DDL_AERHH
ID DDL_AERHH Reviewed; 329 AA.
AC A0KKW8;
DT 15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT 12-DEC-2006, sequence version 1.
DT 03-AUG-2022, entry version 95.
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=AHA_2404;
OS Aeromonas hydrophila subsp. hydrophila (strain ATCC 7966 / DSM 30187 / BCRC
OS 13018 / CCUG 14551 / JCM 1027 / KCTC 2358 / NCIMB 9240 / NCTC 8049).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Aeromonadales;
OC Aeromonadaceae; Aeromonas.
OX NCBI_TaxID=380703;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 7966 / DSM 30187 / BCRC 13018 / CCUG 14551 / JCM 1027 / KCTC
RC 2358 / NCIMB 9240 / NCTC 8049;
RX PubMed=16980456; DOI=10.1128/jb.00621-06;
RA Seshadri R., Joseph S.W., Chopra A.K., Sha J., Shaw J., Graf J., Haft D.H.,
RA Wu M., Ren Q., Rosovitz M.J., Madupu R., Tallon L., Kim M., Jin S.,
RA Vuong H., Stine O.C., Ali A., Horneman A.J., Heidelberg J.F.;
RT "Genome sequence of Aeromonas hydrophila ATCC 7966T: jack of all trades.";
RL J. Bacteriol. 188:8272-8282(2006).
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}.
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DR EMBL; CP000462; ABK38135.1; -; Genomic_DNA.
DR RefSeq; WP_011706238.1; NC_008570.1.
DR RefSeq; YP_856919.1; NC_008570.1.
DR PDB; 6LL9; X-ray; 2.70 A; A/B=1-329.
DR PDBsum; 6LL9; -.
DR AlphaFoldDB; A0KKW8; -.
DR SMR; A0KKW8; -.
DR STRING; 380703.AHA_2404; -.
DR EnsemblBacteria; ABK38135; ABK38135; AHA_2404.
DR KEGG; aha:AHA_2404; -.
DR PATRIC; fig|380703.7.peg.2401; -.
DR eggNOG; COG1181; Bacteria.
DR HOGENOM; CLU_039268_0_0_6; -.
DR OMA; IDFFLTD; -.
DR UniPathway; UPA00219; -.
DR Proteomes; UP000000756; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
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; 3.30.1490.20; -; 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..329
FT /note="D-alanine--D-alanine ligase"
FT /id="PRO_1000030422"
FT DOMAIN 120..326
FT /note="ATP-grasp"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 150..205
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 280
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 293
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 293
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 295
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT STRAND 6..9
FT /evidence="ECO:0007829|PDB:6LL9"
FT HELIX 17..31
FT /evidence="ECO:0007829|PDB:6LL9"
FT STRAND 34..36
FT /evidence="ECO:0007829|PDB:6LL9"
FT STRAND 39..43
FT /evidence="ECO:0007829|PDB:6LL9"
FT STRAND 49..54
FT /evidence="ECO:0007829|PDB:6LL9"
FT STRAND 57..59
FT /evidence="ECO:0007829|PDB:6LL9"
FT STRAND 63..67
FT /evidence="ECO:0007829|PDB:6LL9"
FT STRAND 70..73
FT /evidence="ECO:0007829|PDB:6LL9"
FT STRAND 75..79
FT /evidence="ECO:0007829|PDB:6LL9"
FT TURN 84..88
FT /evidence="ECO:0007829|PDB:6LL9"
FT HELIX 90..96
FT /evidence="ECO:0007829|PDB:6LL9"
FT HELIX 97..99
FT /evidence="ECO:0007829|PDB:6LL9"
FT STRAND 102..104
FT /evidence="ECO:0007829|PDB:6LL9"
FT HELIX 107..114
FT /evidence="ECO:0007829|PDB:6LL9"
FT HELIX 116..125
FT /evidence="ECO:0007829|PDB:6LL9"
FT STRAND 141..144
FT /evidence="ECO:0007829|PDB:6LL9"
FT TURN 147..153
FT /evidence="ECO:0007829|PDB:6LL9"
FT STRAND 154..156
FT /evidence="ECO:0007829|PDB:6LL9"
FT STRAND 158..163
FT /evidence="ECO:0007829|PDB:6LL9"
FT STRAND 174..176
FT /evidence="ECO:0007829|PDB:6LL9"
FT HELIX 177..183
FT /evidence="ECO:0007829|PDB:6LL9"
FT TURN 184..187
FT /evidence="ECO:0007829|PDB:6LL9"
FT STRAND 193..196
FT /evidence="ECO:0007829|PDB:6LL9"
FT STRAND 203..211
FT /evidence="ECO:0007829|PDB:6LL9"
FT STRAND 214..217
FT /evidence="ECO:0007829|PDB:6LL9"
FT STRAND 246..248
FT /evidence="ECO:0007829|PDB:6LL9"
FT HELIX 254..270
FT /evidence="ECO:0007829|PDB:6LL9"
FT STRAND 275..283
FT /evidence="ECO:0007829|PDB:6LL9"
FT STRAND 289..297
FT /evidence="ECO:0007829|PDB:6LL9"
FT STRAND 301..303
FT /evidence="ECO:0007829|PDB:6LL9"
FT HELIX 305..313
FT /evidence="ECO:0007829|PDB:6LL9"
FT HELIX 318..324
FT /evidence="ECO:0007829|PDB:6LL9"
SQ SEQUENCE 329 AA; 36343 MW; BC5B5747304BD548 CRC64;
MKNIHVLLLC GGGGSEHEVS LRSANFLEKQ LSLLPGVEVT RVEMFADRWL SADGRECKLG
LDKLLSFDSV ARPVDYVVPC IHGYPGETGD LQSFLELAGL PYLGCDAEAS KICFNKISTK
LWLSAIGIPN TPYLFLTEQN DAALSEAKAA LAKWGKVFIK AASQGSSVGC YSASNEADLV
KGIADAFGYS EQVLIEKAVK PRELEVAVYQ YGDELVATYP GEICVPQDKF YTYEEKYSSA
SHTETALRAE GLTQAQADAI HEYALKAFRQ LKLTHLSRID FFLTEEGEIL LNEINTFPGM
TSISMFPKLL EHHGHRFADY LEQILRKAV
