DDLA_SALTY
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 03-AUG-2022, entry version 107.
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; Proteobacteria; 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}.
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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; P0A1F0; -.
DR EnsemblBacteria; AAL19334; AAL19334; STM0380.
DR GeneID; 1251899; -.
DR KEGG; stm:STM0380; -.
DR PATRIC; fig|99287.12.peg.403; -.
DR HOGENOM; CLU_039268_0_1_6; -.
DR OMA; IDFFLTD; -.
DR PhylomeDB; P0A1F0; -.
DR BioCyc; SENT99287:STM0380-MON; -.
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; 3.30.1490.20; -; 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; 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
