DDL_VIBCH
ID DDL_VIBCH Reviewed; 334 AA.
AC Q9KM17;
DT 02-AUG-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 127.
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=VC_A0572;
OS Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae;
OC Vibrio.
OX NCBI_TaxID=243277;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 39315 / El Tor Inaba N16961;
RX PubMed=10952301; DOI=10.1038/35020000;
RA Heidelberg J.F., Eisen J.A., Nelson W.C., Clayton R.A., Gwinn M.L.,
RA Dodson R.J., Haft D.H., Hickey E.K., Peterson J.D., Umayam L.A., Gill S.R.,
RA Nelson K.E., Read T.D., Tettelin H., Richardson D.L., Ermolaeva M.D.,
RA Vamathevan J.J., Bass S., Qin H., Dragoi I., Sellers P., McDonald L.A.,
RA Utterback T.R., Fleischmann R.D., Nierman W.C., White O., Salzberg S.L.,
RA Smith H.O., Colwell R.R., Mekalanos J.J., Venter J.C., Fraser C.M.;
RT "DNA sequence of both chromosomes of the cholera pathogen Vibrio
RT cholerae.";
RL Nature 406:477-483(2000).
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; AE003853; AAF96474.1; -; Genomic_DNA.
DR PIR; A82443; A82443.
DR RefSeq; NP_232962.1; NC_002506.1.
DR RefSeq; WP_000169444.1; NZ_LT906615.1.
DR PDB; 6DGI; X-ray; 2.30 A; A/B=1-334.
DR PDBsum; 6DGI; -.
DR AlphaFoldDB; Q9KM17; -.
DR SMR; Q9KM17; -.
DR STRING; 243277.VC_A0572; -.
DR DNASU; 2612376; -.
DR EnsemblBacteria; AAF96474; AAF96474; VC_A0572.
DR GeneID; 57741973; -.
DR KEGG; vch:VC_A0572; -.
DR PATRIC; fig|243277.26.peg.3199; -.
DR eggNOG; COG1181; Bacteria.
DR HOGENOM; CLU_039268_0_0_6; -.
DR OMA; NTTPGMT; -.
DR BioCyc; VCHO:VCA0572-MON; -.
DR UniPathway; UPA00219; -.
DR Proteomes; UP000000584; Chromosome 2.
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; Ligase; Magnesium; Manganese; Metal-binding; Nucleotide-binding;
KW Peptidoglycan synthesis; Reference proteome.
FT CHAIN 1..334
FT /note="D-alanine--D-alanine ligase"
FT /id="PRO_0000177901"
FT DOMAIN 121..327
FT /note="ATP-grasp"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 151..206
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 281
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 294
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 294
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 296
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT STRAND 4..11
FT /evidence="ECO:0007829|PDB:6DGI"
FT HELIX 17..31
FT /evidence="ECO:0007829|PDB:6DGI"
FT STRAND 37..45
FT /evidence="ECO:0007829|PDB:6DGI"
FT STRAND 48..51
FT /evidence="ECO:0007829|PDB:6DGI"
FT STRAND 56..60
FT /evidence="ECO:0007829|PDB:6DGI"
FT TURN 61..64
FT /evidence="ECO:0007829|PDB:6DGI"
FT STRAND 65..67
FT /evidence="ECO:0007829|PDB:6DGI"
FT STRAND 72..74
FT /evidence="ECO:0007829|PDB:6DGI"
FT STRAND 76..81
FT /evidence="ECO:0007829|PDB:6DGI"
FT TURN 85..90
FT /evidence="ECO:0007829|PDB:6DGI"
FT HELIX 91..99
FT /evidence="ECO:0007829|PDB:6DGI"
FT STRAND 103..105
FT /evidence="ECO:0007829|PDB:6DGI"
FT HELIX 108..115
FT /evidence="ECO:0007829|PDB:6DGI"
FT HELIX 117..126
FT /evidence="ECO:0007829|PDB:6DGI"
FT STRAND 134..137
FT /evidence="ECO:0007829|PDB:6DGI"
FT HELIX 142..155
FT /evidence="ECO:0007829|PDB:6DGI"
FT STRAND 156..162
FT /evidence="ECO:0007829|PDB:6DGI"
FT STRAND 171..174
FT /evidence="ECO:0007829|PDB:6DGI"
FT HELIX 177..179
FT /evidence="ECO:0007829|PDB:6DGI"
FT HELIX 180..188
FT /evidence="ECO:0007829|PDB:6DGI"
FT STRAND 192..198
FT /evidence="ECO:0007829|PDB:6DGI"
FT STRAND 203..212
FT /evidence="ECO:0007829|PDB:6DGI"
FT STRAND 215..218
FT /evidence="ECO:0007829|PDB:6DGI"
FT STRAND 222..225
FT /evidence="ECO:0007829|PDB:6DGI"
FT TURN 229..231
FT /evidence="ECO:0007829|PDB:6DGI"
FT HELIX 234..238
FT /evidence="ECO:0007829|PDB:6DGI"
FT STRAND 245..249
FT /evidence="ECO:0007829|PDB:6DGI"
FT HELIX 255..271
FT /evidence="ECO:0007829|PDB:6DGI"
FT STRAND 276..284
FT /evidence="ECO:0007829|PDB:6DGI"
FT STRAND 290..298
FT /evidence="ECO:0007829|PDB:6DGI"
FT HELIX 306..313
FT /evidence="ECO:0007829|PDB:6DGI"
FT HELIX 318..331
FT /evidence="ECO:0007829|PDB:6DGI"
SQ SEQUENCE 334 AA; 37318 MW; B7581B22D766818B CRC64;
MTKTTILLLC GGGSSEHEIS LVSANYIQQQ LELTPEFHVI RVEMKKEGWF SEQGALVYLD
TNSATLNSDK ASYPIDFVVP CIHGFPGETG DIQSMLELAG IPYLGCGPEA SANSFNKITS
KLWYDALDIP NTPYLFLTQN TPSSIDKAKQ AFGHWGSIFV KAARQGSSVG CYKVTTEDQI
APAIEAAFGF SEQVLVEQAV KPRELEVSAY EMNGKLYISK PGEVIAPEGT FYSYEEKYSA
NSHARTVLEA ENLTEKHKEL IQTYAERVFI HMKLRHLSRI DFFLTQEGQI YLNEVNTFPG
MTPISMFPKM LEHNGHRFSE FLVQCVTNTL VNAK
