P0A6P5 (DER_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
GTPase Der

Alternative name(s):
Double era-like domain protein
GTP-binding protein EngA

Gene names

Name:	der
Synonyms:	engA, yfgK
Ordered Locus Names:	b2511, JW5403

Organism

Escherichia coli (strain K12)

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	490 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	GTPase that plays an essential role in the late steps of ribosome biogenesis. GTPase point mutations (but not a deletion mutant) are suppressed by mild overexpression of RelA, probably due to increased levels of the stringent response mediator (p)ppGpp. 50S subunits assembled in the absence of Der are defective and unable to assemble into 70S ribosomes. GTPase activity is stimulated by YihI. Overexpression rescues an rrmJ deletion, stabilizing the 70S ribosome. Der and RrmJ are likely to share a mechanism to stabilize 50S ribosomal subunits at a very late stage of 50S subunit maturation possibly by interacting with 23S rRNA or 23S rRNA/r-protein complex. Ref.5 Ref.7
Subunit structure	Associates with the 50S ribosomal subunit in the presence of GMPPNP, a non-hydrolysable GTP analog, and thus probably also in the presence of GTP, but not in the presence of GDP or in the absence of nucleotide. Interacts with YihI via the last 490 residues. Ref.6 Ref.7 Ref.10
Domain	The 2 G (guanine nucleotide-binding) domains are essential for activity and function cooperatively. The KH-like domain is required for ribosome recognition. Ref.9
Disruption phenotype	Lethality. In a depletion experiment cells grow normally for 4 hours, at which time there is no detectable protein left. After 4 hours cell growth decreases rapidly, the amount of 50S ribosomal subunit decreases, rRNA precursors accumulate. A 40S ribosomal subunit is detected which is missing proteins L9 and L18 and has slightly reduced amounts of L2 and L6 compared to wild-type ribosomes. Ref.4 Ref.6 Ref.7
Sequence similarities	Belongs to the Era/MnmE GTP-binding protein family. Der subfamily. Contains 2 G (guanine nucleotide-binding) domains. Contains 1 KH-like domain.
Biophysicochemical properties	Kinetic parameters: Vmax increases 35% in the presence of full length YihI and 90% in the presence of YihI missing the first 45 residues. KM=125 µM for GTP (to 143 µM) in the absence of YihI Ref.7 Ref.10 KM=59.2 µM for GTP in the presence of full-length YihI KM=50.1 µM for GTP in the presence of N-terminally truncated YihI

Ontologies

Keywords
Biological process	Ribosome biogenesis
Domain	Repeat
Ligand	GTP-binding Nucleotide-binding
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	ribosomal large subunit assembly Inferred from mutant phenotype Ref.7Ref.6. Source: EcoCyc
Cellular component	cytoplasm Inferred from direct assay. Source: EcoCyc
Molecular function	GTP binding Inferred from electronic annotation. Source: UniProtKB-KW GTPase activating protein binding Inferred from physical interaction Ref.10. Source: EcoCyc GTPase activity Inferred from direct assay Ref.6. Source: EcoCyc ribosome binding Inferred from direct assay Ref.7Ref.6. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 490	490	GTPase Der HAMAP MF_00195		PRO_0000178991
Regions
	Domain	14 – 119	106	G 1
	Domain	214 – 322	109	G 2
	Domain	376 – 461	86	KH-like
	Nucleotide binding	9 – 16	8	GTP 1 Potential
	Nucleotide binding	56 – 60	5	GTP 1 Potential
	Nucleotide binding	118 – 121	4	GTP 1 Potential
	Nucleotide binding	209 – 216	8	GTP 2 Potential
	Nucleotide binding	256 – 260	5	GTP 2 Potential
	Nucleotide binding	321 – 324	4	GTP 2 Potential
Experimental info
	Mutagenesis	15	1	K → A: Complements a disruption mutant, KM for GTP 695 uM. Ref.6
	Mutagenesis	16	1	S → A: Does not complement a disruption mutant, KM for GTP 4.9 mM. Decreased GTPase activity, no stimulation by YihI. Ref.6 Ref.10
	Mutagenesis	118	1	N → D: 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. Ref.7
	Mutagenesis	118	1	N → D: Does not complement a disruption mutant at 42 degrees Celsius, diminished association with 50S ribosomal subunits; when associated with D-321. Ref.7
	Mutagenesis	215	1	K → A: Does not complement a disruption mutant, KM for GTP 6.7 mM. Ref.6
	Mutagenesis	216	1	S → A: Does not complement a disruption mutant, considerably decreased GTPase activity, KM for GTP 4.8 mM, no stimulation by YihI. Ref.6 Ref.10
	Mutagenesis	321	1	N → D: 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. Ref.7
	Mutagenesis	414	1	G → R: Does not complement rrmJ deletion, complements der disruption at 42 degrees Celsius. Ref.9
	Mutagenesis	424	1	G → D: Does not complement rrmJ deletion, nor the der disruption at 42 degrees Celsius. Ref.9
	Mutagenesis	469	1	N → K: Does not complement rrmJ deletion, complements der disruption at 42 degrees Celsius. Ref.9
	Mutagenesis	472	1	T → A: Does not complement rrmJ deletion, complements der disruption at 42 degrees Celsius. Ref.9

Sequences

	Sequence		Length	Mass (Da)
	P0A6P5 [UniParc]. Last modified May 10, 2005. Version 1. Checksum: 0321511F5A5A7E3D	FASTA	490	55,036
	10 20 30 40 50 60 MVPVVALVGR PNVGKSTLFN RLTRTRDALV ADFPGLTRDR KYGRAEIEGR EFICIDTGGI 70 80 90 100 110 120 DGTEDGVETR MAEQSLLAIE EADVVLFMVD ARAGLMPADE AIAKHLRSRE KPTFLVANKT 130 140 150 160 170 180 DGLDPDQAVV DFYSLGLGEI YPIAASHGRG VLSLLEHVLL PWMEDLAPQE EVDEDAEYWA 190 200 210 220 230 240 QFEAEENGEE EEEDDFDPQS LPIKLAIVGR PNVGKSTLTN RILGEERVVV YDMPGTTRDS 250 260 270 280 290 300 IYIPMERDGR EYVLIDTAGV RKRGKITDAV EKFSVIKTLQ AIEDANVVML VIDAREGISD 310 320 330 340 350 360 QDLSLLGFIL NSGRSLVIVV NKWDGLSQEV KEQVKETLDF RLGFIDFARV HFISALHGSG 370 380 390 400 410 420 VGNLFESVRE AYDSSTRRVG TSMLTRIMTM AVEDHQPPLV RGRRVKLKYA HAGGYNPPIV 430 440 450 460 470 480 VIHGNQVKDL PDSYKRYLMN YFRKSLDVMG SPIRIQFKEG ENPYANKRNT LTPTQMRKRK 490 RLMKHIKKNK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features." Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T. , Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T. DNA Res. 4:91-113(1997) [PubMed: 9205837] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[2]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[3]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]	"An essential GTPase, der, containing double GTP-binding domains from Escherichia coli and Thermotoga maritima." Hwang J., Inouye M. J. Biol. Chem. 276:31415-31421(2001) [PubMed: 11387344] [Abstract] Cited for: DISRUPTION PHENOTYPE.
[5]	"Overexpression of two different GTPases rescues a null mutation in a heat-induced rRNA methyltransferase." Tan J., Jakob U., Bardwell J.C.A. J. Bacteriol. 184:2692-2698(2002) [PubMed: 11976298] [Abstract] Cited for: FUNCTION. Strain: K12 / MG1655 / ATCC 47076.
[6]	"Cooperative and critical roles for both G domains in the GTPase activity and cellular function of ribosome-associated Escherichia coli EngA." Bharat A., Jiang M., Sullivan S.M., Maddock J.R., Brown E.D. J. Bacteriol. 188:7992-7996(2006) [PubMed: 16963571] [Abstract] Cited for: INTERACTION WITH 50S RIBOSOMAL SUBUNIT, MUTAGENESIS OF LYS-15; SER-16; LYS-215 AND SER-216, DISRUPTION PHENOTYPE. Strain: K12 / EB1208.
[7]	"The tandem GTPase, Der, is essential for the biogenesis of 50S ribosomal subunits in Escherichia coli." Hwang J., Inouye M. Mol. Microbiol. 61:1660-1672(2006) [PubMed: 16930151] [Abstract] Cited for: FUNCTION IN 50S RIBOSOMAL SUBUNIT BIOGENESIS, BIOPHYSICOCHEMICAL PROPERTIES, INTERACTION WITH 50S RIBOSOMAL SUBUNIT, MUTAGENESIS OF ASN-118 AND ASN-321, DISRUPTION PHENOTYPE. Strain: K12 / BW25113.
[8]	"RelA functionally suppresses the growth defect caused by a mutation in the G domain of the essential Der protein." Hwang J., Inouye M. J. Bacteriol. 190:3236-3243(2008) [PubMed: 18296517] [Abstract] Cited for: SUPPRESSION BY RELA AND (P)PPGPP. Strain: K12 / BW25113.
[9]	"Interaction of an essential Escherichia coli GTPase, Der, with the 50S ribosome via the KH-like domain." Hwang J., Inouye M. J. Bacteriol. 192:2277-2283(2010) [PubMed: 20172997] [Abstract] Cited for: DOMAIN KH-LIKE, MUTAGENESIS OF GLY-414; GLY-424; ASN-469 AND THR-472.
[10]	"A bacterial GAP-like protein, YihI, regulating the GTPase of Der, an essential GTP-binding protein in Escherichia coli." Hwang J., Inouye M. J. Mol. Biol. 399:759-772(2010) [PubMed: 20434458] [Abstract] Cited for: STIMULATION OF GTPASE BY YIHI, BIOPHYSICOCHEMICAL PROPERTIES, INTERACTION WITH YIHI, MUTAGENESIS OF SER-16 AND SER-216.

Cross-references

Sequence databases
EMBL GenBank DDBJ	U00096 Genomic DNA. Translation: AAC75564.2. AP009048 Genomic DNA. Translation: BAA16397.2.
PIR	F65027.
RefSeq	NP_417006.2. NC_000913.2.
3D structure databases
ProteinModelPortal	P0A6P5.
SMR	P0A6P5. Positions 2-461.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-48272N.
IntAct	P0A6P5. 6 interactions.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	EBESCT00000000698; EBESCP00000000698; EBESCG00000000584. EBESCT00000017218; EBESCP00000016509; EBESCG00000016277.
GeneID	946983.
GenomeReviews	Gene locus JW5403 in contig AP009048_GR. Gene locus b2511 in contig U00096_GR.
KEGG	ecj:JW5403. eco:b2511.
PATRIC	32120415. VBIEscCol129921_2610.
Organism-specific databases
EchoBASE	EB3959.
EcoGene	EG14207. der.
Phylogenomic databases
eggNOG	COG1160.
GeneTree	EBGT00050000010178.
HOGENOM	HBG592135.
OMA	LAVNKCE.
PhylomeDB	P0A6P5.
ProtClustDB	PRK00093.
Enzyme and pathway databases
BioCyc	EcoCyc:G7319-MONOMER. MetaCyc:G7319-MONOMER.
Gene expression databases
Genevestigator	P0A6P5.
Family and domain databases
HAMAP	MF_00195. GTPase_Der. [Tree]
InterPro	IPR016484. GTP-bd_EngA. IPR006073. GTP_binding_domain. IPR015946. KH_dom-like_a/b. IPR005225. Small_GTP-bd_dom. [Graphical view]
Gene3D	G3DSA:3.30.300.20. KH_prok. 1 hit.
KO	K03977.
PANTHER	PTHR11649:SF5. PTHR11649:SF5. 1 hit.
Pfam	PF01926. MMR_HSR1. 2 hits. [Graphical view]
PIRSF	PIRSF006485. GTP-binding_EngA. 1 hit.
PRINTS	PR00326. GTP1OBG.
TIGRFAMs	TIGR03594. GTPase_EngA. 1 hit. TIGR00231. Small_GTP. 2 hits.
ProtoNet	Search...

Entry information

Entry name

DER_ECOLI

Accession

Primary (citable) accession number: P0A6P5
Secondary accession number(s): P77254, Q8X4Y1

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 10, 2005
Last sequence update:	May 10, 2005
Last modified:	January 25, 2012
This is version 62 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program