DER_ECOLI
ID DER_ECOLI Reviewed; 490 AA.
AC P0A6P5; P77254; Q8X4Y1;
DT 10-MAY-2005, integrated into UniProtKB/Swiss-Prot.
DT 10-MAY-2005, sequence version 1.
DT 03-AUG-2022, entry version 132.
DE RecName: Full=GTPase Der;
DE AltName: Full=Double era-like domain protein;
DE AltName: Full=GTP-binding protein EngA;
GN Name=der; Synonyms=engA, yfgK; OrderedLocusNames=b2511, JW5403;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9205837; DOI=10.1093/dnares/4.2.91;
RA Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K.,
RA Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T., Oyama S.,
RA Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H.,
RA Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.;
RT "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12
RT genome corresponding to 50.0-68.8 min on the linkage map and analysis of
RT its sequence features.";
RL DNA Res. 4:91-113(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [4]
RP DISRUPTION PHENOTYPE.
RX PubMed=11387344; DOI=10.1074/jbc.m104455200;
RA Hwang J., Inouye M.;
RT "An essential GTPase, der, containing double GTP-binding domains from
RT Escherichia coli and Thermotoga maritima.";
RL J. Biol. Chem. 276:31415-31421(2001).
RN [5]
RP FUNCTION.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=11976298; DOI=10.1128/jb.184.10.2692-2698.2002;
RA Tan J., Jakob U., Bardwell J.C.A.;
RT "Overexpression of two different GTPases rescues a null mutation in a heat-
RT induced rRNA methyltransferase.";
RL J. Bacteriol. 184:2692-2698(2002).
RN [6]
RP INTERACTION WITH 50S RIBOSOMAL SUBUNIT, MUTAGENESIS OF LYS-15; SER-16;
RP LYS-215 AND SER-216, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12 / EB1208;
RX PubMed=16963571; DOI=10.1128/jb.00959-06;
RA Bharat A., Jiang M., Sullivan S.M., Maddock J.R., Brown E.D.;
RT "Cooperative and critical roles for both G domains in the GTPase activity
RT and cellular function of ribosome-associated Escherichia coli EngA.";
RL J. Bacteriol. 188:7992-7996(2006).
RN [7]
RP FUNCTION IN 50S RIBOSOMAL SUBUNIT BIOGENESIS, BIOPHYSICOCHEMICAL
RP PROPERTIES, INTERACTION WITH 50S RIBOSOMAL SUBUNIT, MUTAGENESIS OF ASN-118
RP AND ASN-321, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12 / BW25113;
RX PubMed=16930151; DOI=10.1111/j.1365-2958.2006.05348.x;
RA Hwang J., Inouye M.;
RT "The tandem GTPase, Der, is essential for the biogenesis of 50S ribosomal
RT subunits in Escherichia coli.";
RL Mol. Microbiol. 61:1660-1672(2006).
RN [8]
RP SUPPRESSION BY RELA AND (P)PPGPP.
RC STRAIN=K12 / BW25113;
RX PubMed=18296517; DOI=10.1128/jb.01758-07;
RA Hwang J., Inouye M.;
RT "RelA functionally suppresses the growth defect caused by a mutation in the
RT G domain of the essential Der protein.";
RL J. Bacteriol. 190:3236-3243(2008).
RN [9]
RP DOMAIN KH-LIKE, AND MUTAGENESIS OF GLY-414; GLY-424; ASN-469 AND THR-472.
RX PubMed=20172997; DOI=10.1128/jb.00045-10;
RA Hwang J., Inouye M.;
RT "Interaction of an essential Escherichia coli GTPase, Der, with the 50S
RT ribosome via the KH-like domain.";
RL J. Bacteriol. 192:2277-2283(2010).
RN [10]
RP STIMULATION OF GTPASE BY YIHI, BIOPHYSICOCHEMICAL PROPERTIES, INTERACTION
RP WITH YIHI, AND MUTAGENESIS OF SER-16 AND SER-216.
RX PubMed=20434458; DOI=10.1016/j.jmb.2010.04.040;
RA Hwang J., Inouye M.;
RT "A bacterial GAP-like protein, YihI, regulating the GTPase of Der, an
RT essential GTP-binding protein in Escherichia coli.";
RL J. Mol. Biol. 399:759-772(2010).
CC -!- FUNCTION: GTPase that plays an essential role in the late steps of
CC ribosome biogenesis. GTPase point mutations (but not a deletion mutant)
CC are suppressed by mild overexpression of RelA, probably due to
CC increased levels of the stringent response mediator (p)ppGpp. 50S
CC subunits assembled in the absence of Der are defective and unable to
CC assemble into 70S ribosomes. GTPase activity is stimulated by YihI.
CC Overexpression rescues an rrmJ deletion, stabilizing the 70S ribosome.
CC Der and RrmJ are likely to share a mechanism to stabilize 50S ribosomal
CC subunits at a very late stage of 50S subunit maturation possibly by
CC interacting with 23S rRNA or 23S rRNA/r-protein complex.
CC {ECO:0000269|PubMed:11976298, ECO:0000269|PubMed:16930151}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=125 uM for GTP (to 143 uM) in the absence of YihI
CC {ECO:0000269|PubMed:16930151, ECO:0000269|PubMed:20434458};
CC KM=59.2 uM for GTP in the presence of full-length YihI
CC {ECO:0000269|PubMed:16930151, ECO:0000269|PubMed:20434458};
CC KM=50.1 uM for GTP in the presence of N-terminally truncated YihI
CC {ECO:0000269|PubMed:16930151, ECO:0000269|PubMed:20434458};
CC Note=Vmax increases 35% in the presence of full-length YihI and 90%
CC in the presence of YihI missing the first 45 residues.;
CC -!- SUBUNIT: Associates with the 50S ribosomal subunit in the presence of
CC GMPPNP, a non-hydrolysable GTP analog, and thus probably also in the
CC presence of GTP, but not in the presence of GDP or in the absence of
CC nucleotide. Interacts with YihI via the last 490 residues.
CC {ECO:0000269|PubMed:16930151, ECO:0000269|PubMed:16963571,
CC ECO:0000269|PubMed:20434458}.
CC -!- DOMAIN: The 2 G (guanine nucleotide-binding) domains are essential for
CC activity and function cooperatively. The KH-like domain is required for
CC ribosome recognition. {ECO:0000269|PubMed:20172997}.
CC -!- DISRUPTION PHENOTYPE: Lethality. In a depletion experiment cells grow
CC normally for 4 hours, at which time there is no detectable protein
CC left. After 4 hours cell growth decreases rapidly, the amount of 50S
CC ribosomal subunit decreases, rRNA precursors accumulate. A 40S
CC ribosomal subunit is detected which is missing proteins L9 and L18 and
CC has slightly reduced amounts of L2 and L6 compared to wild-type
CC ribosomes. {ECO:0000269|PubMed:11387344, ECO:0000269|PubMed:16930151,
CC ECO:0000269|PubMed:16963571}.
CC -!- SIMILARITY: Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like
CC GTPase superfamily. EngA (Der) GTPase family. {ECO:0000305}.
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DR EMBL; U00096; AAC75564.2; -; Genomic_DNA.
DR EMBL; AP009048; BAA16397.2; -; Genomic_DNA.
DR PIR; F65027; F65027.
DR RefSeq; NP_417006.2; NC_000913.3.
DR RefSeq; WP_000249410.1; NZ_STEB01000011.1.
DR PDB; 3J8G; EM; 5.00 A; X=1-490.
DR PDBsum; 3J8G; -.
DR AlphaFoldDB; P0A6P5; -.
DR SMR; P0A6P5; -.
DR BioGRID; 4263153; 69.
DR BioGRID; 851322; 1.
DR DIP; DIP-48272N; -.
DR IntAct; P0A6P5; 7.
DR STRING; 511145.b2511; -.
DR jPOST; P0A6P5; -.
DR PaxDb; P0A6P5; -.
DR PRIDE; P0A6P5; -.
DR EnsemblBacteria; AAC75564; AAC75564; b2511.
DR EnsemblBacteria; BAA16397; BAA16397; BAA16397.
DR GeneID; 66673601; -.
DR GeneID; 946983; -.
DR KEGG; ecj:JW5403; -.
DR KEGG; eco:b2511; -.
DR PATRIC; fig|1411691.4.peg.4225; -.
DR EchoBASE; EB3959; -.
DR eggNOG; COG1160; Bacteria.
DR HOGENOM; CLU_016077_6_2_6; -.
DR InParanoid; P0A6P5; -.
DR OMA; KFRFLEY; -.
DR PhylomeDB; P0A6P5; -.
DR BioCyc; EcoCyc:G7319-MON; -.
DR BioCyc; MetaCyc:G7319-MON; -.
DR BRENDA; 3.6.5.2; 2026.
DR PRO; PR:P0A6P5; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0005525; F:GTP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0003924; F:GTPase activity; IDA:EcoCyc.
DR GO; GO:0097216; F:guanosine tetraphosphate binding; IDA:EcoCyc.
DR GO; GO:0043023; F:ribosomal large subunit binding; IDA:EcoCyc.
DR GO; GO:0043022; F:ribosome binding; IDA:EcoCyc.
DR GO; GO:0000027; P:ribosomal large subunit assembly; IMP:EcoCyc.
DR Gene3D; 3.30.300.20; -; 1.
DR Gene3D; 3.40.50.300; -; 2.
DR HAMAP; MF_00195; GTPase_Der; 1.
DR InterPro; IPR031166; G_ENGA.
DR InterPro; IPR006073; GTP-bd.
DR InterPro; IPR016484; GTP-bd_EngA.
DR InterPro; IPR032859; KH_dom-like.
DR InterPro; IPR015946; KH_dom-like_a/b.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR005225; Small_GTP-bd_dom.
DR Pfam; PF14714; KH_dom-like; 1.
DR Pfam; PF01926; MMR_HSR1; 2.
DR PIRSF; PIRSF006485; GTP-binding_EngA; 1.
DR PRINTS; PR00326; GTP1OBG.
DR SUPFAM; SSF52540; SSF52540; 2.
DR TIGRFAMs; TIGR03594; GTPase_EngA; 1.
DR TIGRFAMs; TIGR00231; small_GTP; 2.
DR PROSITE; PS51712; G_ENGA; 2.
PE 1: Evidence at protein level;
KW 3D-structure; GTP-binding; Nucleotide-binding; Reference proteome; Repeat;
KW Ribosome biogenesis.
FT CHAIN 1..490
FT /note="GTPase Der"
FT /id="PRO_0000178991"
FT DOMAIN 3..166
FT /note="EngA-type G 1"
FT DOMAIN 203..376
FT /note="EngA-type G 2"
FT DOMAIN 377..461
FT /note="KH-like"
FT BINDING 9..16
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /ligand_label="1"
FT /evidence="ECO:0000255"
FT BINDING 56..60
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /ligand_label="1"
FT /evidence="ECO:0000255"
FT BINDING 118..121
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /ligand_label="1"
FT /evidence="ECO:0000255"
FT BINDING 209..216
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /ligand_label="2"
FT /evidence="ECO:0000255"
FT BINDING 256..260
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /ligand_label="2"
FT /evidence="ECO:0000255"
FT BINDING 321..324
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /ligand_label="2"
FT /evidence="ECO:0000255"
FT MUTAGEN 15
FT /note="K->A: Complements a disruption mutant, KM for GTP
FT 695 uM."
FT /evidence="ECO:0000269|PubMed:16963571"
FT MUTAGEN 16
FT /note="S->A: Does not complement a disruption mutant, KM
FT for GTP 4.9 mM. Decreased GTPase activity, no stimulation
FT by YihI."
FT /evidence="ECO:0000269|PubMed:16963571,
FT ECO:0000269|PubMed:20434458"
FT MUTAGEN 118
FT /note="N->D: Complements a disruption mutant at 42 degrees
FT Celsius, very poor complementation at 30 degrees Celsius.
FT Reduces affinity for the 50S ribosomal subunit at 30
FT degrees Celsius. RelA suppresses this point mutation at 30
FT degrees Celsius."
FT /evidence="ECO:0000269|PubMed:16930151"
FT MUTAGEN 118
FT /note="N->D: Does not complement a disruption mutant at 42
FT degrees Celsius, diminished association with 50S ribosomal
FT subunits; when associated with D-321."
FT /evidence="ECO:0000269|PubMed:16930151"
FT MUTAGEN 215
FT /note="K->A: Does not complement a disruption mutant, KM
FT for GTP 6.7 mM."
FT /evidence="ECO:0000269|PubMed:16963571"
FT MUTAGEN 216
FT /note="S->A: Does not complement a disruption mutant,
FT considerably decreased GTPase activity, KM for GTP 4.8 mM,
FT no stimulation by YihI."
FT /evidence="ECO:0000269|PubMed:16963571,
FT ECO:0000269|PubMed:20434458"
FT MUTAGEN 321
FT /note="N->D: Complements a disruption mutant at 42 degrees
FT Celsius, no complementation at 30 degrees Celsius. Greatly
FT reduces affinity for the 50S ribosomal subunit at 30
FT degrees Celsius. RelA suppresses this point mutation at 30
FT degrees Celsius."
FT /evidence="ECO:0000269|PubMed:16930151"
FT MUTAGEN 414
FT /note="G->R: Does not complement rrmJ deletion, complements
FT der disruption at 42 degrees Celsius."
FT /evidence="ECO:0000269|PubMed:20172997"
FT MUTAGEN 424
FT /note="G->D: Does not complement rrmJ deletion, nor the der
FT disruption at 42 degrees Celsius."
FT /evidence="ECO:0000269|PubMed:20172997"
FT MUTAGEN 469
FT /note="N->K: Does not complement rrmJ deletion, complements
FT der disruption at 42 degrees Celsius."
FT /evidence="ECO:0000269|PubMed:20172997"
FT MUTAGEN 472
FT /note="T->A: Does not complement rrmJ deletion, complements
FT der disruption at 42 degrees Celsius."
FT /evidence="ECO:0000269|PubMed:20172997"
SQ SEQUENCE 490 AA; 55036 MW; 0321511F5A5A7E3D CRC64;
MVPVVALVGR PNVGKSTLFN RLTRTRDALV ADFPGLTRDR KYGRAEIEGR EFICIDTGGI
DGTEDGVETR MAEQSLLAIE EADVVLFMVD ARAGLMPADE AIAKHLRSRE KPTFLVANKT
DGLDPDQAVV DFYSLGLGEI YPIAASHGRG VLSLLEHVLL PWMEDLAPQE EVDEDAEYWA
QFEAEENGEE EEEDDFDPQS LPIKLAIVGR PNVGKSTLTN RILGEERVVV YDMPGTTRDS
IYIPMERDGR EYVLIDTAGV RKRGKITDAV EKFSVIKTLQ AIEDANVVML VIDAREGISD
QDLSLLGFIL NSGRSLVIVV NKWDGLSQEV KEQVKETLDF RLGFIDFARV HFISALHGSG
VGNLFESVRE AYDSSTRRVG TSMLTRIMTM AVEDHQPPLV RGRRVKLKYA HAGGYNPPIV
VIHGNQVKDL PDSYKRYLMN YFRKSLDVMG SPIRIQFKEG ENPYANKRNT LTPTQMRKRK
RLMKHIKKNK
