DDL_COXBU
ID DDL_COXBU Reviewed; 372 AA.
AC Q83BZ9;
DT 15-DEC-2003, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 109.
DE RecName: Full=D-alanine--D-alanine ligase {ECO:0000255|HAMAP-Rule:MF_00047};
DE EC=6.3.2.4 {ECO:0000255|HAMAP-Rule:MF_00047};
DE AltName: Full=D-Ala-D-Ala ligase {ECO:0000255|HAMAP-Rule:MF_00047};
DE AltName: Full=D-alanylalanine synthetase {ECO:0000255|HAMAP-Rule:MF_00047};
GN Name=ddl {ECO:0000255|HAMAP-Rule:MF_00047}; OrderedLocusNames=CBU_1338;
OS Coxiella burnetii (strain RSA 493 / Nine Mile phase I).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Legionellales; Coxiellaceae;
OC Coxiella.
OX NCBI_TaxID=227377;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=RSA 493 / Nine Mile phase I;
RX PubMed=12704232; DOI=10.1073/pnas.0931379100;
RA Seshadri R., Paulsen I.T., Eisen J.A., Read T.D., Nelson K.E., Nelson W.C.,
RA Ward N.L., Tettelin H., Davidsen T.M., Beanan M.J., DeBoy R.T.,
RA Daugherty S.C., Brinkac L.M., Madupu R., Dodson R.J., Khouri H.M.,
RA Lee K.H., Carty H.A., Scanlan D., Heinzen R.A., Thompson H.A., Samuel J.E.,
RA Fraser C.M., Heidelberg J.F.;
RT "Complete genome sequence of the Q-fever pathogen, Coxiella burnetii.";
RL Proc. Natl. Acad. Sci. U.S.A. 100:5455-5460(2003).
CC -!- FUNCTION: Cell wall formation. {ECO:0000255|HAMAP-Rule:MF_00047}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + 2 D-alanine = ADP + D-alanyl-D-alanine + H(+) +
CC phosphate; Xref=Rhea:RHEA:11224, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:43474, ChEBI:CHEBI:57416,
CC ChEBI:CHEBI:57822, ChEBI:CHEBI:456216; EC=6.3.2.4;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00047};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
CC Note=Binds 2 magnesium or manganese ions per subunit. {ECO:0000250};
CC -!- PATHWAY: Cell wall biogenesis; peptidoglycan biosynthesis.
CC {ECO:0000255|HAMAP-Rule:MF_00047}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00047}.
CC -!- SIMILARITY: Belongs to the D-alanine--D-alanine ligase family.
CC {ECO:0000255|HAMAP-Rule:MF_00047}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAO90841.2; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; AE016828; AAO90841.2; ALT_INIT; Genomic_DNA.
DR RefSeq; NP_820327.2; NC_002971.3.
DR PDB; 3TQT; X-ray; 1.88 A; A/B=1-372.
DR PDBsum; 3TQT; -.
DR AlphaFoldDB; Q83BZ9; -.
DR SMR; Q83BZ9; -.
DR STRING; 227377.CBU_1338; -.
DR EnsemblBacteria; AAO90841; AAO90841; CBU_1338.
DR GeneID; 1209244; -.
DR KEGG; cbu:CBU_1338; -.
DR PATRIC; fig|227377.7.peg.1330; -.
DR eggNOG; COG1181; Bacteria.
DR HOGENOM; CLU_039268_0_0_6; -.
DR OMA; IDFFLTD; -.
DR UniPathway; UPA00219; -.
DR Proteomes; UP000002671; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0008716; F:D-alanine-D-alanine ligase activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
DR GO; GO:0009252; P:peptidoglycan biosynthetic process; IBA:GO_Central.
DR GO; GO:0008360; P:regulation of cell shape; IEA:UniProtKB-KW.
DR Gene3D; 3.30.1490.20; -; 1.
DR HAMAP; MF_00047; Dala_Dala_lig; 1.
DR InterPro; IPR011761; ATP-grasp.
DR InterPro; IPR013815; ATP_grasp_subdomain_1.
DR InterPro; IPR000291; D-Ala_lig_Van_CS.
DR InterPro; IPR005905; D_ala_D_ala.
DR InterPro; IPR011095; Dala_Dala_lig_C.
DR InterPro; IPR011127; Dala_Dala_lig_N.
DR InterPro; IPR016185; PreATP-grasp_dom_sf.
DR Pfam; PF07478; Dala_Dala_lig_C; 1.
DR Pfam; PF01820; Dala_Dala_lig_N; 1.
DR PIRSF; PIRSF039102; Ddl/VanB; 1.
DR SUPFAM; SSF52440; SSF52440; 1.
DR TIGRFAMs; TIGR01205; D_ala_D_alaTIGR; 1.
DR PROSITE; PS50975; ATP_GRASP; 1.
DR PROSITE; PS00843; DALA_DALA_LIGASE_1; 1.
DR PROSITE; PS00844; DALA_DALA_LIGASE_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Cell shape; Cell wall biogenesis/degradation;
KW Cytoplasm; Ligase; Magnesium; Manganese; Metal-binding; Nucleotide-binding;
KW Peptidoglycan synthesis; Reference proteome.
FT CHAIN 1..372
FT /note="D-alanine--D-alanine ligase"
FT /id="PRO_0000177813"
FT DOMAIN 145..349
FT /note="ATP-grasp"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 176..231
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 303
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 316
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 316
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 318
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT STRAND 4..12
FT /evidence="ECO:0007829|PDB:3TQT"
FT HELIX 18..31
FT /evidence="ECO:0007829|PDB:3TQT"
FT TURN 34..36
FT /evidence="ECO:0007829|PDB:3TQT"
FT STRAND 37..44
FT /evidence="ECO:0007829|PDB:3TQT"
FT STRAND 50..53
FT /evidence="ECO:0007829|PDB:3TQT"
FT HELIX 56..61
FT /evidence="ECO:0007829|PDB:3TQT"
FT HELIX 64..70
FT /evidence="ECO:0007829|PDB:3TQT"
FT STRAND 73..78
FT /evidence="ECO:0007829|PDB:3TQT"
FT STRAND 87..89
FT /evidence="ECO:0007829|PDB:3TQT"
FT STRAND 100..104
FT /evidence="ECO:0007829|PDB:3TQT"
FT TURN 109..112
FT /evidence="ECO:0007829|PDB:3TQT"
FT HELIX 115..122
FT /evidence="ECO:0007829|PDB:3TQT"
FT STRAND 127..129
FT /evidence="ECO:0007829|PDB:3TQT"
FT HELIX 132..139
FT /evidence="ECO:0007829|PDB:3TQT"
FT HELIX 141..150
FT /evidence="ECO:0007829|PDB:3TQT"
FT STRAND 159..161
FT /evidence="ECO:0007829|PDB:3TQT"
FT HELIX 170..177
FT /evidence="ECO:0007829|PDB:3TQT"
FT STRAND 183..189
FT /evidence="ECO:0007829|PDB:3TQT"
FT HELIX 193..195
FT /evidence="ECO:0007829|PDB:3TQT"
FT STRAND 196..199
FT /evidence="ECO:0007829|PDB:3TQT"
FT HELIX 202..212
FT /evidence="ECO:0007829|PDB:3TQT"
FT TURN 213..215
FT /evidence="ECO:0007829|PDB:3TQT"
FT STRAND 219..223
FT /evidence="ECO:0007829|PDB:3TQT"
FT STRAND 227..239
FT /evidence="ECO:0007829|PDB:3TQT"
FT STRAND 246..249
FT /evidence="ECO:0007829|PDB:3TQT"
FT STRAND 268..271
FT /evidence="ECO:0007829|PDB:3TQT"
FT HELIX 277..293
FT /evidence="ECO:0007829|PDB:3TQT"
FT STRAND 298..306
FT /evidence="ECO:0007829|PDB:3TQT"
FT STRAND 312..320
FT /evidence="ECO:0007829|PDB:3TQT"
FT HELIX 328..335
FT /evidence="ECO:0007829|PDB:3TQT"
FT HELIX 340..370
FT /evidence="ECO:0007829|PDB:3TQT"
SQ SEQUENCE 372 AA; 41218 MW; C983B28F92B519EC CRC64;
MAEKLHISVL CGGQSTEHEI SIQSAKNIVN TLDAAKYLIS VIFIDHVGRW YLIDQPEMFL
AHSPDHLVKE GSARPITIAF GDAAKPWQSL NGDGRRYSAD CVFPMVHGTQ GEDGALQGLL
ELLNLPYVGA NVQSSAVCME KDLTKTVLRA GGIPVVDWHT LSPRDATEGV YQRLLDRWGT
SELFVKAVSL GSSVATLPVK TETEFTKAVK EVFRYDDRLM VEPRIRGREI ECAVLGNGAP
KASLPGEIIP HHDYYSYDAK YLDPNGATTT TSVDLSESVT KQIQQIAIDA FKMVHCSGMA
RVDFFVTPNN KVLVNEINTI PGFTNISMYP KMWEASGLPC PNLLDQLIEL AIDRHQEQQK
LIRCYEVKAR SL
