YMDB_BACSU
ID YMDB_BACSU Reviewed; 264 AA.
AC O31775;
DT 20-JAN-2009, integrated into UniProtKB/Swiss-Prot.
DT 16-JUN-2009, sequence version 2.
DT 03-AUG-2022, entry version 114.
DE RecName: Full=2',3'-cyclic-nucleotide 2'-phosphodiesterase {ECO:0000305};
DE EC=3.1.4.16 {ECO:0000269|PubMed:24163345};
DE AltName: Full=Global regulator YmdB {ECO:0000305};
GN Name=ymdB; OrderedLocusNames=BSU16970;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
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 [2]
RP SEQUENCE REVISION TO 135-136.
RX PubMed=19383706; DOI=10.1099/mic.0.027839-0;
RA Barbe V., Cruveiller S., Kunst F., Lenoble P., Meurice G., Sekowska A.,
RA Vallenet D., Wang T., Moszer I., Medigue C., Danchin A.;
RT "From a consortium sequence to a unified sequence: the Bacillus subtilis
RT 168 reference genome a decade later.";
RL Microbiology 155:1758-1775(2009).
RN [3]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=168, and
RC 168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 / NCIMB 3610 /
RC NRRL NRS-744 / VKM B-501;
RX PubMed=21856853; DOI=10.1128/jb.05360-11;
RA Diethmaier C., Pietack N., Gunka K., Wrede C., Lehnik-Habrink M.,
RA Herzberg C., Huebner S., Stuelke J.;
RT "A novel factor controlling bistability in Bacillus subtilis: the YmdB
RT protein affects flagellin expression and biofilm formation.";
RL J. Bacteriol. 193:5997-6007(2011).
RN [4]
RP FUNCTION, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF ASP-8.
RX PubMed=26904951; DOI=10.1016/j.celrep.2016.01.071;
RA Mamou G., Malli Mohan G.B., Rouvinski A., Rosenberg A., Ben-Yehuda S.;
RT "Early developmental program shapes colony morphology in bacteria.";
RL Cell Rep. 14:1850-1857(2016).
RN [5]
RP FUNCTION, SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
RC STRAIN=168 / PY79;
RX PubMed=26906740; DOI=10.1016/j.devcel.2016.01.013;
RA Dubey G.P., Malli Mohan G.B., Dubrovsky A., Amen T., Tsipshtein S.,
RA Rouvinski A., Rosenberg A., Kaganovich D., Sherman E., Medalia O.,
RA Ben-Yehuda S.;
RT "Architecture and characteristics of bacterial nanotubes.";
RL Dev. Cell 36:453-461(2016).
RN [6] {ECO:0007744|PDB:4B2O}
RP X-RAY CRYSTALLOGRAPHY (1.64 ANGSTROMS) IN COMPLEX WITH IRON, FUNCTION,
RP CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT,
RP DISRUPTION PHENOTYPE, ACTIVE SITE, AND MUTAGENESIS OF GLU-39.
RC STRAIN=168, and
RC 168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 / NCIMB 3610 /
RC NRRL NRS-744 / VKM B-501;
RX PubMed=24163345; DOI=10.1128/jb.00826-13;
RA Diethmaier C., Newman J.A., Kovacs A.T., Kaever V., Herzberg C.,
RA Rodrigues C., Boonstra M., Kuipers O.P., Lewis R.J., Stulke J.;
RT "The YmdB phosphodiesterase is a global regulator of late adaptive
RT responses in Bacillus subtilis.";
RL J. Bacteriol. 196:265-275(2014).
CC -!- FUNCTION: Plays a central, regulatory role in the late adaptive
CC responses and affects the levels of many genes (PubMed:24163345). May
CC act via regulation of cAMP levels (PubMed:26904951). Decreases the
CC expression of motility genes and induces genes involved in biofilm
CC formation, by controlling the expression of SlrR (PubMed:21856853).
CC Required for formation of intercellular nanotubes that bridge
CC neighboring cells to allow molecular exchange (PubMed:26906740). Plays
CC a key role in directing the early stages of colony development
CC (PubMed:26904951). In vitro, has a metal-dependent phosphodiesterase
CC activity against 2',3'-cAMP and 2',3'-cGMP. Has also 3',5'-cyclic-
CC nucleotide phosphodiesterase activity, but cannot use cyclic di-AMP or
CC cyclic di-GMP, and does not have phosphatase activity
CC (PubMed:24163345). {ECO:0000269|PubMed:21856853,
CC ECO:0000269|PubMed:24163345, ECO:0000269|PubMed:26904951,
CC ECO:0000269|PubMed:26906740, ECO:0000305|PubMed:26904951}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a nucleoside 2',3'-cyclic phosphate + H2O = a nucleoside 3'-
CC phosphate + H(+); Xref=Rhea:RHEA:19621, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:66949, ChEBI:CHEBI:66954; EC=3.1.4.16;
CC Evidence={ECO:0000269|PubMed:24163345};
CC -!- COFACTOR:
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC Evidence={ECO:0000269|PubMed:24163345};
CC Note=Corresponds to iron 2 in the structure.
CC {ECO:0000305|PubMed:24163345};
CC -!- COFACTOR:
CC Name=Fe(3+); Xref=ChEBI:CHEBI:29034;
CC Evidence={ECO:0000269|PubMed:24163345};
CC Note=Corresponds to iron 1 in the structure.
CC {ECO:0000305|PubMed:24163345};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.2 mM for 2',3'-cAMP {ECO:0000269|PubMed:24163345};
CC KM=0.29 mM for 2',3'-cGMP {ECO:0000269|PubMed:24163345};
CC KM=1.3 mM for 3',5'-cAMP {ECO:0000269|PubMed:24163345};
CC KM=0.85 mM for 3',5'-cGMP {ECO:0000269|PubMed:24163345};
CC KM=0.94 mM for bis-pNPP {ECO:0000269|PubMed:24163345};
CC Vmax=0.83 umol/min/mg enzyme with 2',3'-cAMP as substrate
CC {ECO:0000269|PubMed:24163345};
CC Vmax=1.02 umol/min/mg enzyme with 2',3'-cGMP as substrate
CC {ECO:0000269|PubMed:24163345};
CC Vmax=0.45 umol/min/mg enzyme with 3',5'-cAMP as substrate
CC {ECO:0000269|PubMed:24163345};
CC Vmax=0.37 umol/min/mg enzyme with 3',5'-cGMP as substrate
CC {ECO:0000269|PubMed:24163345};
CC Vmax=105 umol/min/mg enzyme with bis-pNPP as substrate
CC {ECO:0000269|PubMed:24163345};
CC Note=kcat is 15.0 min(-1) with 2',3'-cAMP as substrate. kcat is 22.1
CC min(-1) with 2',3'-cGMP as substrate. kcat is 9.2 min(-1) with 3',5'-
CC cAMP as substrate. kcat is 7.7 min(-1) with 3',5'-cGMP as substrate.
CC {ECO:0000269|PubMed:24163345};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:24163345}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:26906740}.
CC Note=Localizes to the cytoplasm, cell periphery and nanotubes.
CC {ECO:0000269|PubMed:26906740}.
CC -!- DISRUPTION PHENOTYPE: Deletion of the gene affects the levels of over
CC 800 mRNAs (PubMed:24163345). Deletion mutant overexpresses flagellin
CC and other genes of the sigma-D-dependent motility regulon. In contrast,
CC the two major operons for biofilm formation are not expressed and the
CC mutant is unable to form biofilms. All cells are short and motile
CC (PubMed:21856853). Deletion also results in a significant decrease in
CC intercellular molecular exchange (PubMed:26906740). Mutant displays
CC aberrant developmental patterns and forms smaller colonies
CC (PubMed:26904951). {ECO:0000269|PubMed:21856853,
CC ECO:0000269|PubMed:24163345, ECO:0000269|PubMed:26904951,
CC ECO:0000269|PubMed:26906740}.
CC -!- SIMILARITY: Belongs to the YmdB-like family. {ECO:0000305}.
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DR EMBL; AL009126; CAB13570.2; -; Genomic_DNA.
DR PIR; G69884; G69884.
DR RefSeq; NP_389579.2; NC_000964.3.
DR RefSeq; WP_003245138.1; NZ_JNCM01000035.1.
DR PDB; 4B2O; X-ray; 1.64 A; A/B/C/D=1-264.
DR PDBsum; 4B2O; -.
DR AlphaFoldDB; O31775; -.
DR SMR; O31775; -.
DR STRING; 224308.BSU16970; -.
DR PaxDb; O31775; -.
DR PRIDE; O31775; -.
DR EnsemblBacteria; CAB13570; CAB13570; BSU_16970.
DR GeneID; 50133449; -.
DR GeneID; 939441; -.
DR KEGG; bsu:BSU16970; -.
DR PATRIC; fig|224308.179.peg.1838; -.
DR eggNOG; COG1692; Bacteria.
DR InParanoid; O31775; -.
DR OMA; NHIWDKK; -.
DR PhylomeDB; O31775; -.
DR BioCyc; BSUB:BSU16970-MON; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0008663; F:2',3'-cyclic-nucleotide 2'-phosphodiesterase activity; IEA:UniProtKB-EC.
DR GO; GO:0004113; F:2',3'-cyclic-nucleotide 3'-phosphodiesterase activity; IDA:CACAO.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR Gene3D; 3.60.21.10; -; 1.
DR InterPro; IPR029052; Metallo-depent_PP-like.
DR InterPro; IPR005235; YmdB-like.
DR PANTHER; PTHR36303; PTHR36303; 1.
DR Pfam; PF13277; YmdB; 1.
DR PIRSF; PIRSF004789; DR1281; 1.
DR SUPFAM; SSF56300; SSF56300; 1.
DR TIGRFAMs; TIGR00282; TIGR00282; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Hydrolase; Iron; Metal-binding;
KW Reference proteome.
FT CHAIN 1..264
FT /note="2',3'-cyclic-nucleotide 2'-phosphodiesterase"
FT /id="PRO_0000361092"
FT ACT_SITE 68
FT /note="Proton donor"
FT /evidence="ECO:0000305|PubMed:24163345"
FT BINDING 8
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:24163345,
FT ECO:0007744|PDB:4B2O"
FT BINDING 39
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:24163345,
FT ECO:0007744|PDB:4B2O"
FT BINDING 39
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:24163345,
FT ECO:0007744|PDB:4B2O"
FT BINDING 40
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:24163345,
FT ECO:0007744|PDB:4B2O"
FT BINDING 67
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:24163345,
FT ECO:0007744|PDB:4B2O"
FT BINDING 150
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:24163345,
FT ECO:0007744|PDB:4B2O"
FT BINDING 175
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:24163345,
FT ECO:0007744|PDB:4B2O"
FT BINDING 177
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:24163345,
FT ECO:0007744|PDB:4B2O"
FT MUTAGEN 8
FT /note="D->A: Increases cAMP levels. Displays aberrant
FT colony morphologies."
FT /evidence="ECO:0000269|PubMed:26904951"
FT MUTAGEN 39
FT /note="E->Q: Abolishes phosphodiesterase activity.
FT Overexpresses flagellin and forms smooth colonies. Does not
FT affect stability of the protein."
FT /evidence="ECO:0000269|PubMed:24163345"
FT STRAND 2..6
FT /evidence="ECO:0007829|PDB:4B2O"
FT HELIX 11..29
FT /evidence="ECO:0007829|PDB:4B2O"
FT STRAND 32..37
FT /evidence="ECO:0007829|PDB:4B2O"
FT TURN 41..44
FT /evidence="ECO:0007829|PDB:4B2O"
FT HELIX 49..57
FT /evidence="ECO:0007829|PDB:4B2O"
FT STRAND 61..64
FT /evidence="ECO:0007829|PDB:4B2O"
FT TURN 67..70
FT /evidence="ECO:0007829|PDB:4B2O"
FT HELIX 75..78
FT /evidence="ECO:0007829|PDB:4B2O"
FT TURN 79..81
FT /evidence="ECO:0007829|PDB:4B2O"
FT STRAND 83..85
FT /evidence="ECO:0007829|PDB:4B2O"
FT STRAND 99..105
FT /evidence="ECO:0007829|PDB:4B2O"
FT STRAND 108..116
FT /evidence="ECO:0007829|PDB:4B2O"
FT HELIX 127..139
FT /evidence="ECO:0007829|PDB:4B2O"
FT STRAND 145..150
FT /evidence="ECO:0007829|PDB:4B2O"
FT HELIX 154..163
FT /evidence="ECO:0007829|PDB:4B2O"
FT STRAND 168..178
FT /evidence="ECO:0007829|PDB:4B2O"
FT STRAND 191..194
FT /evidence="ECO:0007829|PDB:4B2O"
FT STRAND 199..205
FT /evidence="ECO:0007829|PDB:4B2O"
FT HELIX 210..219
FT /evidence="ECO:0007829|PDB:4B2O"
FT STRAND 232..241
FT /evidence="ECO:0007829|PDB:4B2O"
FT TURN 243..245
FT /evidence="ECO:0007829|PDB:4B2O"
FT STRAND 248..257
FT /evidence="ECO:0007829|PDB:4B2O"
SQ SEQUENCE 264 AA; 29289 MW; B0A58FF04DC56D3F CRC64;
MRILFIGDVV GSPGRDMVKE YVPKLKTKYK PHFTIINGEN AAHGKGLTEK IYHSLIQSGA
DAITMGNHTW DKKEIFDFID DVPNLVRPAN FPEGTPGKGI TYVKANGKEL AVINLQGRTF
LPPLDDPFLK ADELIAEAAK RTPYIFIDFH AEATSEKLAL GWYTDGRASA VVGTHTHVQT
ADNRILPKGT AYITDVGMTG PYDGILGMDR ETIIKRFKTN LPVRFTVAEG KTTLSGVVID
IDDQTKKAVK IERILINDDH MFFE
