CDNE_ELIME
ID CDNE_ELIME Reviewed; 292 AA.
AC P0DSP2;
DT 18-SEP-2019, integrated into UniProtKB/Swiss-Prot.
DT 18-SEP-2019, sequence version 1.
DT 03-AUG-2022, entry version 13.
DE RecName: Full=Cyclic dipurine nucleotide synthase {ECO:0000305|PubMed:30787435};
DE EC=2.7.7.- {ECO:0000269|PubMed:30787435};
DE AltName: Full=Cyclic GMP-AMP synthase {ECO:0000305|PubMed:30787435};
DE Short=cGAMP synthase {ECO:0000305|PubMed:30787435};
DE AltName: Full=c-di-AMP synthase {ECO:0000305|PubMed:30787435};
DE EC=2.7.7.85 {ECO:0000269|PubMed:30787435};
DE AltName: Full=c-di-GMP synthase {ECO:0000305|PubMed:30787435};
DE EC=2.7.7.65 {ECO:0000269|PubMed:30787435};
DE AltName: Full=cGAS/DncV-like nucleotidyltransferase {ECO:0000303|PubMed:30787435};
DE Short=CD-NTase {ECO:0000303|PubMed:30787435};
GN Name=cdnE01 {ECO:0000303|PubMed:30787435};
GN ORFNames=NCTC10016_00133 {ECO:0000312|EMBL:SQG05247.1};
OS Elizabethkingia meningoseptica (Chryseobacterium meningosepticum).
OC Bacteria; Bacteroidetes; Flavobacteriia; Flavobacteriales; Weeksellaceae;
OC Elizabethkingia.
OX NCBI_TaxID=238;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 13253 / DSM 2800 / CCUG 214 / CIP 60.57 / LMG 12279 / NBRC
RC 12535 / NCTC 100 / 1416;
RG Pathogen Informatics;
RA Doyle S.;
RL Submitted (JUN-2018) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP CLASSIFICATION AND NOMENCLATURE.
RX PubMed=32839535; DOI=10.1038/s41564-020-0777-y;
RA Millman A., Melamed S., Amitai G., Sorek R.;
RT "Diversity and classification of cyclic-oligonucleotide-based anti-phage
RT signalling systems.";
RL Nat. Microbiol. 5:1608-1615(2020).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.25 ANGSTROMS) IN COMPLEXES WITH GTP;
RP NON-HYDROLYSABLE ATP AND MAGNESIUM, FUNCTION, CATALYTIC ACTIVITY, COFACTOR,
RP NOMENCLATURE, SIMILARITY, AND MUTAGENESIS OF SER-169.
RC STRAIN=ATCC 13253 / DSM 2800 / CCUG 214 / CIP 60.57 / LMG 12279 / NBRC
RC 12535 / NCTC 100 / 1416;
RX PubMed=30787435; DOI=10.1038/s41586-019-0953-5;
RA Whiteley A.T., Eaglesham J.B., de Oliveira Mann C.C., Morehouse B.R.,
RA Lowey B., Nieminen E.A., Danilchanka O., King D.S., Lee A.S.Y.,
RA Mekalanos J.J., Kranzusch P.J.;
RT "Bacterial cGAS-like enzymes synthesize diverse nucleotide signals.";
RL Nature 567:194-199(2019).
CC -!- FUNCTION: CBASS (cyclic oligonucleotide-based antiphage signaling
CC system) provides immunity against bacteriophage. The CD-NTase protein
CC synthesizes cyclic nucleotides in response to infection; these serve as
CC specific second messenger signals. The signals activate a diverse range
CC of effectors, leading to bacterial cell death and thus abortive phage
CC infection. A type I-A(GA) CBASS system (PubMed:32839535).
CC {ECO:0000303|PubMed:32839535, ECO:0000305}.
CC -!- FUNCTION: Cyclic dinucleotide synthase that catalyzes the synthesis of
CC 3'3'-cyclic GMP-AMP (cGAMP) from GTP and ATP, and of c-di-AMP and c-di-
CC GMP, that are second messengers for cell signal transduction.
CC {ECO:0000269|PubMed:30787435}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2 ATP = 3',3'-c-di-AMP + 2 diphosphate; Xref=Rhea:RHEA:35655,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:33019, ChEBI:CHEBI:71500; EC=2.7.7.85;
CC Evidence={ECO:0000269|PubMed:30787435};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:35656;
CC Evidence={ECO:0000305|PubMed:30787435};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2 GTP = cyclic di-3',5'-guanylate + 2 diphosphate;
CC Xref=Rhea:RHEA:24898, ChEBI:CHEBI:33019, ChEBI:CHEBI:37565,
CC ChEBI:CHEBI:58805; EC=2.7.7.65;
CC Evidence={ECO:0000269|PubMed:30787435};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:24899;
CC Evidence={ECO:0000305|PubMed:30787435};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + GTP = 3',3'-cGAMP + 2 diphosphate; Xref=Rhea:RHEA:35647,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:33019, ChEBI:CHEBI:37565,
CC ChEBI:CHEBI:71501; Evidence={ECO:0000269|PubMed:30787435};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:35648;
CC Evidence={ECO:0000305|PubMed:30787435};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:30787435};
CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000269|PubMed:30787435};
CC -!- SIMILARITY: Belongs to the CD-NTase family. E01 subfamily.
CC {ECO:0000305|PubMed:30787435}.
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DR EMBL; LS483376; SQG05247.1; -; Genomic_DNA.
DR RefSeq; WP_016200549.1; NZ_MAHZ01000011.1.
DR PDB; 6E0M; X-ray; 1.52 A; A=1-292.
DR PDB; 6E0N; X-ray; 1.50 A; A=1-292.
DR PDB; 6E0O; X-ray; 1.25 A; A=1-292.
DR PDBsum; 6E0M; -.
DR PDBsum; 6E0N; -.
DR PDBsum; 6E0O; -.
DR AlphaFoldDB; P0DSP2; -.
DR SMR; P0DSP2; -.
DR STRING; 1216967.L100_16065; -.
DR KEGG; emg:BBD33_11290; -.
DR GO; GO:0140701; F:3',3'-cyclic GMP-AMP synthase activity; IDA:UniProtKB.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0106408; F:diadenylate cyclase activity; IEA:UniProtKB-EC.
DR GO; GO:0052621; F:diguanylate cyclase activity; IEA:UniProtKB-EC.
DR GO; GO:0005525; F:GTP binding; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0051607; P:defense response to virus; IEA:UniProtKB-KW.
DR GO; GO:0009117; P:nucleotide metabolic process; IEA:UniProtKB-KW.
DR CDD; cd05400; NT_2-5OAS_ClassI-CCAase; 1.
DR Gene3D; 3.30.460.10; -; 1.
DR InterPro; IPR006116; NT_2-5OAS_ClassI-CCAase.
DR InterPro; IPR043519; NT_sf.
DR SUPFAM; SSF81301; SSF81301; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Antiviral defense; ATP-binding; GTP-binding; Magnesium;
KW Metal-binding; Nucleotide metabolism; Nucleotide-binding;
KW Nucleotidyltransferase; Transferase.
FT CHAIN 1..292
FT /note="Cyclic dipurine nucleotide synthase"
FT /id="PRO_0000447702"
FT BINDING 47
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:30787435"
FT BINDING 48..52
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000269|PubMed:30787435"
FT BINDING 61
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:30787435"
FT BINDING 63
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:30787435"
FT BINDING 63
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:30787435"
FT BINDING 121..122
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:30787435"
FT BINDING 136
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:30787435"
FT BINDING 136
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:30787435"
FT BINDING 197
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000269|PubMed:30787435"
FT BINDING 216
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000269|PubMed:30787435"
FT MUTAGEN 169
FT /note="S->N: Changes substrate specificity, loses
FT preference for producing cyclic dipurine molecules and
FT instead produces more pyrimidine-containing CDN products."
FT /evidence="ECO:0000269|PubMed:30787435"
FT HELIX 5..11
FT /evidence="ECO:0007829|PDB:6E0N"
FT HELIX 21..38
FT /evidence="ECO:0007829|PDB:6E0N"
FT HELIX 39..41
FT /evidence="ECO:0007829|PDB:6E0N"
FT STRAND 42..47
FT /evidence="ECO:0007829|PDB:6E0N"
FT HELIX 48..52
FT /evidence="ECO:0007829|PDB:6E0N"
FT STRAND 62..68
FT /evidence="ECO:0007829|PDB:6E0N"
FT TURN 70..72
FT /evidence="ECO:0007829|PDB:6E0N"
FT HELIX 98..113
FT /evidence="ECO:0007829|PDB:6E0N"
FT HELIX 114..116
FT /evidence="ECO:0007829|PDB:6E0N"
FT STRAND 117..119
FT /evidence="ECO:0007829|PDB:6E0N"
FT STRAND 121..126
FT /evidence="ECO:0007829|PDB:6E0N"
FT STRAND 135..147
FT /evidence="ECO:0007829|PDB:6E0N"
FT TURN 148..151
FT /evidence="ECO:0007829|PDB:6E0N"
FT STRAND 152..160
FT /evidence="ECO:0007829|PDB:6E0N"
FT STRAND 166..169
FT /evidence="ECO:0007829|PDB:6E0N"
FT HELIX 171..184
FT /evidence="ECO:0007829|PDB:6E0N"
FT TURN 185..187
FT /evidence="ECO:0007829|PDB:6E0N"
FT HELIX 188..205
FT /evidence="ECO:0007829|PDB:6E0N"
FT HELIX 216..224
FT /evidence="ECO:0007829|PDB:6E0N"
FT HELIX 228..230
FT /evidence="ECO:0007829|PDB:6E0N"
FT HELIX 236..252
FT /evidence="ECO:0007829|PDB:6E0N"
FT STRAND 262..265
FT /evidence="ECO:0007829|PDB:6E0N"
FT HELIX 275..289
FT /evidence="ECO:0007829|PDB:6E0N"
SQ SEQUENCE 292 AA; 34162 MW; 22F1E1B5CB286673 CRC64;
MNFSEQQLIN WSRPVSTTED LKCQNAITQI TAALRAKFGN RVTIFLQGSY RNNTNVRQNS
DVDIVMRYDD AFYPDLQRLS ESDKAIYNAQ RTYSGYNFDE LKADTEEALR NVFTTSVERK
NKCIQVNGNS NRITADVIPC FVLKRFSTLQ SVEAEGIKFY SDDNKEIISF PEQHYSNGTE
KTNQTYRLYK RMVRILKVVN YRLIDDGEIA DNLVSSFFIE CLVYNVPNNQ FISGNYTQTL
RNVIVKIYED MKNNADYTEV NRLFWLFSNR SPRTRQDALG FMQKCWNYLG YQ
