DER_BACSU
ID DER_BACSU Reviewed; 436 AA.
AC P50743;
DT 01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1996, sequence version 1.
DT 03-AUG-2022, entry version 151.
DE RecName: Full=GTPase Der;
DE AltName: Full=GTP-binding protein EngA;
GN Name=der; Synonyms=engA, yphC; OrderedLocusNames=BSU22840;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 / NCIMB
RC 3610 / NRRL NRS-744 / VKM B-501;
RX PubMed=8760912; DOI=10.1099/13500872-142-8-2005;
RA Sorokin A.V., Azevedo V., Zumstein E., Galleron N., Ehrlich S.D.,
RA Serror P.;
RT "Sequence analysis of the Bacillus subtilis chromosome region between the
RT serA and kdg loci cloned in a yeast artificial chromosome.";
RL Microbiology 142:2005-2016(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 185-436.
RC STRAIN=168;
RX PubMed=7592341; DOI=10.1128/jb.177.20.5899-5905.1995;
RA Morbidoni H.R., de Mendoza D., Cronan J.E. Jr.;
RT "Synthesis of sn-glycerol 3-phosphate, a key precursor of membrane lipids,
RT in Bacillus subtilis.";
RL J. Bacteriol. 177:5899-5905(1995).
RN [4]
RP GTP- AND GDP-BINDING, PROTEIN LEVELS, AND DISRUPTION PHENOTYPE.
RC STRAIN=CRK6000;
RX PubMed=12427945; DOI=10.1099/00221287-148-11-3539;
RA Morimoto T., Loh P.C., Hirai T., Asai K., Kobayashi K., Moriya S.,
RA Ogasawara N.;
RT "Six GTP-binding proteins of the Era/Obg family are essential for cell
RT growth in Bacillus subtilis.";
RL Microbiology 148:3539-3552(2002).
RN [5]
RP INTERACTION WITH THE 50S RIBOSOMAL SUBUNIT, AND FUNCTION IN 50S RIBOSOMAL
RP SUBUNIT BIOGENESIS.
RC STRAIN=RB247;
RX PubMed=16997968; DOI=10.1128/jb.01213-06;
RA Schaefer L., Uicker W.C., Wicker-Planquart C., Foucher A.-E., Jault J.-M.,
RA Britton R.A.;
RT "Multiple GTPases participate in the assembly of the large ribosomal
RT subunit in Bacillus subtilis.";
RL J. Bacteriol. 188:8252-8258(2006).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) BOUND TO GDP IN THE PROBABLE OFF
RP STATE.
RX PubMed=16894162; DOI=10.1073/pnas.0602585103;
RA Muench S.P., Xu L., Sedelnikova S.E., Rice D.W.;
RT "The essential GTPase YphC displays a major domain rearrangement associated
RT with nucleotide binding.";
RL Proc. Natl. Acad. Sci. U.S.A. 103:12359-12364(2006).
CC -!- FUNCTION: GTPase that plays an essential role in the late steps of
CC ribosome biogenesis. {ECO:0000269|PubMed:16997968}.
CC -!- SUBUNIT: Cofractionates with the 70S ribosome; association is
CC stabilized by the non-hydrolyzable GTP analog GMPPNP, and inhibited by
CC GTP or GDP.
CC -!- DISRUPTION PHENOTYPE: Essential for growth, it cannot be disrupted.
CC Depletion experiments show that cells become longer and abnormally
CC curved, with nucleoid condensation. Cells have many fewer 70S
CC ribosomes; the large ribosomal subunit is 45S and is missing proteins
CC L16, L27, L36 and interacts with 2 large non-ribosomal proteins.
CC {ECO:0000269|PubMed:12427945}.
CC -!- MISCELLANEOUS: Estimated to be present at 7000 copies per cell.
CC -!- SIMILARITY: Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like
CC GTPase superfamily. EngA (Der) GTPase family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=U32164; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; L47648; AAC83966.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB14200.1; -; Genomic_DNA.
DR EMBL; U32164; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR PIR; A69936; A69936.
DR RefSeq; NP_390165.1; NC_000964.3.
DR RefSeq; WP_003230565.1; NZ_JNCM01000036.1.
DR PDB; 2HJG; X-ray; 2.50 A; A=1-436.
DR PDB; 4DCS; X-ray; 2.25 A; A=1-436.
DR PDB; 4DCT; X-ray; 2.30 A; A=1-436.
DR PDB; 4DCU; X-ray; 2.00 A; A=1-436.
DR PDB; 4DCV; X-ray; 2.60 A; A=1-436.
DR PDB; 5M7H; X-ray; 3.15 A; A=1-436.
DR PDB; 5MBS; X-ray; 3.20 A; A=1-436.
DR PDB; 5X4B; X-ray; 1.50 A; A/B=2-163.
DR PDBsum; 2HJG; -.
DR PDBsum; 4DCS; -.
DR PDBsum; 4DCT; -.
DR PDBsum; 4DCU; -.
DR PDBsum; 4DCV; -.
DR PDBsum; 5M7H; -.
DR PDBsum; 5MBS; -.
DR PDBsum; 5X4B; -.
DR AlphaFoldDB; P50743; -.
DR SMR; P50743; -.
DR STRING; 224308.BSU22840; -.
DR jPOST; P50743; -.
DR PaxDb; P50743; -.
DR PRIDE; P50743; -.
DR EnsemblBacteria; CAB14200; CAB14200; BSU_22840.
DR GeneID; 938988; -.
DR KEGG; bsu:BSU22840; -.
DR PATRIC; fig|224308.179.peg.2489; -.
DR eggNOG; COG1160; Bacteria.
DR InParanoid; P50743; -.
DR OMA; KFRFLEY; -.
DR PhylomeDB; P50743; -.
DR BioCyc; BSUB:BSU22840-MON; -.
DR EvolutionaryTrace; P50743; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0005525; F:GTP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0043022; F:ribosome binding; IBA:GO_Central.
DR GO; GO:0000027; P:ribosomal large subunit assembly; IBA:GO_Central.
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 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..436
FT /note="GTPase Der"
FT /id="PRO_0000178964"
FT DOMAIN 4..167
FT /note="EngA-type G 1"
FT DOMAIN 176..351
FT /note="EngA-type G 2"
FT DOMAIN 352..436
FT /note="KH-like"
FT BINDING 10..17
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /ligand_label="1"
FT /evidence="ECO:0000255"
FT BINDING 57..61
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /ligand_label="1"
FT /evidence="ECO:0000255"
FT BINDING 119..122
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /ligand_label="1"
FT /evidence="ECO:0000255"
FT BINDING 182..189
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /ligand_label="2"
FT /evidence="ECO:0000255"
FT BINDING 229..233
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /ligand_label="2"
FT /evidence="ECO:0000255"
FT BINDING 294..297
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /ligand_label="2"
FT /evidence="ECO:0000255"
FT CONFLICT 186..187
FT /note="VG -> CR (in Ref. 2)"
FT /evidence="ECO:0000305"
FT STRAND 4..9
FT /evidence="ECO:0007829|PDB:5X4B"
FT STRAND 12..15
FT /evidence="ECO:0007829|PDB:5X4B"
FT HELIX 16..23
FT /evidence="ECO:0007829|PDB:5X4B"
FT STRAND 30..32
FT /evidence="ECO:0007829|PDB:5MBS"
FT STRAND 42..48
FT /evidence="ECO:0007829|PDB:5X4B"
FT STRAND 51..57
FT /evidence="ECO:0007829|PDB:5X4B"
FT HELIX 58..60
FT /evidence="ECO:0007829|PDB:5X4B"
FT HELIX 68..82
FT /evidence="ECO:0007829|PDB:5X4B"
FT STRAND 84..91
FT /evidence="ECO:0007829|PDB:5X4B"
FT TURN 92..94
FT /evidence="ECO:0007829|PDB:5X4B"
FT HELIX 98..107
FT /evidence="ECO:0007829|PDB:5X4B"
FT STRAND 114..119
FT /evidence="ECO:0007829|PDB:5X4B"
FT HELIX 124..136
FT /evidence="ECO:0007829|PDB:5X4B"
FT STRAND 137..139
FT /evidence="ECO:0007829|PDB:5X4B"
FT STRAND 141..143
FT /evidence="ECO:0007829|PDB:5X4B"
FT TURN 146..149
FT /evidence="ECO:0007829|PDB:5X4B"
FT HELIX 152..161
FT /evidence="ECO:0007829|PDB:5X4B"
FT HELIX 162..165
FT /evidence="ECO:0007829|PDB:2HJG"
FT STRAND 176..181
FT /evidence="ECO:0007829|PDB:4DCU"
FT STRAND 183..187
FT /evidence="ECO:0007829|PDB:5M7H"
FT HELIX 188..196
FT /evidence="ECO:0007829|PDB:4DCU"
FT STRAND 201..203
FT /evidence="ECO:0007829|PDB:4DCU"
FT STRAND 215..220
FT /evidence="ECO:0007829|PDB:4DCU"
FT STRAND 223..227
FT /evidence="ECO:0007829|PDB:4DCU"
FT HELIX 230..232
FT /evidence="ECO:0007829|PDB:4DCU"
FT TURN 233..235
FT /evidence="ECO:0007829|PDB:4DCU"
FT TURN 236..238
FT /evidence="ECO:0007829|PDB:4DCT"
FT HELIX 245..257
FT /evidence="ECO:0007829|PDB:4DCU"
FT STRAND 259..266
FT /evidence="ECO:0007829|PDB:4DCU"
FT TURN 267..269
FT /evidence="ECO:0007829|PDB:4DCU"
FT HELIX 273..284
FT /evidence="ECO:0007829|PDB:4DCU"
FT STRAND 288..294
FT /evidence="ECO:0007829|PDB:4DCU"
FT HELIX 296..298
FT /evidence="ECO:0007829|PDB:4DCU"
FT HELIX 305..316
FT /evidence="ECO:0007829|PDB:4DCU"
FT HELIX 318..320
FT /evidence="ECO:0007829|PDB:4DCU"
FT STRAND 321..323
FT /evidence="ECO:0007829|PDB:5M7H"
FT STRAND 325..327
FT /evidence="ECO:0007829|PDB:4DCU"
FT TURN 330..332
FT /evidence="ECO:0007829|PDB:4DCU"
FT HELIX 336..338
FT /evidence="ECO:0007829|PDB:4DCU"
FT HELIX 339..350
FT /evidence="ECO:0007829|PDB:4DCU"
FT HELIX 356..369
FT /evidence="ECO:0007829|PDB:4DCU"
FT STRAND 374..377
FT /evidence="ECO:0007829|PDB:4DCV"
FT STRAND 382..389
FT /evidence="ECO:0007829|PDB:4DCU"
FT TURN 390..393
FT /evidence="ECO:0007829|PDB:4DCU"
FT STRAND 394..400
FT /evidence="ECO:0007829|PDB:4DCU"
FT HELIX 402..404
FT /evidence="ECO:0007829|PDB:4DCU"
FT HELIX 407..421
FT /evidence="ECO:0007829|PDB:4DCU"
FT STRAND 429..433
FT /evidence="ECO:0007829|PDB:4DCU"
SQ SEQUENCE 436 AA; 48770 MW; A5CC7028FFB5A442 CRC64;
MGKPVVAIVG RPNVGKSTIF NRIAGERISI VEDTPGVTRD RIYSSAEWLN YDFNLIDTGG
IDIGDEPFLA QIRQQAEIAM DEADVIIFMV NGREGVTAAD EEVAKILYRT KKPVVLAVNK
LDNTEMRANI YDFYSLGFGE PYPISGTHGL GLGDLLDAVA EHFKNIPETK YNEEVIQFCL
IGRPNVGKSS LVNAMLGEER VIVSNVAGTT RDAVDTSFTY NQQEFVIVDT AGMRKKGKVY
ETTEKYSVLR ALKAIDRSEV VAVVLDGEEG IIEQDKRIAG YAHEAGKAVV IVVNKWDAVD
KDESTMKEFE ENIRDHFQFL DYAPILFMSA LTKKRIHTLM PAIIKASENH SLRVQTNVLN
DVIMDAVAMN PTPTHNGSRL KIYYATQVSV KPPSFVVFVN DPELMHFSYE RFLENRIRDA
FGFEGTPIKI FARARK
