Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
twitter

Escherichia coli K-12 substr. MG1655 Enzyme: 50S ribosomal subunit stability factor



Gene: der Accession Numbers: G7319 (EcoCyc), b2511, ECK2507

Synonyms: engA, yfgK

Regulation Summary Diagram: ?

Summary:
The Der protein is a GTPase that is ubiquitously conserved in eubacteria [Bharat06]. It is associated with the large subunit of the ribosome and is required for its stability [Hwang06, Bharat06]. In E. coli, Der is essential for growth [Hwang01, Baba06, Hwang06, Bharat06].

GTP hydrolysis appears to regulate the specificity of interactions of Der with ribosomal subunits [Tomar09]. The GAP-like protein YihI interacts with Der and activates its GTPase activity [Hwang10]. The KH-like C-terminal domain of Der plays a role in recognition of the ribosome [Hwang10a].

The Der protein appears to be evenly distributed throughout the cytoplasm [Watt07].

Mutants containing substitutions in either of the two predicted GTP binding domains of Der are not able to complement the lethal phenotype of the der null mutant at low temperature and are defective in ribosome biogenesis [Hwang06, Bharat06]. Depletion of Der results in the accumulation of 23S and 16S rRNA precursors and accumulation of aberrant 50S ribosomal subunits at low concentrations of Mg2+ [Hwang06]. Overexpression of RelA suppresses the growth defect of a der mutant [Hwang08].

Overexpression of der suppresses the growth and ribosome-related defects of a mutant lacking the RrmJ rRNA methyltransferase [Tan02]. Both the GTP binding domains and the C-terminal KH-like domain of Der are required for suppression [Hwang10a].

Der: "double-Era-like domains" [Hwang01]

Reviews: [Mittenhuber01, Caldon01]

Gene Citations: [Rhodius05]

Locations: cytosol

Map Position: [2,633,906 <- 2,635,378] (56.77 centisomes)
Length: 1473 bp / 490 aa

Molecular Weight of Polypeptide: 55.036 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0008270 , DIP:DIP-48272N , EchoBASE:EB3959 , EcoGene:EG14207 , EcoliWiki:b2511 , ModBase:P0A6P5 , OU-Microarray:b2511 , PortEco:der , PR:PRO_000022516 , Pride:P0A6P5 , Protein Model Portal:P0A6P5 , RefSeq:NP_417006 , RegulonDB:G7319 , SMR:P0A6P5 , String:511145.b2511 , UniProt:P0A6P5

Relationship Links: InterPro:IN-FAMILY:IPR005225 , InterPro:IN-FAMILY:IPR006073 , InterPro:IN-FAMILY:IPR015946 , InterPro:IN-FAMILY:IPR016484 , InterPro:IN-FAMILY:IPR027417 , Panther:IN-FAMILY:PTHR11649:SF5 , Pfam:IN-FAMILY:PF01926 , Prints:IN-FAMILY:PR00326

In Paralogous Gene Group: 77 (16 members)

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0000027 - ribosomal large subunit assembly Inferred from experiment [Bharat06, Hwang06]
GO:0006184 - GTP catabolic process Inferred from experiment [Bharat06]
GO:0042254 - ribosome biogenesis Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0003924 - GTPase activity Inferred from experiment [Bharat06]
GO:0032794 - GTPase activating protein binding Inferred from experiment [Hwang10]
GO:0043022 - ribosome binding Inferred from experiment [Hwang06, Bharat06]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0005525 - GTP binding Inferred by computational analysis [UniProtGOA11, GOA06, GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, Watt07]

MultiFun Terms: cell structure ribosomes

Essentiality data for der knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 1]

Credits:
Last-Curated ? 10-May-2010 by Keseler I , SRI International


Enzymatic reaction of: GTPase (50S ribosomal subunit stability factor)

EC Number: 3.6.5.1/3.6.5.2/3.6.5.3/3.6.5.4/3.6.5.5/3.6.5.6

GTP + H2O <=> GDP + phosphate + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

Activators (Unknown Mechanism): GAP-like protein that activates GTPase activity of Der [Hwang10]

Kinetic Parameters:

Substrate
Km (μM)
Citations
GTP
143.0
[Bharat06]


Sequence Features

Feature Class Location Citations Comment
Nucleotide-Phosphate-Binding-Region 9 -> 16
[UniProt10a]
UniProt: GTP 1; Non-Experimental Qualifier: potential;
Conserved-Region 14 -> 119
[UniProt10b]
UniProt: G 1;
Mutagenesis-Variant 15
[Bharat06, UniProt11]
Alternate sequence: K → A; UniProt: Complements a disruption mutant, KM for GTP 695 uM.
Mutagenesis-Variant 16
[Bharat06, Hwang10, UniProt11]
Alternate sequence: S → A; UniProt: Does not complement a disruption mutant, KM for GTP 4.9 mM. Decreased GTPase activity, no stimulation by YihI.
Nucleotide-Phosphate-Binding-Region 56 -> 60
[UniProt10a]
UniProt: GTP 1; Non-Experimental Qualifier: potential;
Mutagenesis-Variant 118
[Hwang06, UniProt11]
Alternate sequence: N → D; UniProt: Complements a disruption mutant at 42 degrees Celsius, very poor complementation at 30 degrees Celsius. Reduces affinity for the 50S ribosomal subunit at 30 degrees Celsius. RelA suppresses this point mutation at 30 degrees Celsius.
Nucleotide-Phosphate-Binding-Region 118 -> 121
[UniProt10a]
UniProt: GTP 1; Non-Experimental Qualifier: potential;
Nucleotide-Phosphate-Binding-Region 209 -> 216
[UniProt10a]
UniProt: GTP 2; Non-Experimental Qualifier: potential;
Conserved-Region 214 -> 322
[UniProt10b]
UniProt: G 2;
Mutagenesis-Variant 215
[Bharat06, UniProt11]
Alternate sequence: K → A; UniProt: Does not complement a disruption mutant, KM for GTP 6.7 mM.
Mutagenesis-Variant 216
[Bharat06, Hwang10, UniProt11]
Alternate sequence: S → A; UniProt: Does not complement a disruption mutant, considerably decreased GTPase activity, KM for GTP 4.8 mM, no stimulation by YihI.
Nucleotide-Phosphate-Binding-Region 256 -> 260
[UniProt10a]
UniProt: GTP 2; Non-Experimental Qualifier: potential;
Mutagenesis-Variant 321
[Hwang06, UniProt11]
Alternate sequence: N → D; UniProt: Complements a disruption mutant at 42 degrees Celsius, no complementation at 30 degrees Celsius. Greatly reduces affinity for the 50S ribosomal subunit at 30 degrees Celsius. RelA suppresses this point mutation at 30 degrees Celsius.
Nucleotide-Phosphate-Binding-Region 321 -> 324
[UniProt10a]
UniProt: GTP 2; Non-Experimental Qualifier: potential;
Conserved-Region 376 -> 461
[UniProt10b]
UniProt: KH-like;
Mutagenesis-Variant 414
[Hwang10a, UniProt11]
Alternate sequence: G → R; UniProt: Does not complement rrmJ deletion, complements der disruption at 42 degrees Celsius.
Mutagenesis-Variant 424
[Hwang10a, UniProt11]
Alternate sequence: G → D; UniProt: Does not complement rrmJ deletion, nor the der disruption at 42 degrees Celsius.
Mutagenesis-Variant 469
[Hwang10a, UniProt11]
Alternate sequence: N → K; UniProt: Does not complement rrmJ deletion, complements der disruption at 42 degrees Celsius.
Mutagenesis-Variant 472
[Hwang10a, UniProt11]
Alternate sequence: T → A; UniProt: Does not complement rrmJ deletion, complements der disruption at 42 degrees Celsius.


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Peter D. Karp on Wed Jan 18, 2006:
Gene right-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


References

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Bharat06: Bharat A, Jiang M, Sullivan SM, Maddock JR, Brown ED (2006). "Cooperative and critical roles for both G domains in the GTPase activity and cellular function of ribosome-associated Escherichia coli EngA." J Bacteriol 188(22);7992-6. PMID: 16963571

Caldon01: Caldon CE, Yoong P, March PE (2001). "Evolution of a molecular switch: universal bacterial GTPases regulate ribosome function." Mol Microbiol 41(2);289-97. PMID: 11489118

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Hwang01: Hwang J, Inouye M (2001). "An essential GTPase, der, containing double GTP-binding domains from Escherichia coli and Thermotoga maritima." J Biol Chem 276(33);31415-21. PMID: 11387344

Hwang06: Hwang J, Inouye M (2006). "The tandem GTPase, Der, is essential for the biogenesis of 50S ribosomal subunits in Escherichia coli." Mol Microbiol 61;1660-1672. PMID: 16930151

Hwang08: Hwang J, Inouye M (2008). "RelA functionally suppresses the growth defect caused by a mutation in the G domain of the essential Der protein." J Bacteriol 190(9);3236-43. PMID: 18296517

Hwang10: Hwang J, Inouye M (2010). "A Bacterial GAP-like protein, YihI, regulating GTPase of Der, an essential GTP-binding protein in Escherichia coli." J Mol Biol 399(5);759-72. PMID: 20434458

Hwang10a: Hwang J, Inouye M (2010). "The interaction of an essential E. coli GTPase, Der with 50S ribosome via the KH-like domain." J Bacteriol 192(8):2277-83. PMID: 20172997

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Mittenhuber01: Mittenhuber G (2001). "Comparative genomics of prokaryotic GTP-binding proteins (the Era, Obg, EngA, ThdF (TrmE), YchF and YihA families) and their relationship to eukaryotic GTP-binding proteins (the DRG, ARF, RAB, RAN, RAS and RHO families)." J Mol Microbiol Biotechnol 2001;3(1);21-35. PMID: 11200227

Rhodius05: Rhodius VA, Suh WC, Nonaka G, West J, Gross CA (2005). "Conserved and variable functions of the sigmaE stress response in related genomes." PLoS Biol 4(1);e2. PMID: 16336047

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

Tan02: Tan J, Jakob U, Bardwell JC (2002). "Overexpression of two different GTPases rescues a null mutation in a heat-induced rRNA methyltransferase." J Bacteriol 184(10);2692-8. PMID: 11976298

Tomar09: Tomar SK, Dhimole N, Chatterjee M, Prakash B (2009). "Distinct GDP/GTP bound states of the tandem G-domains of EngA regulate ribosome binding." Nucleic Acids Res 37(7);2359-70. PMID: 19246542

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt10b: UniProt Consortium (2010). "UniProt version 2010-12 released on 2010-12-01 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Watt07: Watt RM, Wang J, Leong M, Kung HF, Cheah KS, Liu D, Danchin A, Huang JD (2007). "Visualizing the proteome of Escherichia coli: an efficient and versatile method for labeling chromosomal coding DNA sequences (CDSs) with fluorescent protein genes." Nucleic Acids Res 35(6);e37. PMID: 17272300


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Sun Dec 21, 2014, biocyc14.