NUCC_ECOM1
ID NUCC_ECOM1 Reviewed; 241 AA.
AC D7Y2H5;
DT 10-FEB-2021, integrated into UniProtKB/Swiss-Prot.
DT 05-OCT-2010, sequence version 1.
DT 03-AUG-2022, entry version 23.
DE RecName: Full=Endodeoxyribonuclease NucC {ECO:0000303|PubMed:31932165};
DE EC=3.1.-.- {ECO:0000269|PubMed:31932165};
DE AltName: Full=NucC nuclease;
GN Name=nucC {ECO:0000303|PubMed:31932165};
GN ORFNames=HMPREF9540_01761 {ECO:0000312|EMBL:EFJ98159.1};
OS Escherichia coli (strain MS 115-1).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=749537;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MS 115-1;
RA Weinstock G., Sodergren E., Clifton S., Fulton L., Fulton B., Courtney L.,
RA Fronick C., Harrison M., Strong C., Farmer C., Delahaunty K., Markovic C.,
RA Hall O., Minx P., Tomlinson C., Mitreva M., Hou S., Chen J., Wollam A.,
RA Pepin K.H., Johnson M., Bhonagiri V., Zhang X., Suruliraj S., Warren W.,
RA Chinwalla A., Mardis E.R., Wilson R.K.;
RL Submitted (MAY-2010) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP FUNCTION, ACTIVITY REGULATION, SUBUNIT, AND MUTAGENESIS OF ASP-73.
RC STRAIN=MS 115-1;
RX PubMed=31932165; DOI=10.1016/j.molcel.2019.12.009;
RA Ye Q., Lau R.K., Mathews I.T., Birkholz E.A., Watrous J.D., Azimi C.S.,
RA Pogliano J., Jain M., Corbett K.D.;
RT "HORMA Domain Proteins and a Trip13-like ATPase Regulate Bacterial cGAS-
RT like Enzymes to Mediate Bacteriophage Immunity.";
RL Mol. Cell 77:709-722(2020).
RN [3]
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 [4] {ECO:0007744|PDB:6P7O, ECO:0007744|PDB:6P7P, ECO:0007744|PDB:6P7Q}
RP X-RAY CRYSTALLOGRAPHY (1.66 ANGSTROMS) OF 2-240 IN COMPLEX WITH MAGNESIUM
RP AND IN COMPLEX WITH SECOND MESSENGERS, FUNCTION, POSSIBLE ACTIVE SITES,
RP COFACTOR, SUBUNIT, AND MUTAGENESIS OF TRP-4; LEU-19; ALA-27; PHE-28;
RP ARG-53; ASP-73; TYR-81; HIS-136; TYR-141 AND THR-226.
RC STRAIN=MS 115-1;
RX PubMed=31932164; DOI=10.1016/j.molcel.2019.12.010;
RA Lau R.K., Ye Q., Birkholz E.A., Berg K.R., Patel L., Mathews I.T.,
RA Watrous J.D., Ego K., Whiteley A.T., Lowey B., Mekalanos J.J.,
RA Kranzusch P.J., Jain M., Pogliano J., Corbett K.D.;
RT "Structure and Mechanism of a Cyclic Trinucleotide-Activated Bacterial
RT Endonuclease Mediating Bacteriophage Immunity.";
RL Mol. Cell 77:723-733(2020).
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 III-C(AAA) CBASS system (PubMed:32839535).
CC {ECO:0000269|PubMed:31932165, ECO:0000303|PubMed:32839535}.
CC -!- FUNCTION: A cyclic nucleotide-activated dsDNase. In the presence of
CC 3',3',3'-cyclic AMP-AMP-AMP (cAAA), and to a lesser extent 3',3',3'-
CC cyclic AMP-AMP-GMP (cAAG) and cyclic-di-AMP (c-di-AMP),
CC endonucleolytically degrades dsDNA (PubMed:31932165, PubMed:31932164).
CC Binds one cAAA in a pocket on one surface of the trimer; cAAA binding
CC promotes hexamerization, which is necessary for nuclease activation.
CC Also binds c-diAMP or linear di-AMP with lower affinity. The nuclease
CC digests dsDNA to about 50 bp lengths with a 2-base 3' overhang and a
CC consensus recognition site of 5'-Axx|T-3'. DNA has been modeled to
CC contact a pair of juxtaposed active sites (one from each layer of the
CC hexamer), accounting for cleavage on both strands and the 2-base
CC overhang (PubMed:31932164). {ECO:0000269|PubMed:31932164,
CC ECO:0000269|PubMed:31932165}.
CC -!- FUNCTION: Protects E.coli strain JP313 against bacteriophage lambda
CC cI- infection. When the cdnC-cap7-cap6-nucC operon is transformed into
CC a susceptible strain it confers bacteriophage immunity. Mutations in
CC the sensor (Cap7 also called HORMA) or effector proteins (CdnC, NucC)
CC but not the disassembly protein (Cap6 also called Trip13) no longer
CC confer immunity. The presence of the intact operon leads to culture
CC collapse and cell death which occurs before the phage has finished its
CC replication cycle, thus protecting non-infected bacteria by aborting
CC the phage infection and preventing its propagation.
CC {ECO:0000269|PubMed:31932164, ECO:0000269|PubMed:31932165}.
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:31932164, ECO:0007744|PDB:6P7O};
CC -!- ACTIVITY REGULATION: Activated by cAAA and to a lesser extent cAA and
CC cAAG; cAAA and cAA are products of its cognate CD-NTase. Cyclic
CC nucleotide binding causes hexamerization (PubMed:31932165). Cyclic
CC nucleotide binding causes a series of shifts that enclose the cAAA
CC molecule, enable hexamer formation and juxtapose pairs of active sites
CC to allow dsDNA cleavage (PubMed:31932164).
CC {ECO:0000269|PubMed:31932164, ECO:0000269|PubMed:31932165}.
CC -!- SUBUNIT: Self-oligomerizes (PubMed:31932165). Forms homotrimers; in the
CC presence of cAAA the trimers associate face-to-face to form
CC homohexamers. The 2 cAAA-binding sites are on the exterior of the
CC hexamer at the three-way junction, there are maximally 2 cyclic
CC nucleotides per hexamer (PubMed:31932164).
CC {ECO:0000269|PubMed:31932164, ECO:0000269|PubMed:31932165}.
CC -!- SIMILARITY: Belongs to the NucC endonuclease family.
CC {ECO:0000305|PubMed:31932164}.
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DR EMBL; ADTL01000141; EFJ98159.1; -; Genomic_DNA.
DR RefSeq; WP_001286625.1; NZ_GG771785.1.
DR PDB; 6P7O; X-ray; 1.75 A; A=4-240.
DR PDB; 6P7P; X-ray; 1.67 A; A/B/C=2-240.
DR PDB; 6P7Q; X-ray; 1.66 A; A/B/C=2-240.
DR PDBsum; 6P7O; -.
DR PDBsum; 6P7P; -.
DR PDBsum; 6P7Q; -.
DR AlphaFoldDB; D7Y2H5; -.
DR SMR; D7Y2H5; -.
DR EnsemblBacteria; EFJ98159; EFJ98159; HMPREF9540_01761.
DR HOGENOM; CLU_078737_0_0_6; -.
DR Proteomes; UP000032708; Unassembled WGS sequence.
DR GO; GO:0004519; F:endonuclease activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR GO; GO:0051607; P:defense response to virus; IEA:UniProtKB-KW.
PE 1: Evidence at protein level;
KW 3D-structure; Antiviral defense; Endonuclease; Hydrolase; Magnesium;
KW Metal-binding; Nuclease; Nucleotide-binding.
FT CHAIN 1..241
FT /note="Endodeoxyribonuclease NucC"
FT /id="PRO_0000451845"
FT ACT_SITE 73
FT /evidence="ECO:0000305|PubMed:31932164"
FT ACT_SITE 104
FT /evidence="ECO:0000305|PubMed:31932164"
FT ACT_SITE 106
FT /evidence="ECO:0000305|PubMed:31932164"
FT BINDING 73
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:31932164,
FT ECO:0007744|PDB:6P7O"
FT BINDING 104
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:31932164,
FT ECO:0007744|PDB:6P7O"
FT SITE 53
FT /note="Binds cAAA"
FT /evidence="ECO:0000269|PubMed:31932164,
FT ECO:0007744|PDB:6P7P"
FT SITE 81
FT /note="Binds cAAA"
FT /evidence="ECO:0000269|PubMed:31932164,
FT ECO:0007744|PDB:6P7P"
FT SITE 136
FT /note="Gate loop latch"
FT /evidence="ECO:0000269|PubMed:31932164,
FT ECO:0007744|PDB:6P7P"
FT SITE 141
FT /note="Gate loop latch"
FT /evidence="ECO:0000269|PubMed:31932164,
FT ECO:0007744|PDB:6P7P"
FT SITE 226
FT /note="Binds cAAA"
FT /evidence="ECO:0000269|PubMed:31932164,
FT ECO:0007744|PDB:6P7P"
FT MUTAGEN 4
FT /note="W->A: Decreased hexamer formation, retains
FT endonuclease activity."
FT /evidence="ECO:0000269|PubMed:31932164"
FT MUTAGEN 19
FT /note="L->A: Wild-type hexamer and endonuclease activity."
FT /evidence="ECO:0000269|PubMed:31932164"
FT MUTAGEN 19
FT /note="L->D: No hexamer formation, no endonuclease
FT activity."
FT /evidence="ECO:0000269|PubMed:31932164"
FT MUTAGEN 27
FT /note="A->E,K: No hexamer formation, no endonuclease
FT activity."
FT /evidence="ECO:0000269|PubMed:31932164"
FT MUTAGEN 28
FT /note="F->A: No hexamer formation, no endonuclease
FT activity, no phage immunity."
FT /evidence="ECO:0000269|PubMed:31932164"
FT MUTAGEN 53
FT /note="R->A: Loss of endonuclease activity."
FT /evidence="ECO:0000269|PubMed:31932164"
FT MUTAGEN 73
FT /note="D->N: Loss of endonuclease activity, no phage
FT immunity."
FT /evidence="ECO:0000269|PubMed:31932164,
FT ECO:0000269|PubMed:31932165"
FT MUTAGEN 81
FT /note="Y->A: Loss of endonuclease activity."
FT /evidence="ECO:0000269|PubMed:31932164"
FT MUTAGEN 136
FT /note="H->A: Loss of endonuclease activity."
FT /evidence="ECO:0000269|PubMed:31932164"
FT MUTAGEN 141
FT /note="Y->A: Loss of endonuclease activity."
FT /evidence="ECO:0000269|PubMed:31932164"
FT MUTAGEN 226
FT /note="T->Y: Loss of endonuclease activity."
FT /evidence="ECO:0000269|PubMed:31932164"
FT HELIX 6..27
FT /evidence="ECO:0007829|PDB:6P7Q"
FT HELIX 31..49
FT /evidence="ECO:0007829|PDB:6P7Q"
FT STRAND 55..62
FT /evidence="ECO:0007829|PDB:6P7Q"
FT STRAND 72..77
FT /evidence="ECO:0007829|PDB:6P7Q"
FT TURN 79..81
FT /evidence="ECO:0007829|PDB:6P7O"
FT STRAND 85..88
FT /evidence="ECO:0007829|PDB:6P7Q"
FT STRAND 91..95
FT /evidence="ECO:0007829|PDB:6P7Q"
FT HELIX 96..98
FT /evidence="ECO:0007829|PDB:6P7Q"
FT STRAND 99..109
FT /evidence="ECO:0007829|PDB:6P7Q"
FT HELIX 111..125
FT /evidence="ECO:0007829|PDB:6P7Q"
FT STRAND 134..136
FT /evidence="ECO:0007829|PDB:6P7Q"
FT STRAND 139..141
FT /evidence="ECO:0007829|PDB:6P7Q"
FT STRAND 150..162
FT /evidence="ECO:0007829|PDB:6P7Q"
FT HELIX 166..172
FT /evidence="ECO:0007829|PDB:6P7Q"
FT STRAND 183..186
FT /evidence="ECO:0007829|PDB:6P7Q"
FT TURN 187..189
FT /evidence="ECO:0007829|PDB:6P7Q"
FT STRAND 190..195
FT /evidence="ECO:0007829|PDB:6P7Q"
FT TURN 196..199
FT /evidence="ECO:0007829|PDB:6P7Q"
FT STRAND 200..207
FT /evidence="ECO:0007829|PDB:6P7Q"
FT HELIX 209..224
FT /evidence="ECO:0007829|PDB:6P7Q"
FT HELIX 232..236
FT /evidence="ECO:0007829|PDB:6P7Q"
FT HELIX 237..239
FT /evidence="ECO:0007829|PDB:6P7Q"
SQ SEQUENCE 241 AA; 26728 MW; BCEEC0B4E3B8082D CRC64;
MSDWSLSQLF ASLHEDIQLR LGTARKAFQH PGAKGDASEG VWIEMLDTYL PKRYQAANAF
VVDSLGNFSD QIDVVVFDRQ YSPFIFKFNE QIIVPAESVY AVFEAKQSAS ADLVAYAQRK
VASVRRLHRT SLPIPHAGGT YPAKPLIPIL GGLLTFESDW SPALGMSFDK ALNGDLSDGR
LDMGCVASHG HFYFNNIDSK FNFEHGNKPA TAFLFRLIAQ LQFSGTVPMI DIDAYGKWLA
N
