RIZA_BACIU
ID RIZA_BACIU Reviewed; 413 AA.
AC B5UAT8;
DT 09-DEC-2015, integrated into UniProtKB/Swiss-Prot.
DT 25-NOV-2008, sequence version 1.
DT 03-AUG-2022, entry version 40.
DE RecName: Full=L-arginine-specific L-amino acid ligase {ECO:0000305};
DE EC=6.3.2.48 {ECO:0000269|PubMed:19352016};
DE AltName: Full=L-amino acid ligase RizA {ECO:0000303|PubMed:19352016};
GN Name=rizA {ECO:0000303|PubMed:19352016};
OS Bacillus subtilis.
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=1423;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-25, FUNCTION,
RP CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, AND SUBUNIT.
RC STRAIN=ATCC 6633 / PCI 219 / NRS 231;
RX PubMed=19352016; DOI=10.1271/bbb.80842;
RA Kino K., Kotanaka Y., Arai T., Yagasaki M.;
RT "A novel L-amino acid ligase from Bacillus subtilis NBRC3134, a
RT microorganism producing peptide-antibiotic rhizocticin.";
RL Biosci. Biotechnol. Biochem. 73:901-907(2009).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).
RC STRAIN=ATCC 6633 / PCI 219 / NRS 231;
RX PubMed=26323296; DOI=10.1107/s2053230x15012698;
RA Kagawa W., Arai T., Ishikura S., Kino K., Kurumizaka H.;
RT "Structure of RizA, an L-amino-acid ligase from Bacillus subtilis.";
RL Acta Crystallogr. F 71:1125-1130(2015).
CC -!- FUNCTION: Catalyzes the synthesis of Arg-Xaa dipeptides in an ATP-
CC dependent manner. Has strict specificity toward arginine as the N-
CC terminal substrate. {ECO:0000269|PubMed:19352016}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=an L-alpha-amino acid + ATP + L-arginine = ADP + H(+) + L-
CC arginyl-L-alpha-amino acid + phosphate; Xref=Rhea:RHEA:44336,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:30616, ChEBI:CHEBI:32682,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:59869, ChEBI:CHEBI:84315,
CC ChEBI:CHEBI:456216; EC=6.3.2.48;
CC Evidence={ECO:0000269|PubMed:19352016};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|PROSITE-ProRule:PRU00409,
CC ECO:0000269|PubMed:19352016};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000255|PROSITE-ProRule:PRU00409,
CC ECO:0000269|PubMed:19352016};
CC Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Evidence={ECO:0000269|PubMed:19352016};
CC Note=Activity is maximal in the presence of Mg(2+). The use of Mn(2+)
CC or Co(2+) decreases ligase activity. {ECO:0000269|PubMed:19352016};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 9.5. {ECO:0000269|PubMed:19352016};
CC Temperature dependence:
CC Optimum temperature is 37 degrees Celsius.
CC {ECO:0000269|PubMed:19352016};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:19352016}.
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DR EMBL; AB437349; BAG72134.1; -; Genomic_DNA.
DR PDB; 4WD3; X-ray; 2.80 A; A/B=1-413.
DR PDBsum; 4WD3; -.
DR AlphaFoldDB; B5UAT8; -.
DR SMR; B5UAT8; -.
DR KEGG; ag:BAG72134; -.
DR BioCyc; MetaCyc:MON-18696; -.
DR BRENDA; 6.3.2.48; 658.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016874; F:ligase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR Gene3D; 3.30.1490.20; -; 1.
DR InterPro; IPR011761; ATP-grasp.
DR InterPro; IPR013815; ATP_grasp_subdomain_1.
DR PROSITE; PS50975; ATP_GRASP; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Cobalt; Direct protein sequencing; Ligase;
KW Magnesium; Manganese; Metal-binding; Nucleotide-binding.
FT CHAIN 1..413
FT /note="L-arginine-specific L-amino acid ligase"
FT /id="PRO_0000434829"
FT DOMAIN 115..312
FT /note="ATP-grasp"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00409"
FT BINDING 141..202
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00409"
FT BINDING 268
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00409"
FT BINDING 268
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00409"
FT BINDING 281
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00409"
FT BINDING 281
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00409"
FT STRAND 2..7
FT /evidence="ECO:0007829|PDB:4WD3"
FT HELIX 12..24
FT /evidence="ECO:0007829|PDB:4WD3"
FT STRAND 28..34
FT /evidence="ECO:0007829|PDB:4WD3"
FT HELIX 36..41
FT /evidence="ECO:0007829|PDB:4WD3"
FT TURN 42..45
FT /evidence="ECO:0007829|PDB:4WD3"
FT STRAND 47..51
FT /evidence="ECO:0007829|PDB:4WD3"
FT HELIX 58..71
FT /evidence="ECO:0007829|PDB:4WD3"
FT STRAND 75..79
FT /evidence="ECO:0007829|PDB:4WD3"
FT HELIX 82..84
FT /evidence="ECO:0007829|PDB:4WD3"
FT HELIX 85..94
FT /evidence="ECO:0007829|PDB:4WD3"
FT STRAND 98..100
FT /evidence="ECO:0007829|PDB:4WD3"
FT HELIX 102..107
FT /evidence="ECO:0007829|PDB:4WD3"
FT HELIX 111..121
FT /evidence="ECO:0007829|PDB:4WD3"
FT STRAND 129..132
FT /evidence="ECO:0007829|PDB:4WD3"
FT HELIX 134..136
FT /evidence="ECO:0007829|PDB:4WD3"
FT HELIX 137..144
FT /evidence="ECO:0007829|PDB:4WD3"
FT STRAND 146..155
FT /evidence="ECO:0007829|PDB:4WD3"
FT TURN 158..160
FT /evidence="ECO:0007829|PDB:4WD3"
FT STRAND 162..164
FT /evidence="ECO:0007829|PDB:4WD3"
FT HELIX 167..175
FT /evidence="ECO:0007829|PDB:4WD3"
FT TURN 177..180
FT /evidence="ECO:0007829|PDB:4WD3"
FT HELIX 181..185
FT /evidence="ECO:0007829|PDB:4WD3"
FT STRAND 190..194
FT /evidence="ECO:0007829|PDB:4WD3"
FT STRAND 199..208
FT /evidence="ECO:0007829|PDB:4WD3"
FT STRAND 211..220
FT /evidence="ECO:0007829|PDB:4WD3"
FT STRAND 232..236
FT /evidence="ECO:0007829|PDB:4WD3"
FT HELIX 244..257
FT /evidence="ECO:0007829|PDB:4WD3"
FT STRAND 262..271
FT /evidence="ECO:0007829|PDB:4WD3"
FT STRAND 277..285
FT /evidence="ECO:0007829|PDB:4WD3"
FT HELIX 290..299
FT /evidence="ECO:0007829|PDB:4WD3"
FT HELIX 303..311
FT /evidence="ECO:0007829|PDB:4WD3"
FT STRAND 324..332
FT /evidence="ECO:0007829|PDB:4WD3"
FT STRAND 336..338
FT /evidence="ECO:0007829|PDB:4WD3"
FT HELIX 345..349
FT /evidence="ECO:0007829|PDB:4WD3"
FT STRAND 354..361
FT /evidence="ECO:0007829|PDB:4WD3"
FT STRAND 378..387
FT /evidence="ECO:0007829|PDB:4WD3"
FT HELIX 388..400
FT /evidence="ECO:0007829|PDB:4WD3"
SQ SEQUENCE 413 AA; 46345 MW; 12A2229ADE4E066B CRC64;
MLRILLINSD KPEPIQFFQK DKETNDSINI SVITRSCYAP LYSHWADHVY IVDDVTDLTV
MKSLMLEILK VGPFDHIVST TEKSILTGGF LRSYFGIAGP GFETALYMTN KLAMKTKLKM
EGIPVADFLC VSQVEDIPAA GEKLGWPIIV KPALGSGALN TFIIHSLDHY EDLYSTSGGL
GELKKNNSLM IAEKCIEMEE FHCDTLYADG EILFVSISKY TVPLLKGMAK IQGSFILSQN
DPVYAEILEL QKSVAQAFRI TDGPGHLEIY RTHSGELIVG EIAMRIGGGG ISRMIEKKFN
ISLWESSLNI SVYRDPNLTV NPIEGTVGYF SLPCRNGTIK EFTPIEEWEK LAGILEVELL
YQEGDVVDEK QSSSFDLARL YFCLENENEV QHLLALVKQT YYLHLTEDHM MNQ
