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InterPro: IPR014721 Ribosomal protein S5 domain 2-type fold, subgroup

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23604 proteins

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Accession

IPR014721 Ribosomal_S5_D2-typ_fold_subgr

Type

Domain

Signatures Help

Database	ID	Name	Proteins
Gene3D	G3DSA:3.30.230.10	Ribosomal_S5_D2-type_fold	23604
Signatures in BioMart

InterPro Relationships Help

Parent

IPR020568 Ribosomal protein S5 domain 2-type fold

Children

IPR000100 Ribonuclease P
IPR000754 Ribosomal protein S9
IPR005324 Ribosomal protein S5, C-terminal
IPR005517 Translation elongation factor EFG/EF2, domain IV
IPR013506 DNA topoisomerase, type IIA, subunit B, region 2
IPR013507 DNA mismatch repair protein, C-terminal
IPR015192 Switch protein XOL-1, N-terminal
IPR015320 DNA topoisomerase VI, subunit B, transducer

Found in

IPR000705 Galactokinase
IPR000870 Homoserine kinase
IPR001174 Galactokinase/homoserine kinase
IPR002099 DNA mismatch repair protein
IPR004424 4-diphosphocytidyl-2C-methyl-D-erythritol kinase
IPR004540 Translation elongation factor EFG/EF2
IPR004543 Translation elongation factor EFG/EF2, archaeal
IPR005734 DNA topoisomerase VI, subunit B
IPR005916 Phosphomevalonate kinase, eukaryotic
IPR005917 Phosphomevalonate kinase, Gram-positive
IPR005935 Diphosphomevalonate decarboxylase
IPR006205 Mevalonate kinase
IPR006206 Mevalonate/galactokinase
IPR010189 Shikimate kinase, archaea
IPR012369 Galactokinase, glycosyltransferase
IPR014606 D,D-heptose 7-phosphate kinase
IPR014763 DNA mismatch repair protein, N-terminal
IPR015434 Post Meiotic Segregation 2
IPR016005 Phosphomevalonate kinase, ERG8
IPR020667 DNA mismatch repair protein, MutL

Contains

IPR006203 GHMP kinase, ATP-binding, conserved site
IPR006204 GHMP kinase
IPR019539 Galactokinase galactose-binding domain
IPR019741 Galactokinase, conserved site
IPR020539 Ribonuclease P, conserved site
IPR020574 Ribosomal protein S9, conserved site

InterPro annotation

Entry Details in BioMart

Abstract

Domain 2 of the ribosomal protein S5 has a left-handed beta-alpha-beta fold that is found in numerous RNA/DNA-binding proteins, as well as in kinases from the GHMP kinase family. Proteins containing this beta-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].
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 (EC:2.7.1.6), homoserine kinase (EC: 2.7.1.39), and mevalonate kinase (EC: 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].

Structural links Help

PDB - click here

SCOP: d.14.1.1 , d.14.1.2 , d.14.1.3 , d.14.1.5 , d.14.1.6 , d.50.1.2 , d.58.11.1 , d.58.26.3 , d.58.26.6 , d.58.26.7 , i.1.1.1 , i.1.1.3

CATH: 3.30.230.10 , 3.30.70.240 , 3.30.70.870 , 3.30.70.890

Taxonomic coverage Help

Overlapping InterPro entries Help

IPR014721

Numbers of overlapping proteins

Average numbers of overlapping amino acids

Example proteins Help

O08810 116 kDa U5 small nuclear ribonucleoprotein component

P04385 Galactokinase

P13060 Elongation factor 2

P51570 Galactokinase

Q23229 XO lethal protein 1

More proteins

Example Proteins Key

InterPro entry accession number/name and structure databases		Colour code
IPR020568	Ribosomal protein S5 domain 2-type fold
IPR019741	Galactokinase, conserved site
IPR006206	Mevalonate/galactokinase
IPR006203	GHMP kinase, ATP-binding, conserved site
IPR006204	GHMP kinase
IPR013750	GHMP kinase, C-terminal
IPR000640	Translation elongation factor EFG/EF2, C-terminal
IPR015193	Switch protein XOL-1, GHMP-like
IPR004161	Translation elongation factor EFTu/EF1A, domain 2
IPR015192	Switch protein XOL-1, N-terminal
IPR009022	Elongation factor G/III/V
IPR005225	Small GTP-binding protein
IPR009000	Translation elongation/initiation factor/Ribosomal, beta-barrel
IPR000705	Galactokinase
IPR005517	Translation elongation factor EFG/EF2, domain IV
IPR014721	Ribosomal protein S5 domain 2-type fold, subgroup
IPR000795	Protein synthesis factor, GTP-binding
IPR019539	Galactokinase galactose-binding domain
	PDB Chain
	ModBase
	CATH Domain
	SWISS-MODEL
	SCOP Domain

Publications Open in usermanual
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.	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
4.	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
5.	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
6.	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

Additional Reading Open in usermanual
	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
	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
	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

InterPro 23.1