DPAL_ECOLI
ID DPAL_ECOLI Reviewed; 398 AA.
AC P66899; Q2M9W9; Q46804;
DT 11-OCT-2004, integrated into UniProtKB/Swiss-Prot.
DT 11-OCT-2004, sequence version 1.
DT 03-AUG-2022, entry version 117.
DE RecName: Full=Diaminopropionate ammonia-lyase;
DE Short=DAPAL;
DE EC=4.3.1.15 {ECO:0000269|PubMed:12596860};
DE AltName: Full=2,3-diaminopropionate ammonia-lyase;
DE AltName: Full=Alpha,beta-diaminopropionate ammonia-lyase;
DE AltName: Full=Diaminopropionatase;
GN Name=ygeX; OrderedLocusNames=b2871, JW2839;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, ACTIVE SITE, BIOPHYSICOCHEMICAL PROPERTIES,
RP SUBSTRATES, AND SUBUNIT.
RX PubMed=12596860; DOI=10.1271/bbb.66.2639;
RA Uo T., Yoshimura T., Nishiyama T., Esaki N.;
RT "Gene cloning, purification, and characterization of 2,3-diaminopropionate
RT ammonia-lyase from Escherichia coli.";
RL Biosci. Biotechnol. Biochem. 66:2639-2644(2002).
RN [4]
RP FUNCTION, COFACTOR, AND SUBUNIT.
RX PubMed=12821154; DOI=10.1016/s0006-291x(03)01100-8;
RA Khan F., Jala V.R., Rao N.A., Savithri H.S.;
RT "Characterization of recombinant diaminopropionate ammonia-lyase from
RT Escherichia coli and Salmonella typhimurium.";
RL Biochem. Biophys. Res. Commun. 306:1083-1088(2003).
RN [5]
RP FUNCTION, INDUCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12;
RX PubMed=22904288; DOI=10.1128/jb.01362-12;
RA Kalyani J.N., Ramachandra N., Kachroo A.H., Mahadevan S., Savithri H.S.;
RT "Functional analysis of the genes encoding diaminopropionate ammonia lyase
RT in Escherichia coli and Salmonella enterica serovar Typhimurium.";
RL J. Bacteriol. 194:5604-5612(2012).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) ALONE AND IN COMPLEX WITH SUBSTRATE,
RP FUNCTION, REACTION MECHANISM, COFACTOR, ACTIVE SITE, SUBUNIT, DISULFIDE
RP BOND, AND MUTAGENESIS OF LYS-77; ASP-120 AND ASP-189.
RX PubMed=22505717; DOI=10.1074/jbc.m112.351809;
RA Bisht S., Rajaram V., Bharath S.R., Kalyani J.N., Khan F., Rao A.N.,
RA Savithri H.S., Murthy M.R.;
RT "Crystal structure of Escherichia coli diaminopropionate ammonia-lyase
RT reveals mechanism of enzyme activation and catalysis.";
RL J. Biol. Chem. 287:20369-20381(2012).
CC -!- FUNCTION: Catalyzes the alpha,beta-elimination reaction of both L- and
CC D-alpha,beta-diaminopropionate (DAP) to form pyruvate and ammonia. In
CC vitro the D-isomer of serine is degraded to pyruvate, though very
CC poorly; other amino acids (L-serine, D- and L-threonine, D- and L-beta-
CC Cl-alanine) are not substrates. In vivo allows poor growth on L-DAP or
CC a DL-DAP mixture but not on D-DAP alone, this may be due to a poor
CC promoter. DL-DAP is toxic in the absence of this enzyme, it may inhibit
CC enzymes involved in the synthesis of pyruvate and aspartate, as well as
CC amino acids derived from them. {ECO:0000269|PubMed:12596860,
CC ECO:0000269|PubMed:12821154, ECO:0000269|PubMed:22505717,
CC ECO:0000269|PubMed:22904288}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(S)-2,3-diaminopropanoate + H(+) + H2O = 2 NH4(+) + pyruvate;
CC Xref=Rhea:RHEA:22084, ChEBI:CHEBI:15361, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:28938, ChEBI:CHEBI:57721; EC=4.3.1.15;
CC Evidence={ECO:0000269|PubMed:12596860};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(R)-2,3-diaminopropanoate + H(+) + H2O = 2 NH4(+) + pyruvate;
CC Xref=Rhea:RHEA:52432, ChEBI:CHEBI:15361, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:28938, ChEBI:CHEBI:136599;
CC EC=4.3.1.15; Evidence={ECO:0000269|PubMed:12596860};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000269|PubMed:12821154, ECO:0000269|PubMed:22505717};
CC Note=Binds 1 pyridoxal phosphate per subunit.
CC {ECO:0000269|PubMed:12821154, ECO:0000269|PubMed:22505717};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.10 mM for D-DAP {ECO:0000269|PubMed:12596860};
CC KM=0.048 mM for L-DAP {ECO:0000269|PubMed:12596860};
CC Vmax=48 umol/min/mg enzyme for D-DAP {ECO:0000269|PubMed:12596860};
CC Vmax=25 umol/min/mg enzyme for L-DAP {ECO:0000269|PubMed:12596860};
CC pH dependence:
CC Optimum pH is 8.0. {ECO:0000269|PubMed:12596860};
CC -!- SUBUNIT: Homodimer. {ECO:0000305|PubMed:12596860,
CC ECO:0000305|PubMed:12821154, ECO:0000305|PubMed:22505717}.
CC -!- INDUCTION: Slightly induced by DL-DAP. {ECO:0000269|PubMed:22904288}.
CC -!- DISRUPTION PHENOTYPE: No growth on minimal medium plus DL-DAP; growth
CC can be restored by a mix of 8 amino acids (Arg, Asn, Cys, Glu, Ile,
CC Leu, Met and Thr). {ECO:0000269|PubMed:22904288}.
CC -!- SIMILARITY: Belongs to the diaminopropionate ammonia-lyase family.
CC {ECO:0000305}.
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DR EMBL; U28375; AAA83052.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75909.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76937.1; -; Genomic_DNA.
DR PIR; G65070; G65070.
DR RefSeq; NP_417347.1; NC_000913.3.
DR RefSeq; WP_000110493.1; NZ_STEB01000001.1.
DR PDB; 4D9G; X-ray; 2.45 A; A/B=1-398.
DR PDB; 4D9I; X-ray; 2.00 A; A/B=1-398.
DR PDB; 4D9K; X-ray; 2.19 A; A/B/C/D=1-398.
DR PDB; 4D9M; X-ray; 2.50 A; A/B=1-398.
DR PDB; 4D9N; X-ray; 2.50 A; A/B=1-398.
DR PDBsum; 4D9G; -.
DR PDBsum; 4D9I; -.
DR PDBsum; 4D9K; -.
DR PDBsum; 4D9M; -.
DR PDBsum; 4D9N; -.
DR AlphaFoldDB; P66899; -.
DR SMR; P66899; -.
DR BioGRID; 4262322; 13.
DR IntAct; P66899; 1.
DR STRING; 511145.b2871; -.
DR jPOST; P66899; -.
DR PaxDb; P66899; -.
DR PRIDE; P66899; -.
DR EnsemblBacteria; AAC75909; AAC75909; b2871.
DR EnsemblBacteria; BAE76937; BAE76937; BAE76937.
DR GeneID; 66673256; -.
DR GeneID; 947012; -.
DR KEGG; ecj:JW2839; -.
DR KEGG; eco:b2871; -.
DR PATRIC; fig|1411691.4.peg.3863; -.
DR EchoBASE; EB2866; -.
DR eggNOG; COG1171; Bacteria.
DR HOGENOM; CLU_021802_8_0_6; -.
DR InParanoid; P66899; -.
DR OMA; VMQGYTA; -.
DR PhylomeDB; P66899; -.
DR BioCyc; EcoCyc:G7490-MON; -.
DR BioCyc; MetaCyc:G7490-MON; -.
DR BRENDA; 4.3.1.15; 2026.
DR SABIO-RK; P66899; -.
DR PRO; PR:P66899; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0008838; F:diaminopropionate ammonia-lyase activity; IDA:EcoCyc.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IDA:EcoCyc.
DR Gene3D; 3.40.50.1100; -; 2.
DR InterPro; IPR010081; DiNH2opropionate_NH3_lyase.
DR InterPro; IPR019871; DiNH2propionate_NH3-lyase_sub.
DR InterPro; IPR001926; PLP-dep.
DR InterPro; IPR036052; Trypto_synt_PLP_dependent.
DR Pfam; PF00291; PALP; 1.
DR SUPFAM; SSF53686; SSF53686; 1.
DR TIGRFAMs; TIGR03528; 2_3_DAP_am_ly; 1.
DR TIGRFAMs; TIGR01747; diampropi_NH3ly; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Disulfide bond; Lyase; Pyridoxal phosphate;
KW Reference proteome.
FT CHAIN 1..398
FT /note="Diaminopropionate ammonia-lyase"
FT /id="PRO_0000185590"
FT ACT_SITE 77
FT /note="Proton acceptor; for D-DAP ammonia-lyase activity"
FT /evidence="ECO:0000305"
FT ACT_SITE 120
FT /note="Proton acceptor; for L-DAP ammonia-lyase activity"
FT /evidence="ECO:0000305"
FT MOD_RES 77
FT /note="N6-(pyridoxal phosphate)lysine"
FT DISULFID 265..291
FT /evidence="ECO:0000269|PubMed:22505717"
FT MUTAGEN 77
FT /note="K->H,R: No longer binds cofactor, loss of enzymatic
FT activity."
FT /evidence="ECO:0000269|PubMed:22505717"
FT MUTAGEN 120
FT /note="D->N: No activity on D-DAP, 150-fold reduced
FT catalytic efficiency for L-DAP; alters substrate
FT stereospecificity."
FT /evidence="ECO:0000269|PubMed:22505717"
FT MUTAGEN 189
FT /note="D->N: 10000-fold reduced catalytic efficiency for
FT both D- and L-DAP."
FT /evidence="ECO:0000269|PubMed:22505717"
FT STRAND 8..12
FT /evidence="ECO:0007829|PDB:4D9I"
FT HELIX 22..24
FT /evidence="ECO:0007829|PDB:4D9K"
FT HELIX 26..36
FT /evidence="ECO:0007829|PDB:4D9I"
FT STRAND 47..49
FT /evidence="ECO:0007829|PDB:4D9I"
FT HELIX 51..57
FT /evidence="ECO:0007829|PDB:4D9I"
FT STRAND 59..66
FT /evidence="ECO:0007829|PDB:4D9I"
FT HELIX 67..69
FT /evidence="ECO:0007829|PDB:4D9I"
FT TURN 71..74
FT /evidence="ECO:0007829|PDB:4D9I"
FT HELIX 81..93
FT /evidence="ECO:0007829|PDB:4D9I"
FT HELIX 97..99
FT /evidence="ECO:0007829|PDB:4D9I"
FT HELIX 102..107
FT /evidence="ECO:0007829|PDB:4D9I"
FT STRAND 114..118
FT /evidence="ECO:0007829|PDB:4D9I"
FT HELIX 122..134
FT /evidence="ECO:0007829|PDB:4D9I"
FT STRAND 137..142
FT /evidence="ECO:0007829|PDB:4D9I"
FT HELIX 148..155
FT /evidence="ECO:0007829|PDB:4D9I"
FT TURN 156..158
FT /evidence="ECO:0007829|PDB:4D9I"
FT STRAND 160..163
FT /evidence="ECO:0007829|PDB:4D9I"
FT HELIX 168..182
FT /evidence="ECO:0007829|PDB:4D9I"
FT HELIX 197..219
FT /evidence="ECO:0007829|PDB:4D9I"
FT STRAND 225..230
FT /evidence="ECO:0007829|PDB:4D9I"
FT STRAND 232..234
FT /evidence="ECO:0007829|PDB:4D9I"
FT HELIX 235..248
FT /evidence="ECO:0007829|PDB:4D9I"
FT HELIX 250..252
FT /evidence="ECO:0007829|PDB:4D9K"
FT STRAND 254..260
FT /evidence="ECO:0007829|PDB:4D9I"
FT HELIX 261..263
FT /evidence="ECO:0007829|PDB:4D9G"
FT HELIX 265..272
FT /evidence="ECO:0007829|PDB:4D9I"
FT HELIX 296..305
FT /evidence="ECO:0007829|PDB:4D9I"
FT STRAND 308..312
FT /evidence="ECO:0007829|PDB:4D9I"
FT HELIX 315..325
FT /evidence="ECO:0007829|PDB:4D9I"
FT HELIX 338..352
FT /evidence="ECO:0007829|PDB:4D9I"
FT HELIX 356..362
FT /evidence="ECO:0007829|PDB:4D9I"
FT STRAND 370..375
FT /evidence="ECO:0007829|PDB:4D9I"
FT STRAND 379..381
FT /evidence="ECO:0007829|PDB:4D9K"
FT HELIX 382..389
FT /evidence="ECO:0007829|PDB:4D9I"
SQ SEQUENCE 398 AA; 43328 MW; FAF1277E86D60232 CRC64;
MSVFSLKIDI ADNKFFNGET SPLFSQSQAK LARQFHQKIA GYRPTPLCAL DDLANLFGVK
KILVKDESKR FGLNAFKMLG GAYAIAQLLC EKYHLDIETL SFEHLKNAIG EKMTFATTTD
GNHGRGVAWA AQQLGQNAVI YMPKGSAQER VDAILNLGAE CIVTDMNYDD TVRLTMQHAQ
QHGWEVVQDT AWEGYTKIPT WIMQGYATLA DEAVEQMREM GVTPTHVLLQ AGVGAMAGGV
LGYLVDVYSP QNLHSIIVEP DKADCIYRSG VKGDIVNVGG DMATIMAGLA CGEPNPLGWE
ILRNCATQFI SCQDSVAALG MRVLGNPYGN DPRIISGESG AVGLGVLAAV HYHPQRQSLM
EKLALNKDAV VLVISTEGDT DVKHYREVVW EGKHAVAP
