A.
2.40.30.230
Class: Mainly Beta
Architecture: Beta Barrel
Topology: Elongation Factor Tu (Ef-tu); domain 3
Homology: Elongation Factor Tu (Ef-tu); domain 3
Occurring in:
  1. Regulator of nonsense transcripts 1
The deposited structure of PDB entry 2gk6 contains 2 copies of CATH domain 2.40.30.230 (Elongation Factor Tu (Ef-tu); domain 3) in Regulator of nonsense transcripts 1. Showing 1 copy in chain A.

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