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3WO0

Crystal structure of Bacillus subtilis YwfE, an L-amino acid ligase, with bound ADP-Mg-Ala

Functional Information from GO Data
ChainGOidnamespacecontents
A0003824molecular_functioncatalytic activity
A0005524molecular_functionATP binding
A0016874molecular_functionligase activity
A0017000biological_processantibiotic biosynthetic process
A0034026molecular_functionL-amino-acid alpha-ligase activity
A0046872molecular_functionmetal ion binding
Functional Information from PDB Data
site_idAC1
Number of Residues22
DetailsBINDING SITE FOR RESIDUE ADP A 501
ChainResidue
ALYS138
ALEU229
AGLN268
APHE271
AGLU311
AGLU324
AMG502
AMG503
AHOH1001
AHOH1029
AHOH1032
ALYS178
AHOH1033
AHOH1181
AHOH1200
AALA183
ASER184
ASER185
AVAL188
AGLU226
AGLU227
APHE228

site_idAC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG A 502
ChainResidue
AGLU311
AGLU324
AADP501
AMG503
AHOH1001
AHOH1032

site_idAC3
Number of Residues7
DetailsBINDING SITE FOR RESIDUE MG A 503
ChainResidue
ALYS138
AGLU324
AADP501
AMG502
AHOH1029
AHOH1030
AHOH1200

site_idAC4
Number of Residues9
DetailsBINDING SITE FOR RESIDUE ALA A 504
ChainResidue
AGLU273
AHIS309
AGLU311
AARG328
AGLY331
AMET334
AHOH1001
AHOH1003
AHOH1202

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues2
DetailsBINDING: BINDING => ECO:0000269|PubMed:22407814
ChainResidueDetails
AGLU109
ALEU182

site_idSWS_FT_FI2
Number of Residues9
DetailsBINDING: BINDING => ECO:0000269|PubMed:22407814, ECO:0000269|PubMed:24702628
ChainResidueDetails
ALYS138
ALYS178
ASER184
AGLU226
AGLN268
AHIS309
AGLU311
AGLU324
AARG328

site_idSWS_FT_FI3
Number of Residues1
DetailsBINDING: BINDING => ECO:0000269|PubMed:24702628
ChainResidueDetails
AGLU273

site_idSWS_FT_FI4
Number of Residues1
DetailsSITE: Plays a key role in restricting the N-terminal substrate specificity to small amino acids such as L-Ala => ECO:0000269|PubMed:24702628
ChainResidueDetails
ATRP332

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PDB entries from 2024-07-31

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