InterPro : IPR020568

Name  Ribosomal protein S5 domain 2-type fold Short Name  Ribosomal_S5_D2-typ_fold
Type  Domain Description  Domain 2 of the ribosomal protein S5 has a left-handed, 2-layer alpha/beta fold with a core structure consisting of beta(3)-alpha-beta-alpha. Domains with this fold are found in numerous RNA/DNA-binding proteins, as well as in kinases from the GHMP kinase family. Proteins containing this alpha/beta fold domain include: Translational machinery components (ribosomal proteins S5 and S9, and domain IV of elongation factors EF-G and eEF-2) [].Ribonuclease P protein (RNase P) [].Ribonuclease PH (domain 1) [], as well as various exosome complex exonucleases (RRP41, RRP42, RRP43, RRP45, RRP46, MTR3, ECX1, ECX2) [].DNA modification proteins (DNA mismatch repair proteins MutL and PMS2, DNA gyrase B, DNA topoisomerase II, IV-B and VI-B) []. GHMP kinases that transfer a phosphoryl group from ATP to an acceptor (galactokinase (), homoserine kinase (), and mevalonate kinase ()) [, ].Caenorhabditis elegansearly switch protein Xol-1 (a divergent member of the GHMP kinase family that has lost the ATP-binding site) [].Hsp90 chaperone (middle domain), which is related to the DNA gyrase/MutL family []; this domain contains an extra C-terminal alpha/beta subdomain.Imidazole glycerol phosphate dehydratase, which contains a duplication consisting of two structural repeats of this fold [].The catalytic domain of ATP-dependent protease Lon (La), which contains an extra C-terminal alpha/beta subdomain [].Formaldehyde-activating enzyme FAE, which contains a modification of this fold consisting of an extra alpha/beta unit after strand 2 [].

Sequence Features

GO Displayer


InterPro protein domain ID --> Contigs



6 Child Features

Id Name Short Name Type
IPR001247 Exoribonuclease, phosphorolytic domain 1 ExoRNase_PH_dom1 Domain
IPR001498 Impact, N-terminal Impact_N Domain
IPR008269 Peptidase S16, Lon C-terminal Pept_S16_C Domain
IPR014721 Ribosomal protein S5 domain 2-type fold, subgroup Ribosomal_S5_D2-typ_fold_subgr Domain
IPR015870 UDP-3-O-acyl N-acetylglucosamine deacetylase, N-terminal UDP-acyl_N-AcGlcN_deAcase_N Domain
IPR011334 UDP-3-O-acyl N-acetylglucosamine deacetylase, C-terminal UDP-acyl_GlcNac_deAcase_C Domain

10 Contains

Id Name Short Name Type
IPR006204 GHMP kinase N-terminal domain GHMP_kinase_N_dom Domain
IPR019539 Galactokinase galactose-binding domain GalKase_gal-bd Domain
IPR020574 Ribosomal protein S9, conserved site Ribosomal_S9_CS Conserved_site
IPR019741 Galactokinase, conserved site Galactokinase_CS Conserved_site
IPR008268 Peptidase S16, active site Peptidase_S16_AS Active_site
IPR006203 GHMP kinase, ATP-binding, conserved site GHMP_knse_ATP-bd_CS Conserved_site
IPR020569 Uncharacterised protein family UPF0029, Impact, conserved site UPF0029_Impact_CS Conserved_site
IPR018336 Ribonuclease PH, conserved site RNase_PH_CS Conserved_site
IPR020539 Ribonuclease P, conserved site RNase_P_CS Conserved_site
IPR020565 Imidazoleglycerol-phosphate dehydratase, conserved site ImidazoleglycerP_deHydtase_CS Conserved_site

45 Found In

Id Name Short Name Type
IPR001404 Heat shock protein Hsp90 family Hsp90_fam Family
IPR000851 Ribosomal protein S5 Ribosomal_S5 Family
IPR006206 Mevalonate/galactokinase Mevalonate/galactokinase Family
IPR000705 Galactokinase Galactokinase Family
IPR006205 Mevalonate kinase Mev_gal_kin Family
IPR005935 Diphosphomevalonate/phosphomevalonate decarboxylase Mev_decarb Family
IPR001241 DNA topoisomerase, type IIA Topo_IIA Family
IPR002099 DNA mismatch repair protein family DNA_mismatch_repair_fam Family
IPR004540 Translation elongation factor EFG/EF2 Transl_elong_EFG/EF2 Family
IPR005711 Ribosomal protein S5, eukaryotic/archaeal Ribosomal_S5_euk/arc Family
IPR004815 Lon protease, bacterial/eukaryotic-type Lon_bac/euk-typ Family
IPR011186 DNA mismatch repair protein Mlh1/HexB DNA_mismatch_repair_MLH1/HexB Family
IPR004504 DNA repair protein RadA DNA_repair_RadA Family
IPR002381 Ribonuclease phosphorolytic, bacterial-type RNase_PH_bac-type Family
IPR012162 Polyribonucleotide nucleotidyltransferase PNPase Family
IPR004463 UDP-3-O-acyl N-acetylglucosamine deacetylase UDP-acyl_GlcNac_deAcase Family
IPR000807 Imidazoleglycerol-phosphate dehydratase ImidazoleglycerolP_deHydtase Family
IPR004482 Mg chelatase-related protein Mg_chelat-rel Family
IPR005740 DNA topoisomerase 4 subunit B, Gram-positive ParE Family
IPR011557 DNA gyrase, subunit B GyrB Family
IPR005737 DNA topoisomerase IV, subunit B, Gram-negative TopoIV_B_Gneg Family
IPR000565 DNA topoisomerase, type IIA, subunit B Topo_IIA_B Family
IPR014069 Guanosine pentaphosphate synthetase I/polyribonucleotide nucleotidyltransferase pppGpp_PNP Family
IPR004543 Translation elongation factor EFG/EF2, archaeal Transl_elong_EFG/EF2_arc Family
IPR016005 Phosphomevalonate kinase, ERG8 Pmev_kin_ERG8 Family
IPR005916 Phosphomevalonate kinase, eukaryotic Pmev_kin_euk Family
IPR004424 4-diphosphocytidyl-2C-methyl-D-erythritol kinase IspE Family
IPR004422 GHMP kinase group 1 GHMP_kin Family
IPR004663 Lon protease, archaeal Lon_arc Family
IPR014251 Sporulation protease LonB Spore_LonB Family

0 Parent Features

12 Publications

First Author Title Year Journal Volume Pages
Ramakrishnan V Structures of prokaryotic ribosomal proteins: implications for RNA binding and evolution. 1995 Biochem Cell Biol 73 979-86
Liu Q Reconstitution, activities, and structure of the eukaryotic RNA exosome. 2006 Cell 127 1223-37
Zhou T Structure and mechanism of homoserine kinase: prototype for the GHMP kinase superfamily. 2000 Structure 8 1247-57
Luz JG XOL-1, primary determinant of sexual fate in C. elegans, is a GHMP kinase family member and a structural prototype for a class of developmental regulators. 2003 Genes Dev 17 977-90
Guarné A Structure and function of the N-terminal 40 kDa fragment of human PMS2: a monomeric GHL ATPase. 2001 EMBO J 20 5521-31
Marquez SM Structure and function of eukaryotic Ribonuclease P RNA. 2006 Mol Cell 24 445-56
Andreassi JL 2nd Molecular functions of conserved aspects of the GHMP kinase family. 2004 Biochemistry 43 14594-601
Meyer P Structural basis for recruitment of the ATPase activator Aha1 to the Hsp90 chaperone machinery. 2004 EMBO J 23 1402-10
Sinha SC Crystal structure of imidazole glycerol-phosphate dehydratase: duplication of an unusual fold. 2004 J Biol Chem 279 15491-8
Harlow LS Crystal structure of the phosphorolytic exoribonuclease RNase PH from Bacillus subtilis and implications for its quaternary structure and tRNA binding. 2004 Protein Sci 13 668-77
Botos I The catalytic domain of Escherichia coli Lon protease has a unique fold and a Ser-Lys dyad in the active site. 2004 J Biol Chem 279 8140-8
Acharya P How an enzyme binds the C1 carrier tetrahydromethanopterin. Structure of the tetrahydromethanopterin-dependent formaldehyde-activating enzyme (Fae) from Methylobacterium extorquens AM1. 2005 J Biol Chem 280 13712-9

To cite PlanMine, please refer to the following publication:

Rozanski, A., Moon, H., Brandl, H., Martín-Durán, J. M., Grohme, M., Hüttner, K., Bartscherer, K., Henry, I., & Rink, J. C.
PlanMine 3.0—improvements to a mineable resource of flatworm biology and biodiversity
Nucleic Acids Research, gky1070. doi:10.1093/nar/gky1070 (2018)