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InterPro: IPR020568 Ribosomal protein S5 domain 2-type fold

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UniProtKB
Matches:
43560 proteins
AccessionHelp
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IPR020568 Ribosomal_S5_D2-typ_fold
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Domain
SignaturesHelp
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InterPro RelationshipsHelp
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Children IPR001247 Exoribonuclease, phosphorolytic domain 1
IPR001498 Uncharacterised protein family UPF0029, Impact, N-terminal
IPR008269 Peptidase S16, lon C-terminal
IPR011334 UDP-3-O-acyl N-acetylglucosamine deacetylase, C-terminal
IPR014721 Ribosomal protein S5 domain 2-type fold, subgroup
IPR015870 UDP-3-O-acyl N-acetylglucosamine deacetylase, N-terminal
Found in IPR000565 DNA topoisomerase, type IIA, subunit B
IPR000705 Galactokinase
IPR000807 Imidazoleglycerol-phosphate dehydratase
IPR000851 Ribosomal protein S5
IPR001174 Galactokinase/homoserine kinase
IPR001241 DNA topoisomerase, type IIA, subunit B or N-terminal
IPR001404 Chaperone protein htpG
IPR001984 Peptidase S16, Lon protease, C-terminal
IPR002099 DNA mismatch repair protein
IPR002127 Tetracycline resistance protein, TetO/TetQ/TetM
IPR002381 Ribonuclease phosphorolytic, bacterial-type
IPR004422 GHMP kinase group 1
IPR004424 4-diphosphocytidyl-2C-methyl-D-erythritol kinase
IPR004463 UDP-3-O-acyl N-acetylglucosamine deacetylase
IPR004482 Mg chelatase-related protein
IPR004504 DNA repair protein RadA
IPR004540 Translation elongation factor EFG/EF2
IPR004543 Translation elongation factor EFG/EF2, archaeal
IPR004663 Peptidase S16, archaeal lon homologues
IPR004815 Peptidase S16, ATP-dependent protease La
IPR005711 Ribosomal protein S5, eukaryotic/archaeal
IPR005712 Ribosomal protein S5, bacterial-type
IPR005734 DNA topoisomerase VI, subunit B
IPR005737 DNA topoisomerase IV, subunit B, Gram-negative
IPR005740 DNA topoisomerase IV, subunit B, Gram-positive
IPR005916 Phosphomevalonate kinase, eukaryotic
IPR005917 Phosphomevalonate kinase, Gram-positive
IPR005935 Diphosphomevalonate decarboxylase
IPR006205 Mevalonate kinase
IPR006206 Mevalonate/galactokinase
IPR010189 Shikimate kinase, archaea
IPR011186 DNA mismatch repair protein Mlh1
IPR011557 DNA gyrase, subunit B
IPR011807 Exoribonuclease, phosphorolytic domain-containing, archaea
IPR012043 GHMP kinase-like, archaeal
IPR012162 Polyribonucleotide nucleotidyltransferase
IPR012363 Propanediol utilisation/coumermycin biosynthesis, PduX-related
IPR012369 Galactokinase, glycosyltransferase
IPR013473 Conserved hypothetical protein CHP02653, peptidase S16 non-peptidase homologue
IPR014069 Guanosine pentaphosphate synthetase I/polyribonucleotide nucleotidyltransferase
IPR014251 Sporulation protease LonB
IPR014252 Sporulation protease LonC
IPR014606 D,D-heptose 7-phosphate kinase
IPR014763 DNA mismatch repair protein, N-terminal
IPR015434 Post Meiotic Segregation 2
IPR015566 Molecular chaperone, heat shock protein, endoplasmin
IPR015796 Uncharacterised protein family UPF0029, Impact
IPR016005 Phosphomevalonate kinase, ERG8
IPR020576 Heat shock protein Hsp90, C-terminal
IPR020667 DNA mismatch repair protein, MutL
IPR020869 Exosome complex exonuclease 2, probable
Contains IPR006203 GHMP kinase, ATP-binding, conserved site
IPR006204 GHMP kinase
IPR008268 Peptidase S16, active site
IPR018336 Ribonuclease PH, conserved site
IPR019539 Galactokinase galactose-binding domain
IPR019741 Galactokinase, conserved site
IPR020539 Ribonuclease P, conserved site
IPR020565 Imidazoleglycerol-phosphate dehydratase, conserved site
IPR020569 Uncharacterised protein family UPF0029, Impact, conserved site
IPR020574 Ribosomal protein S9, conserved site
InterPro annotation
BioMart Logo Entry Details in BioMart
AbstractHelp
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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) [1].
  • Ribonuclease P protein (RNase P) [2].
  • Ribonuclease PH (domain 1) [3], as well as various exosome complex exonucleases (RRP41, RRP42, RRP43, RRP45, RRP46, MTR3, ECX1, ECX2) [4].
  • DNA modification proteins (DNA mismatch repair proteins MutL and PMS2, DNA gyrase B, DNA topoisomerase II, IV-B and VI-B) [5].
  • GHMP kinases that transfer a phosphoryl group from ATP to an acceptor (galactokinase (EC:2.7.1.6), homoserine kinase (EC: 2.7.1.39), and mevalonate kinase (EC: 2.7.1.36)) [6, 7].
  • Caenorhabditis elegans early switch protein Xol-1 (a divergent member of the GHMP kinase family that has lost the ATP-binding site) [8].
  • Hsp90 chaperone (middle domain), which is related to the DNA gyrase/MutL family [9]; 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 [10].
  • The catalytic domain of ATP-dependent protease Lon (La), which contains an extra C-terminal alpha/beta subdomain [11].
  • Formaldehyde-activating enzyme FAE, which contains a modification of this fold consisting of an extra alpha/beta unit after strand 2 [12].
Structural linksHelp
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PDB - click here
1a6f , 1b62 , 1b63 , 1bkn , 1d6t , 1dar , 1dv4 , 1e3h , 1e3p , 1ea6 , 1efg , 1ei1 , 1elo , 1fi4 , 1fjg , 1fka , 1fnm , 1fwk , 1fwl , 1gix , 1h72 , 1h73 , 1h74 , 1h7s , 1h7u , 1hk7 , 1hnw , 1hnx , 1hnz , 1hr0 , 1i94 , 1i95 , 1i96 , 1i97 , 1ibk , 1ibl , 1ibm , 1j5e , 1jgo , 1jgp , 1jgq , 1k47 , 1kij , 1kkh , 1ktv , 1kvk , 1mg7 , 1mu5 , 1mx0 , 1n0u , 1n0v , 1n32 , 1n33 , 1n34 , 1n36 , 1nhh , 1nhi , 1nhj , 1nz0 , 1oj4 , 1oyp , 1oyr , 1oys , 1p42 , 1pie , 1pkp , 1pns , 1pnx , 1pvg , 1qd7 , 1qzr , 1r6l , 1r6m , 1rhy , 1rr9 , 1rre , 1s16 , 1s4e , 1u2r , 1udn , 1udo , 1udq , 1uds , 1uek , 1usu , 1usv , 1vi7 , 1vis , 1vs5 , 1vs7 , 1wdt , 1whu , 1wuu , 1xhk , 1xmo , 1xmq , 1xnq , 1xnr , 1xxe , 1yh8 , 1yhc , 1yl4 , 1z59 , 1z5a , 1z5b , 1z5c , 1zm2 , 1zm3 , 1zm4 , 1zm9 , 1zxm , 1zxn , 2ae8 , 2avy , 2aw7 , 2b64 , 2b9m , 2b9o , 2ba0 , 2ba1 , 2bm0 , 2bm1 , 2br2 , 2bv3 , 2c37 , 2c38 , 2c39 , 2cve , 2cz9 , 2dy1 , 2e1r , 2e5l , 2efg , 2f1d , 2f4v , 2go3 , 2go4 , 2hgi , 2hgp , 2hgr , 2hhh , 2hke , 2hkj , 2i2p , 2i2u , 2ier , 2ies , 2j00 , 2j02 , 2j65 , 2je6 , 2jea , 2jeb , 2jt2 , 2nn6 , 2npf , 2o3z , 2ow8 , 2qal , 2qan , 2qb9 , 2qbb , 2qbd , 2qbf , 2qbh , 2qbj , 2qnh , 2qou , 2qow , 2qoy , 2qp0 , 2r42 , 2uu9 , 2uua , 2uub , 2uuc , 2uxb , 2uxc , 2uxd , 2v46 , 2v48 , 2vho , 2vhp , 2vqe , 2vqf , 2z4k , 2z4m , 3d5a , 3d5c , 3df1 , 3df3

Taxonomic coverageHelp
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Overlapping InterPro entriesHelp
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IPR020568 Numbers of overlapping proteins Average numbers of overlapping amino acids

Example proteinsHelp
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P02828 Heat shock protein 83

P02829 ATP-dependent molecular chaperone HSP82

P07900 Heat shock protein HSP 90-alpha

Q23229 XO lethal protein 1

Q8K1R3 Polyribonucleotide nucleotidyltransferase 1, mitochondrial

More proteins


Example Proteins Key


InterPro entry accession number/name and structure databases Colour code
IPR020568 Ribosomal protein S5 domain 2-type fold
IPR019805 Heat shock protein Hsp90, conserved site
IPR001247 Exoribonuclease, phosphorolytic domain 1
IPR003594 ATPase-like, ATP-binding domain
IPR020575 Heat shock protein Hsp90, N-terminal
IPR003029 Ribosomal protein S1, RNA binding domain
IPR020576 Heat shock protein Hsp90, C-terminal
IPR015193 Switch protein XOL-1, GHMP-like
IPR016027 Nucleic acid-binding, OB-fold-like
IPR015192 Switch protein XOL-1, N-terminal
IPR012340 Nucleic acid-binding, OB-fold
IPR004087 K Homology
IPR004088 K Homology, type 1
IPR018111 K Homology, type 1, subgroup
IPR015847 Exoribonuclease, phosphorolytic domain 2
IPR015848 Polynucleotide phosphorylase, phosphorolytic RNA-binding, bacterial/organelle-type
IPR012162 Polyribonucleotide nucleotidyltransferase
IPR001404 Chaperone protein htpG
IPR014721 Ribosomal protein S5 domain 2-type fold, subgroup
PDB Chain
ModBase
CATH Domain
SWISS-MODEL
SCOP Domain

PublicationsHelp
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1. Ramakrishnan V, Davies C, Gerchman SE, Golden BL, Hoffmann DW, Jaishree TN, Kyila JH, Porter S, White SW.
Structures of prokaryotic ribosomal proteins: implications for RNA binding and evolution.
Biochem. Cell Biol. 73 979-86 1995 [PubMed: 8722013]
2. Marquez SM, Chen JL, Evans D, Pace NR.
Structure and function of eukaryotic Ribonuclease P RNA.
Mol. Cell 24 445-56 2006 [PubMed: 17081993]
http://dx.doi.org/10.1016/j.molcel.2006.09.011
3. Harlow LS, Kadziola A, Jensen KF, Larsen S.
Crystal structure of the phosphorolytic exoribonuclease RNase PH from Bacillus subtilis and implications for its quaternary structure and tRNA binding.
Protein Sci. 13 668-77 2004 [PubMed: 14767080]
http://dx.doi.org/10.1110/ps.03477004
4. Liu Q, Greimann JC, Lima CD.
Reconstitution, activities, and structure of the eukaryotic RNA exosome.
Cell 127 1223-37 2006 [PubMed: 17174896]
http://dx.doi.org/10.1016/j.cell.2006.10.037
5. Guarne A, Junop MS, Yang W.
Structure and function of the N-terminal 40 kDa fragment of human PMS2: a monomeric GHL ATPase.
EMBO J. 20 5521-31 2001 [PubMed: 11574484]
http://dx.doi.org/10.1093/emboj/20.19.5521
6. Andreassi JL 2nd, Leyh TS.
Molecular functions of conserved aspects of the GHMP kinase family.
Biochemistry 43 14594-601 2004 [PubMed: 15544330]
http://dx.doi.org/10.1021/bi048963o
7. Zhou T, Daugherty M, Grishin NV, Osterman AL, Zhang H.
Structure and mechanism of homoserine kinase: prototype for the GHMP kinase superfamily.
Structure 8 1247-57 2000 [PubMed: 11188689]
http://dx.doi.org/10.1016/S0969-2126(00)00533-5
8. Luz JG, Hassig CA, Pickle C, Godzik A, Meyer BJ, Wilson IA.
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.
Genes Dev. 17 977-90 2003 [PubMed: 12672694]
http://dx.doi.org/10.1101/gad.1082303
9. Meyer P, Prodromou C, Liao C, Hu B, Roe SM, Vaughan CK, Vlasic I, Panaretou B, Piper PW, Pearl LH.
Structural basis for recruitment of the ATPase activator Aha1 to the Hsp90 chaperone machinery.
EMBO J. 23 1402-10 2004 [PubMed: 15039704]
http://dx.doi.org/10.1038/sj.emboj.7600141
10. Sinha SC, Chaudhuri BN, Burgner JW, Yakovleva G, Davisson VJ, Smith JL.
Crystal structure of imidazole glycerol-phosphate dehydratase: duplication of an unusual fold.
J. Biol. Chem. 279 15491-8 2004 [PubMed: 14724278]
http://dx.doi.org/10.1074/jbc.M312733200
11. Botos I, Melnikov EE, Cherry S, Tropea JE, Khalatova AG, Rasulova F, Dauter Z, Maurizi MR, Rotanova TV, Wlodawer A, Gustchina A.
The catalytic domain of Escherichia coli Lon protease has a unique fold and a Ser-Lys dyad in the active site.
J. Biol. Chem. 279 8140-8 2004 [PubMed: 14665623]
http://dx.doi.org/10.1074/jbc.M312243200
12. Acharya P, Goenrich M, Hagemeier CH, Demmer U, Vorholt JA, Thauer RK, Ermler U.
How an enzyme binds the C1 carrier tetrahydromethanopterin. Structure of the tetrahydromethanopterin-dependent formaldehyde-activating enzyme (Fae) from Methylobacterium extorquens AM1.
J. Biol. Chem. 280 13712-9 2005 [PubMed: 15632161]
http://dx.doi.org/10.1074/jbc.M412320200

Additional ReadingHelp
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Laurberg M, Asahara H, Korostelev A, Zhu J, Trakhanov S, Noller HF.
Structural basis for translation termination on the 70S ribosome.
Nature 454 2008 852-7 [PubMed: 18596689]
http://dx.doi.org/10.1038/nature07115
Kurata S, Weixlbaumer A, Ohtsuki T, Shimazaki T, Wada T, Kirino Y, Takai K, Watanabe K, Ramakrishnan V, Suzuki T.
Modified uridines with C5-methylene substituents at the first position of the tRNA anticodon stabilize U.G wobble pairing during decoding.
J. Biol. Chem. 283 2008 18801-11 [PubMed: 18456657]
http://dx.doi.org/10.1074/jbc.M800233200
Borovinskaya MA, Shoji S, Fredrick K, Cate JH.
Structural basis for hygromycin B inhibition of protein biosynthesis.
RNA 14 2008 1590-9 [PubMed: 18567815]
http://dx.doi.org/10.1261/rna.1076908
Bingel-Erlenmeyer R, Kohler R, Kramer G, Sandikci A, Antolic S, Maier T, Schaffitzel C, Wiedmann B, Bukau B, Ban N.
A peptide deformylase-ribosome complex reveals mechanism of nascent chain processing.
Nature 452 2008 108-11 [PubMed: 18288106]
http://dx.doi.org/10.1038/nature06683
Fu Z, Voynova NE, Herdendorf TJ, Miziorko HM, Kim JJ.
Biochemical and structural basis for feedback inhibition of mevalonate kinase and isoprenoid metabolism.
Biochemistry 47 2008 3715-24 [PubMed: 18302342]
http://dx.doi.org/10.1021/bi7024386
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