ID C7M5V7_CAPOD Unreviewed; 325 AA.
AC C7M5V7;
DT 13-OCT-2009, integrated into UniProtKB/TrEMBL.
DT 13-OCT-2009, sequence version 1.
DT 27-MAR-2024, entry version 89.
DE RecName: Full=D-alanine--D-alanine ligase {ECO:0000256|HAMAP-Rule:MF_00047};
DE EC=6.3.2.4 {ECO:0000256|HAMAP-Rule:MF_00047};
DE AltName: Full=D-Ala-D-Ala ligase {ECO:0000256|HAMAP-Rule:MF_00047};
DE AltName: Full=D-alanylalanine synthetase {ECO:0000256|HAMAP-Rule:MF_00047};
GN Name=ddl {ECO:0000256|HAMAP-Rule:MF_00047};
GN OrderedLocusNames=Coch_1370 {ECO:0000313|EMBL:ACU92916.1};
OS Capnocytophaga ochracea (strain ATCC 27872 / DSM 7271 / JCM 12966 / NCTC
OS 12371 / VPI 2845) (Bacteroides ochraceus).
OC Bacteria; Bacteroidota; Flavobacteriia; Flavobacteriales;
OC Flavobacteriaceae; Capnocytophaga.
OX NCBI_TaxID=521097 {ECO:0000313|EMBL:ACU92916.1, ECO:0000313|Proteomes:UP000006650};
RN [1] {ECO:0000313|EMBL:ACU92916.1, ECO:0000313|Proteomes:UP000006650}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 27872 / DSM 7271 / JCM 12966 / VPI 2845
RC {ECO:0000313|Proteomes:UP000006650};
RX PubMed=21304645; DOI=10.4056/sigs.15195;
RA Mavrommatis K., Gronow S., Saunders E., Land M., Lapidus A., Copeland A.,
RA Glavina Del Rio T., Nolan M., Lucas S., Chen F., Tice H., Cheng J.F.,
RA Bruce D., Goodwin L., Pitluck S., Pati A., Ivanova N., Chen A.,
RA Palaniappan K., Chain P., Hauser L., Chang Y.J., Jeffries C.D., Brettin T.,
RA Detter J.C., Han C., Bristow J., Goker M., Rohde M., Eisen J.A.,
RA Markowitz V., Kyrpides N.C., Klenk H.P., Hugenholtz P.;
RT "Complete genome sequence of Capnocytophaga ochracea type strain (VPI
RT 2845).";
RL Stand. Genomic Sci. 1:101-109(2009).
CC -!- FUNCTION: Cell wall formation. {ECO:0000256|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:0000256|HAMAP-Rule:MF_00047};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000256|PIRSR:PIRSR039102-3};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000256|PIRSR:PIRSR039102-3};
CC Note=Binds 2 magnesium or manganese ions per subunit.
CC {ECO:0000256|PIRSR:PIRSR039102-3};
CC -!- PATHWAY: Cell wall biogenesis; peptidoglycan biosynthesis.
CC {ECO:0000256|HAMAP-Rule:MF_00047}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00047}.
CC -!- SIMILARITY: Belongs to the D-alanine--D-alanine ligase family.
CC {ECO:0000256|ARBA:ARBA00010871, ECO:0000256|HAMAP-Rule:MF_00047}.
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DR EMBL; CP001632; ACU92916.1; -; Genomic_DNA.
DR RefSeq; WP_015782507.1; NC_013162.1.
DR AlphaFoldDB; C7M5V7; -.
DR STRING; 521097.Coch_1370; -.
DR GeneID; 29674868; -.
DR KEGG; coc:Coch_1370; -.
DR eggNOG; COG1181; Bacteria.
DR HOGENOM; CLU_039268_1_1_10; -.
DR UniPathway; UPA00219; -.
DR Proteomes; UP000006650; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0008716; F:D-alanine-D-alanine ligase activity; IEA:UniProtKB-UniRule.
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; IEA:UniProtKB-UniRule.
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:SF0; D-ALANINE-D-ALANINE LIGASE FAMILY; 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 3: Inferred from homology;
KW ATP-binding {ECO:0000256|ARBA:ARBA00022840, ECO:0000256|PROSITE-
KW ProRule:PRU00409};
KW Cell shape {ECO:0000256|ARBA:ARBA00022960, ECO:0000256|HAMAP-
KW Rule:MF_00047};
KW Cell wall biogenesis/degradation {ECO:0000256|ARBA:ARBA00023316,
KW ECO:0000256|HAMAP-Rule:MF_00047};
KW Cytoplasm {ECO:0000256|ARBA:ARBA00022490, ECO:0000256|HAMAP-Rule:MF_00047};
KW Ligase {ECO:0000256|ARBA:ARBA00022598, ECO:0000256|HAMAP-Rule:MF_00047};
KW Magnesium {ECO:0000256|PIRSR:PIRSR039102-3};
KW Manganese {ECO:0000256|PIRSR:PIRSR039102-3};
KW Metal-binding {ECO:0000256|PIRSR:PIRSR039102-3};
KW Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741, ECO:0000256|PROSITE-
KW ProRule:PRU00409};
KW Peptidoglycan synthesis {ECO:0000256|ARBA:ARBA00022984, ECO:0000256|HAMAP-
KW Rule:MF_00047}; Reference proteome {ECO:0000313|Proteomes:UP000006650}.
FT DOMAIN 121..320
FT /note="ATP-grasp"
FT /evidence="ECO:0000259|PROSITE:PS50975"
FT BINDING 287
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|PIRSR:PIRSR039102-3"
FT BINDING 287
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000256|PIRSR:PIRSR039102-3"
FT BINDING 289
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|PIRSR:PIRSR039102-3"
SQ SEQUENCE 325 AA; 36262 MW; 51741B31CCAD2224 CRC64;
MKKNIAIIMG GYSNEAPVSL KSAAVVAKNL NQDKYVPYPV RIDRDKWVYV DTQNNEHPID
KNDFSVTVNG RKITFDAVFN AIHGTPGEDG YLQAYFNLIG LPLTGCSMYA SALTFNKRDM
LSVLKPFGIL SAPSYYLNKG EDYNTADIVA KVGLPCFVKA NKSGSSFGVY KVYEEAQLPM
YIDKAFEVDD EILIETFLKG TEISIGVINY RGKIKVLPMT EIVSENDFFD YDAKYNGKSQ
EITPARLSAE MTAKINALAE RVYRLLKMEG FSRSEFIIVG DTPYLLEMNT TPGLSEASLL
PQQAKVAGIS LEELFESEIE RVLNH
//
