ID DDLA_SALTY Reviewed; 364 AA. AC P0A1F0; P15051; DT 01-MAR-2005, integrated into UniProtKB/Swiss-Prot. DT 23-JAN-2007, sequence version 2. DT 27-MAR-2024, entry version 115. DE RecName: Full=D-alanine--D-alanine ligase A; DE EC=6.3.2.4; DE AltName: Full=D-Ala-D-Ala ligase A; DE AltName: Full=D-alanylalanine synthetase A; GN Name=ddlA; OrderedLocusNames=STM0380; OS Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720). OC Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; OC Enterobacteriaceae; Salmonella. OX NCBI_TaxID=99287; RN [1] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 2-36. RX PubMed=2841972; DOI=10.1021/bi00410a027; RA Daub E., Zawadzke L.E., Botstein D., Walsh C.T.; RT "Isolation, cloning, and sequencing of the Salmonella typhimurium ddlA gene RT with purification and characterization of its product, D-alanine:D-alanine RT ligase (ADP forming)."; RL Biochemistry 27:3701-3708(1988). RN [2] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=LT2 / SGSC1412 / ATCC 700720; RX PubMed=11677609; DOI=10.1038/35101614; RA McClelland M., Sanderson K.E., Spieth J., Clifton S.W., Latreille P., RA Courtney L., Porwollik S., Ali J., Dante M., Du F., Hou S., Layman D., RA Leonard S., Nguyen C., Scott K., Holmes A., Grewal N., Mulvaney E., RA Ryan E., Sun H., Florea L., Miller W., Stoneking T., Nhan M., Waterston R., RA Wilson R.K.; RT "Complete genome sequence of Salmonella enterica serovar Typhimurium LT2."; RL Nature 413:852-856(2001). CC -!- FUNCTION: Cell wall formation. 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 -!- 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 -!- SUBCELLULAR LOCATION: Cytoplasm. CC -!- SIMILARITY: Belongs to the D-alanine--D-alanine ligase family. CC {ECO:0000305}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; M20793; AAA27056.1; -; Genomic_DNA. DR EMBL; AE006468; AAL19334.1; -; Genomic_DNA. DR PIR; A28642; CEEBDT. DR RefSeq; NP_459375.1; NC_003197.2. DR RefSeq; WP_001096588.1; NC_003197.2. DR PDB; 3I12; X-ray; 2.20 A; A/B/C/D=1-364. DR PDB; 3Q1K; X-ray; 2.20 A; A/B/C/D=1-364. DR PDBsum; 3I12; -. DR PDBsum; 3Q1K; -. DR AlphaFoldDB; P0A1F0; -. DR SMR; P0A1F0; -. DR STRING; 99287.STM0380; -. DR PaxDb; 99287-STM0380; -. DR GeneID; 1251899; -. DR KEGG; stm:STM0380; -. DR PATRIC; fig|99287.12.peg.403; -. DR HOGENOM; CLU_039268_0_1_6; -. DR OMA; NMHSKYF; -. DR PhylomeDB; P0A1F0; -. DR BioCyc; SENT99287:STM0380-MONOMER; -. DR UniPathway; UPA00219; -. DR EvolutionaryTrace; P0A1F0; -. DR Proteomes; UP000001014; 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; 3.40.50.20; -; 1. DR Gene3D; 3.30.1490.20; ATP-grasp fold, A domain; 1. DR Gene3D; 3.30.470.20; ATP-grasp fold, B domain; 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 NCBIfam; TIGR01205; D_ala_D_alaTIGR; 1. DR PANTHER; PTHR23132; D-ALANINE--D-ALANINE LIGASE; 1. DR PANTHER; PTHR23132:SF25; D-ALANINE--D-ALANINE LIGASE A; 1. DR Pfam; PF07478; Dala_Dala_lig_C; 1. DR Pfam; PF01820; Dala_Dala_lig_N; 1. DR PIRSF; PIRSF039102; Ddl/VanB; 1. DR SUPFAM; SSF56059; Glutathione synthetase ATP-binding domain-like; 1. DR SUPFAM; SSF52440; PreATP-grasp domain; 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; Direct protein sequencing; Ligase; Magnesium; Manganese; KW Metal-binding; Nucleotide-binding; Peptidoglycan synthesis; KW Reference proteome. FT INIT_MET 1 FT /note="Removed" FT /evidence="ECO:0000269|PubMed:2841972" FT CHAIN 2..364 FT /note="D-alanine--D-alanine ligase A" FT /id="PRO_0000177868" FT DOMAIN 145..348 FT /note="ATP-grasp" FT BINDING 175..230 FT /ligand="ATP" FT /ligand_id="ChEBI:CHEBI:30616" FT /evidence="ECO:0000250" FT BINDING 302 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="1" FT /evidence="ECO:0000250" FT BINDING 315 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="1" FT /evidence="ECO:0000250" FT BINDING 315 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="2" FT /evidence="ECO:0000250" FT BINDING 317 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="2" FT /evidence="ECO:0000250" FT VARIANT 17 FT /note="H -> A" FT STRAND 4..11 FT /evidence="ECO:0007829|PDB:3I12" FT HELIX 17..30 FT /evidence="ECO:0007829|PDB:3I12" FT TURN 33..35 FT /evidence="ECO:0007829|PDB:3I12" FT STRAND 36..43 FT /evidence="ECO:0007829|PDB:3I12" FT STRAND 49..52 FT /evidence="ECO:0007829|PDB:3I12" FT STRAND 54..60 FT /evidence="ECO:0007829|PDB:3I12" FT TURN 64..66 FT /evidence="ECO:0007829|PDB:3I12" FT STRAND 75..78 FT /evidence="ECO:0007829|PDB:3I12" FT STRAND 83..85 FT /evidence="ECO:0007829|PDB:3I12" FT STRAND 87..89 FT /evidence="ECO:0007829|PDB:3I12" FT TURN 90..92 FT /evidence="ECO:0007829|PDB:3I12" FT STRAND 100..104 FT /evidence="ECO:0007829|PDB:3I12" FT TURN 109..112 FT /evidence="ECO:0007829|PDB:3I12" FT HELIX 115..122 FT /evidence="ECO:0007829|PDB:3I12" FT STRAND 127..129 FT /evidence="ECO:0007829|PDB:3I12" FT HELIX 132..139 FT /evidence="ECO:0007829|PDB:3I12" FT HELIX 141..150 FT /evidence="ECO:0007829|PDB:3I12" FT STRAND 158..162 FT /evidence="ECO:0007829|PDB:3I12" FT TURN 163..165 FT /evidence="ECO:0007829|PDB:3I12" FT HELIX 166..168 FT /evidence="ECO:0007829|PDB:3I12" FT HELIX 171..178 FT /evidence="ECO:0007829|PDB:3I12" FT STRAND 180..186 FT /evidence="ECO:0007829|PDB:3I12" FT TURN 191..194 FT /evidence="ECO:0007829|PDB:3I12" FT STRAND 196..200 FT /evidence="ECO:0007829|PDB:3I12" FT HELIX 201..214 FT /evidence="ECO:0007829|PDB:3I12" FT STRAND 216..222 FT /evidence="ECO:0007829|PDB:3I12" FT STRAND 226..238 FT /evidence="ECO:0007829|PDB:3I12" FT STRAND 240..248 FT /evidence="ECO:0007829|PDB:3I12" FT TURN 257..260 FT /evidence="ECO:0007829|PDB:3I12" FT HELIX 262..265 FT /evidence="ECO:0007829|PDB:3I12" FT STRAND 267..271 FT /evidence="ECO:0007829|PDB:3I12" FT HELIX 276..292 FT /evidence="ECO:0007829|PDB:3I12" FT STRAND 297..305 FT /evidence="ECO:0007829|PDB:3I12" FT STRAND 311..319 FT /evidence="ECO:0007829|PDB:3I12" FT HELIX 327..333 FT /evidence="ECO:0007829|PDB:3I12" FT TURN 334..336 FT /evidence="ECO:0007829|PDB:3I12" FT HELIX 339..359 FT /evidence="ECO:0007829|PDB:3I12" SQ SEQUENCE 364 AA; 39357 MW; 00AB43A06746E276 CRC64; MAKLRVGIVF GGKSAEHEVS LQSAKNIVDA IDKTRFDVVL LGIDKAGQWH VNDAENYLQN ADDPAHIALR PSAISLAQVP GKHQHQLINA QNGQPLPTVD VIFPIVHGTL GEDGSLQGML RVANLPFVGS DVLSSAACMD KDVAKRLLRD AGLNIAPFIT LTRTNRHAFS FAEVESRLGL PLFVKPANQG SSVGVSKVAN EAQYQQAVAL AFEFDHKVVV EQGIKGREIE CAVLGNDNPQ ASTCGEIVLN SEFYAYDTKY IDDNGAQVVV PAQIPSEVND KIRAIAIQAY QTLGCAGMAR VDVFLTADNE VVINEINTLP GFTNISMYPK LWQASGLGYT DLISRLIELA LERHTANNAL KTTM //