UniProtKB - O31775 (YMDB_BACSU)
2',3'-cyclic-nucleotide 2'-phosphodiesterase
ymdB
Functioni
Plays a central, regulatory role in the late adaptive responses and affects the levels of many genes (PubMed:24163345).
May act via regulation of cAMP levels (PubMed:26904951).
Decreases the expression of motility genes and induces genes involved in biofilm formation, by controlling the expression of SlrR (PubMed:21856853).
Required for formation of intercellular nanotubes that bridge neighboring cells to allow molecular exchange (PubMed:26906740).
Plays a key role in directing the early stages of colony development (PubMed:26904951).
In vitro, has a metal-dependent phosphodiesterase activity against 2',3'-cAMP and 2',3'-cGMP. Has also 3',5'-cyclic-nucleotide phosphodiesterase activity, but cannot use cyclic di-AMP or cyclic di-GMP, and does not have phosphatase activity (PubMed:24163345).
1 Publication4 PublicationsCatalytic activityi
- EC:3.1.4.161 Publication
Cofactori
Protein has several cofactor binding sites:- Fe2+1 PublicationNote: Corresponds to iron 2 in the structure.1 Publication
- Fe3+1 PublicationNote: Corresponds to iron 1 in the structure.1 Publication
Kineticsi
- KM=0.2 mM for 2',3'-cAMP1 Publication
- KM=0.29 mM for 2',3'-cGMP1 Publication
- KM=1.3 mM for 3',5'-cAMP1 Publication
- KM=0.85 mM for 3',5'-cGMP1 Publication
- KM=0.94 mM for bis-pNPP1 Publication
- Vmax=0.83 µmol/min/mg enzyme with 2',3'-cAMP as substrate1 Publication
- Vmax=1.02 µmol/min/mg enzyme with 2',3'-cGMP as substrate1 Publication
- Vmax=0.45 µmol/min/mg enzyme with 3',5'-cAMP as substrate1 Publication
- Vmax=0.37 µmol/min/mg enzyme with 3',5'-cGMP as substrate1 Publication
- Vmax=105 µmol/min/mg enzyme with bis-pNPP as substrate1 Publication
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Metal bindingi | 8 | Iron 1Combined sources1 Publication | 1 | |
Metal bindingi | 39 | Iron 1Combined sources1 Publication | 1 | |
Metal bindingi | 39 | Iron 2Combined sources1 Publication | 1 | |
Metal bindingi | 40 | Iron 1Combined sources1 Publication | 1 | |
Metal bindingi | 67 | Iron 2Combined sources1 Publication | 1 | |
Active sitei | 68 | Proton donor1 Publication | 1 | |
Metal bindingi | 150 | Iron 2; via tele nitrogenCombined sources1 Publication | 1 | |
Metal bindingi | 175 | Iron 2; via pros nitrogenCombined sources1 Publication | 1 | |
Metal bindingi | 177 | Iron 1; via tele nitrogenCombined sources1 Publication | 1 |
GO - Molecular functioni
- 2',3'-cyclic-nucleotide 2'-phosphodiesterase activity Source: UniProtKB-EC
- 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity Source: CACAO
- metal ion binding Source: UniProtKB-KW
Keywordsi
Molecular function | Hydrolase |
Ligand | Iron, Metal-binding |
Enzyme and pathway databases
BioCyci | BSUB:BSU16970-MONOMER |
Names & Taxonomyi
Protein namesi | Recommended name: 2',3'-cyclic-nucleotide 2'-phosphodiesteraseCurated (EC:3.1.4.161 Publication)Alternative name(s): Global regulator YmdBCurated |
Gene namesi | Name:ymdB Ordered Locus Names:BSU16970 |
Organismi | Bacillus subtilis (strain 168) |
Taxonomic identifieri | 224308 [NCBI] |
Taxonomic lineagei | Bacteria › Firmicutes › Bacilli › Bacillales › Bacillaceae › Bacillus › |
Proteomesi |
|
Subcellular locationi
Cytoplasm and Cytosol
- Cytoplasm 1 Publication
Note: Localizes to the cytoplasm, cell periphery and nanotubes.1 Publication
Other locations
- cytoplasm Source: UniProtKB-SubCell
Keywords - Cellular componenti
CytoplasmPathology & Biotechi
Disruption phenotypei
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 8 | D → A: Increases cAMP levels. Displays aberrant colony morphologies. 1 Publication | 1 | |
Mutagenesisi | 39 | E → Q: Abolishes phosphodiesterase activity. Overexpresses flagellin and forms smooth colonies. Does not affect stability of the protein. 1 Publication | 1 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000361092 | 1 – 264 | 2',3'-cyclic-nucleotide 2'-phosphodiesteraseAdd BLAST | 264 |
Proteomic databases
PaxDbi | O31775 |
PRIDEi | O31775 |
Interactioni
Subunit structurei
Homodimer.
1 PublicationProtein-protein interaction databases
STRINGi | 224308.BSU16970 |
Structurei
Secondary structure
3D structure databases
SMRi | O31775 |
ModBasei | Search... |
PDBe-KBi | Search... |
Family & Domainsi
Sequence similaritiesi
Phylogenomic databases
eggNOGi | COG1692, Bacteria |
InParanoidi | O31775 |
OMAi | NHIWDKK |
PhylomeDBi | O31775 |
Family and domain databases
Gene3Di | 3.60.21.10, 1 hit |
InterProi | View protein in InterPro IPR029052, Metallo-depent_PP-like IPR005235, YmdB-like |
PANTHERi | PTHR36303, PTHR36303, 1 hit |
Pfami | View protein in Pfam PF13277, YmdB, 1 hit |
PIRSFi | PIRSF004789, DR1281, 1 hit |
SUPFAMi | SSF56300, SSF56300, 1 hit |
TIGRFAMsi | TIGR00282, TIGR00282, 1 hit |
i Sequence
Sequence statusi: Complete.
10 20 30 40 50
MRILFIGDVV GSPGRDMVKE YVPKLKTKYK PHFTIINGEN AAHGKGLTEK
60 70 80 90 100
IYHSLIQSGA DAITMGNHTW DKKEIFDFID DVPNLVRPAN FPEGTPGKGI
110 120 130 140 150
TYVKANGKEL AVINLQGRTF LPPLDDPFLK ADELIAEAAK RTPYIFIDFH
160 170 180 190 200
AEATSEKLAL GWYTDGRASA VVGTHTHVQT ADNRILPKGT AYITDVGMTG
210 220 230 240 250
PYDGILGMDR ETIIKRFKTN LPVRFTVAEG KTTLSGVVID IDDQTKKAVK
260
IERILINDDH MFFE
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AL009126 Genomic DNA Translation: CAB13570.2 |
PIRi | G69884 |
RefSeqi | NP_389579.2, NC_000964.3 WP_003245138.1, NZ_JNCM01000035.1 |
Genome annotation databases
EnsemblBacteriai | CAB13570; CAB13570; BSU_16970 |
GeneIDi | 50133449 939441 |
KEGGi | bsu:BSU16970 |
PATRICi | fig|224308.179.peg.1838 |
Similar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AL009126 Genomic DNA Translation: CAB13570.2 |
PIRi | G69884 |
RefSeqi | NP_389579.2, NC_000964.3 WP_003245138.1, NZ_JNCM01000035.1 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
4B2O | X-ray | 1.64 | A/B/C/D | 1-264 | [»] | |
SMRi | O31775 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
STRINGi | 224308.BSU16970 |
Proteomic databases
PaxDbi | O31775 |
PRIDEi | O31775 |
Genome annotation databases
EnsemblBacteriai | CAB13570; CAB13570; BSU_16970 |
GeneIDi | 50133449 939441 |
KEGGi | bsu:BSU16970 |
PATRICi | fig|224308.179.peg.1838 |
Phylogenomic databases
eggNOGi | COG1692, Bacteria |
InParanoidi | O31775 |
OMAi | NHIWDKK |
PhylomeDBi | O31775 |
Enzyme and pathway databases
BioCyci | BSUB:BSU16970-MONOMER |
Family and domain databases
Gene3Di | 3.60.21.10, 1 hit |
InterProi | View protein in InterPro IPR029052, Metallo-depent_PP-like IPR005235, YmdB-like |
PANTHERi | PTHR36303, PTHR36303, 1 hit |
Pfami | View protein in Pfam PF13277, YmdB, 1 hit |
PIRSFi | PIRSF004789, DR1281, 1 hit |
SUPFAMi | SSF56300, SSF56300, 1 hit |
TIGRFAMsi | TIGR00282, TIGR00282, 1 hit |
MobiDBi | Search... |
Entry informationi
Entry namei | YMDB_BACSU | |
Accessioni | O31775Primary (citable) accession number: O31775 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | January 20, 2009 |
Last sequence update: | June 16, 2009 | |
Last modified: | September 29, 2021 | |
This is version 112 of the entry and version 2 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Prokaryotic Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
3D-structure, Reference proteomeDocuments
- PDB cross-references
Index of Protein Data Bank (PDB) cross-references - SIMILARITY comments
Index of protein domains and families