H
IPR020568

Ribosomal protein uS5 domain 2-type superfamily

InterPro entry
Short nameRibosomal_Su5_D2-typ_SF
Overlapping entries
 
Impact, N-terminal (IPR001498)

Description

The founding member of this superfamily is the second domain of the small ribosomal subunit protein uS5. This domain adopts α/β fold consisting of four-stranded mixed β-sheet and two helices packed on one side of it. Typical features for this superfamily are the psi-loop between strands 2 and 3; and the left-handed crossover between strands 3 and 4.

Domain 2 of the ribosomal protein uS5 has a left-handed, 2-layer α/β fold with a core structure consisting of β(3)-α-β-α. 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 α/β 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)
[7]
, as well as various exosome complex exonucleases (RRP41, RRP42, RRP43, RRP45, RRP46, MTR3, ECX1, ECX2)
[8]
.
 * DNA modification proteins (DNA mismatch repair proteins MutL and PMS2, DNA gyrase B, DNA topoisomerase II, IV-B and VI-B)
[3]
.
 * GHMP kinases that transfer a phosphoryl group from ATP to an acceptor (galactokinase (
2.7.1.6
), homoserine kinase (
2.7.1.39
), and mevalonate kinase (
2.7.1.36
))
[4, 5]
.
 * Caenorhabditis elegans early switch protein Xol-1 (a divergent member of the GHMP kinase family that has lost the ATP-binding site)
[6]
.
 * Hsp90 chaperone (middle domain), which is related to the DNA gyrase/MutL family
[9]
; this domain contains an extra C-terminal α/β 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 α/β subdomain
[11]
.
 * Formaldehyde-activating enzyme FAE, which contains a modification of this fold consisting of an extra α/β unit after strand 2
[12]
.

References

1.Structures of prokaryotic ribosomal proteins: implications for RNA binding and evolution. Ramakrishnan V, Davies C, Gerchman SE, Golden BL, Hoffmann DW, Jaishree TN, Kyila JH, Porter S, White SW. Biochem. Cell Biol. 73, 979-86, (1995). PMID: 8722013

2.Structure and function of eukaryotic Ribonuclease P RNA. Marquez SM, Chen JL, Evans D, Pace NR. Mol. Cell 24, 445-56, (2006). View articlePMID: 17081993

3.Structure and function of the N-terminal 40 kDa fragment of human PMS2: a monomeric GHL ATPase. Guarne A, Junop MS, Yang W. EMBO J. 20, 5521-31, (2001). View articlePMID: 11574484

4.Molecular functions of conserved aspects of the GHMP kinase family. Andreassi JL 2nd, Leyh TS. Biochemistry 43, 14594-601, (2004). View articlePMID: 15544330

5.Structure and mechanism of homoserine kinase: prototype for the GHMP kinase superfamily. Zhou T, Daugherty M, Grishin NV, Osterman AL, Zhang H. Structure 8, 1247-57, (2000). View articlePMID: 11188689

6.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. Luz JG, Hassig CA, Pickle C, Godzik A, Meyer BJ, Wilson IA. Genes Dev. 17, 977-90, (2003). View articlePMID: 12672694

7.Crystal structure of the phosphorolytic exoribonuclease RNase PH from Bacillus subtilis and implications for its quaternary structure and tRNA binding. Harlow LS, Kadziola A, Jensen KF, Larsen S. Protein Sci. 13, 668-77, (2004). View articlePMID: 14767080

8.Reconstitution, activities, and structure of the eukaryotic RNA exosome. Liu Q, Greimann JC, Lima CD. Cell 127, 1223-37, (2006). View articlePMID: 17174896

9.Structural basis for recruitment of the ATPase activator Aha1 to the Hsp90 chaperone machinery. Meyer P, Prodromou C, Liao C, Hu B, Roe SM, Vaughan CK, Vlasic I, Panaretou B, Piper PW, Pearl LH. EMBO J. 23, 1402-10, (2004). View articlePMID: 15039704

10.Crystal structure of imidazole glycerol-phosphate dehydratase: duplication of an unusual fold. Sinha SC, Chaudhuri BN, Burgner JW, Yakovleva G, Davisson VJ, Smith JL. J. Biol. Chem. 279, 15491-8, (2004). View articlePMID: 14724278

11.The catalytic domain of Escherichia coli Lon protease has a unique fold and a Ser-Lys dyad in the active site. Botos I, Melnikov EE, Cherry S, Tropea JE, Khalatova AG, Rasulova F, Dauter Z, Maurizi MR, Rotanova TV, Wlodawer A, Gustchina A. J. Biol. Chem. 279, 8140-8, (2004). View articlePMID: 14665623

12.How an enzyme binds the C1 carrier tetrahydromethanopterin. Structure of the tetrahydromethanopterin-dependent formaldehyde-activating enzyme (Fae) from Methylobacterium extorquens AM1. Acharya P, Goenrich M, Hagemeier CH, Demmer U, Vorholt JA, Thauer RK, Ermler U. J. Biol. Chem. 280, 13712-9, (2005). View articlePMID: 15632161

Cross References

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