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Crystal structure of E. coli DEAD-box protein SrmB bound to regulator of ribonuclease activity A (RraA)

Source organism: Escherichia coli K-12
Biochemical function: endoribonuclease inhibitor activity
Biological process: negative regulation of RNA catabolic process
Cellular component: protein-containing complex

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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

GO terms

Sequence families

Pfam Protein families (Pfam)
PF03737
Domain description: Aldolase/RraA
Occurring in:
  1. Regulator of ribonuclease activity A
The deposited structure of PDB entry 2yjt contains 3 copies of Pfam domain PF03737 (Aldolase/RraA) in Regulator of ribonuclease activity A. Showing 1 copy in chain A.

PF00271
Domain description: Helicase conserved C-terminal domain
Occurring in:
  1. ATP-dependent RNA helicase SrmB
The deposited structure of PDB entry 2yjt contains 1 copy of Pfam domain PF00271 (Helicase conserved C-terminal domain) in ATP-dependent RNA helicase SrmB. Showing 1 copy in chain D.

InterPro InterPro annotations
IPR005493
Domain description: Ribonuclease E inhibitor RraA/RraA-like protein
Occurring in:
  1. Regulator of ribonuclease activity A
IPR001650
Domain description: Helicase, C-terminal domain-like
Occurring in:
  1. ATP-dependent RNA helicase SrmB
IPR010203
Domain description: Regulator of ribonuclease activity A
Occurring in:
  1. Regulator of ribonuclease activity A
IPR036704
Domain description: Ribonuclease E inhibitor RraA/RraA-like superfamily
Occurring in:
  1. Regulator of ribonuclease activity A
IPR014339
Domain description: Regulator of ribonuclease activity A, gammaproteobacteria
Occurring in:
  1. Regulator of ribonuclease activity A
IPR027417
Domain description: P-loop containing nucleoside triphosphate hydrolase
Occurring in:
  1. ATP-dependent RNA helicase SrmB

Structure domains

CATH CATH domains
3.50.30.40
Class: Alpha Beta
Architecture: 3-Layer(bba) Sandwich
Topology: Glucose Oxidase; domain 1
Homology: Ribonuclease E inhibitor RraA/RraA-like
Occurring in:
  1. Regulator of ribonuclease activity A
The deposited structure of PDB entry 2yjt contains 3 copies of CATH domain 3.50.30.40 (Glucose Oxidase; domain 1) in Regulator of ribonuclease activity A. Showing 1 copy in chain A.
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. ATP-dependent RNA helicase SrmB
The deposited structure of PDB entry 2yjt contains 1 copy of CATH domain 3.40.50.300 (Rossmann fold) in ATP-dependent RNA helicase SrmB. Showing 1 copy in chain D.

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