ID A0A6F8YQ44_9ACTN Unreviewed; 343 AA.
AC A0A6F8YQ44;
DT 12-AUG-2020, integrated into UniProtKB/TrEMBL.
DT 12-AUG-2020, sequence version 1.
DT 28-JAN-2026, entry version 20.
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 ORFNames=Psuf_054820 {ECO:0000313|EMBL:BCB88169.1};
OS Phytohabitans suffuscus.
OC Bacteria; Bacillati; Actinomycetota; Actinomycetes; Micromonosporales;
OC Micromonosporaceae.
OX NCBI_TaxID=624315 {ECO:0000313|EMBL:BCB88169.1, ECO:0000313|Proteomes:UP000503011};
RN [1] {ECO:0000313|EMBL:BCB88169.1, ECO:0000313|Proteomes:UP000503011}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=NBRC 105367 {ECO:0000313|EMBL:BCB88169.1,
RC ECO:0000313|Proteomes:UP000503011};
RA Komaki H., Tamura T.;
RT "Whole genome shotgun sequence of Phytohabitans suffuscus NBRC 105367.";
RL Submitted (MAR-2020) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:BCB88169.1, ECO:0000313|Proteomes:UP000503011}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=NBRC 105367 {ECO:0000313|EMBL:BCB88169.1,
RC ECO:0000313|Proteomes:UP000503011};
RA Ichikawa N., Kimura A., Kitahashi Y., Uohara A.;
RL Submitted (MAR-2020) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Cell wall formation. {ECO:0000256|HAMAP-Rule:MF_00047}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2 D-alanine + ATP = D-alanyl-D-alanine + ADP + phosphate +
CC H(+); Xref=Rhea:RHEA:11224, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:57416, ChEBI:CHEBI:57822,
CC ChEBI:CHEBI:456216; EC=6.3.2.4; Evidence={ECO:0000256|HAMAP-
CC 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 -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000256|ARBA:ARBA00001936};
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; AP022871; BCB88169.1; -; Genomic_DNA.
DR RefSeq; WP_173159471.1; NZ_AP022871.1.
DR AlphaFoldDB; A0A6F8YQ44; -.
DR KEGG; psuu:Psuf_054820; -.
DR UniPathway; UPA00219; -.
DR Proteomes; UP000503011; Chromosome.
DR GO; GO:0005829; C:cytosol; IEA:TreeGrafter.
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 FunFam; 3.30.470.20:FF:000008; D-alanine--D-alanine ligase; 1.
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 InterPro; IPR058165; VanA-like.
DR NCBIfam; TIGR01205; D_ala_D_alaTIGR; 1.
DR NCBIfam; NF000206; D_ala_D_lac; 1.
DR NCBIfam; NF002528; PRK01966.1-4; 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 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|HAMAP-Rule:MF_00047};
KW Ligase {ECO:0000256|ARBA:ARBA00022598, ECO:0000256|HAMAP-Rule:MF_00047};
KW Magnesium {ECO:0000256|ARBA:ARBA00022842, ECO:0000256|PIRSR:PIRSR039102-3};
KW Manganese {ECO:0000256|ARBA:ARBA00023211, ECO:0000256|PIRSR:PIRSR039102-3};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723,
KW ECO:0000256|PIRSR:PIRSR039102-3};
KW Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741,
KW ECO:0000256|PIRSR:PIRSR039102-2};
KW Peptidoglycan synthesis {ECO:0000256|ARBA:ARBA00022984, ECO:0000256|HAMAP-
KW Rule:MF_00047}; Reference proteome {ECO:0000313|Proteomes:UP000503011}.
FT DOMAIN 137..338
FT /note="ATP-grasp"
FT /evidence="ECO:0000259|PROSITE:PS50975"
FT ACT_SITE 16
FT /evidence="ECO:0000256|PIRSR:PIRSR039102-1"
FT ACT_SITE 177
FT /evidence="ECO:0000256|PIRSR:PIRSR039102-1"
FT ACT_SITE 316
FT /evidence="ECO:0000256|PIRSR:PIRSR039102-1"
FT BINDING 133
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|PIRSR:PIRSR039102-2"
FT BINDING 169..171
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|PIRSR:PIRSR039102-2"
FT BINDING 177..178
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|PIRSR:PIRSR039102-2"
FT BINDING 207..214
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|PIRSR:PIRSR039102-2"
FT BINDING 292
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000256|PIRSR:PIRSR039102-3"
FT BINDING 304..305
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|PIRSR:PIRSR039102-2"
FT BINDING 305
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|PIRSR:PIRSR039102-3"
FT BINDING 305
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000256|PIRSR:PIRSR039102-3"
FT BINDING 307
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|PIRSR:PIRSR039102-3"
SQ SEQUENCE 343 AA; 37004 MW; 9BC88E27D7967252 CRC64;
MSRPRVAVLF GGCSEEHDVS VKSAMEIAAS IDTKRYEPIY VGITKSGVWK ICERPSAQWE
NDDCRRAVIS PDKETHGLLA VENGECRTVH VDAVFPVLHG RSGEDGAVQG LLELSGIPYV
GCDIQSSAIC MDKSLAYIVA RSAGIETPEF SVLHGTDLAV PDELTYPVFV KPARSGSSFG
VRRVDGADGL DDAVAAARQY DDKVLIEQAV TGTEVGCAVL GNGSELVVGE VDQITLRHGI
FRIHQEAEPE KGSENAVITV PADLPEAKRE QIQETAKSIY IALGCKGLSR VDMFLREDGS
IVLNEVNTLP GFTSYSRYPR MMAAAGISLS ELIDRYISLS TGR
//
