ynbA

GTP-binding protein, ribosome-splitting factor, rescues translationally arrested ribosomes

locus: BSU_17430

pI: 9.24

mw: 37.51 kDa

protein length: 420 aa

gene length: 1263 bp

function: rescuing of translationally arrested ribosomes

product: GTP-binding protein, ribosome-splitting factor

essential: no

synonyms

Genomic Context

categories

• [category|SW 3|Information processing] → [category|SW 3.5|Targets of second messengers] → [category|SW 3.5.3|Targets of (p)ppGpp]
• [category|SW 6|Groups of genes] → [category|SW 6.3|GTP-binding proteins]

Gene

Coordinates: 1,875,304 1,876,566

The protein

Catalyzed reaction/ biological activity

• binds and hydrolyzes GTP and readily exchanges GDP for GTP
• rescuing of translationally arrested ribosomes [Pubmed|26458047]

Protein family

• TRAFAC class OBG-HflX-like GTPase superfamily (with [protein|84E7D672DB40B114DC4D96A4D8834958B47401A7|Obg] and [protein|C0F5FAD6DF89DA9E0FFC8F888D7CED6AA42D9C73|YyaF], according to UniProt)

Paralogous protein(s)

• [protein|B2270316642C66BC2DA86EBDCD1BF6A33CC6A1DC|YphC], [protein|C0F5FAD6DF89DA9E0FFC8F888D7CED6AA42D9C73|YyaF], [protein|CB68B3393CA7862C45C624AF7B1ADD188243A01F|Era], [protein|DF1A043F3D9817D9479B8C707F4ACEEF2BF2862C|YsxC], [protein|54CD247926F7FABE4ACE85EB7021B62500B47260|RbgA], [protein|66A6EC4F6CB91EE741BB9D7646913FF3EE602BD7|ThdF], [protein|84E7D672DB40B114DC4D96A4D8834958B47401A7|Obg], [protein|959C0ED7B9DA50F0EADCF1565405B878D36DA206|YqeH]

[SW|Domains]

• Hflx-type G domain (aa 201-363) (according to UniProt)

Effectors of protein activity

• binds ppGpp [Pubmed|26951678], ppGpp may inhibit activity [Pubmed|26951678]

Structure

• [PDB|5ADY] (the protein from ''E. coli'' in complex with the [SW|ribosome], 41% identity) [Pubmed|26458047]

Expression and Regulation

Operons

• genes: [gene|9F6B78C1932FB56F7F71430DB16BC862A312407B|ynbA]-[gene|14EFA3BF4E5DD5368EF02B0733300CEF7A4E0DC7|ynbB]-[gene|641C4BDD9702804642E1753A9C779E80FABB3919|glnR]-[gene|68F4E792B99F86AE9E8F06D2200E128937331F5D|glnA]
  description: [Pubmed|22383849]

  regulation

  • the mRNA is processed between [gene|641C4BDD9702804642E1753A9C779E80FABB3919|glnR] and [gene|68F4E792B99F86AE9E8F06D2200E128937331F5D|glnA] by [protein|872CCB5A49C9000BD95E4B0472556D5F60F7D7A4|RNase Y], this requires the [protein|EE52DFA35B935E551871D079A9BE877DB2001A3B|YmcA]-[protein|6C9A092F38739A3759793EF8B496569CD02C2E3F|YlbF]-[protein|EBD15C174A03B7FCDFFE4C5DB5D86E93F1B9CAC4|YaaT] complex [Pubmed|29794222]

Biological materials

Mutant

• MGNA-A020 (ynbA::erm), available at the [https://shigen.nig.ac.jp/bsub/resource/strainGeneDisrupted/detail/20 NBRP B. subtilis, Japan]
• BKE17430 ([gene|9F6B78C1932FB56F7F71430DB16BC862A312407B|ynbA]::erm trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKE17430 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CAAATGGATGTTCCTTTCTT, downstream forward: _UP4_ATGTAGGAAGGAAATATAAA
• BKK17430 ([gene|9F6B78C1932FB56F7F71430DB16BC862A312407B|ynbA]::kan trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKK17430 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CAAATGGATGTTCCTTTCTT, downstream forward: _UP4_ATGTAGGAAGGAAATATAAA

Expression vector

• pGP2845: IPTG inducible expression, purification in ''E. coli'' with C-terminal Strep-tag, in [SW|pGP574], available in [SW|Jörg Stülke]'s lab
• pGP2846: expression of Strep-''ynbA'' by [SW|pGP380] in ''B. subtilis'' suitable for [SW|SPINE], available in [SW|Jörg Stülke]'s lab

two-hybrid system

• ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([SW|BACTH]), available in [SW|Jörg Stülke]'s lab

labs

• [SW|Naotake Ogasawara], Nara, Japan

References

Reviews

• 21885683

Original publications

• 12427945,26458047,26951678,26951678