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Protein

Diaminopropionate ammonia-lyase

Gene

ygeX

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the alpha,beta-elimination reaction of both L- and D-alpha,beta-diaminopropionate (DAP) to form pyruvate and ammonia. In vitro the D-isomer of serine is degraded to pyruvate, though very poorly; other amino acids (L-serine, D- and L-threonine, D- and L-beta-Cl-alanine) are not substrates. In vivo allows poor growth on L-DAP or a DL-DAP mixture but not on D-DAP alone, this may be due to a poor promoter. DL-DAP is toxic in the absence of this enzyme, it may inhibit enzymes involved in the synthesis of pyruvate and aspartate, as well as amino acids derived from them.4 Publications

Catalytic activityi

2,3-diaminopropionate + H2O = pyruvate + 2 NH3.1 Publication

Cofactori

pyridoxal 5'-phosphate2 PublicationsNote: Binds 1 pyridoxal phosphate per subunit.2 Publications

Kineticsi

  1. KM=0.10 mM for D-DAP1 Publication
  2. KM=0.048 mM for L-DAP1 Publication
  1. Vmax=48 µmol/min/mg enzyme for D-DAP1 Publication
  2. Vmax=25 µmol/min/mg enzyme for L-DAP1 Publication

pH dependencei

Optimum pH is 8.0.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei77 – 771Proton acceptor; for D-DAP ammonia-lyase activityCurated
Active sitei120 – 1201Proton acceptor; for L-DAP ammonia-lyase activityCurated

GO - Molecular functioni

  • diaminopropionate ammonia-lyase activity Source: EcoCyc
  • pyridoxal phosphate binding Source: EcoCyc

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Ligandi

Pyridoxal phosphate

Enzyme and pathway databases

BioCyciEcoCyc:G7490-MONOMER.
ECOL316407:JW2839-MONOMER.
MetaCyc:G7490-MONOMER.
SABIO-RKP66899.

Names & Taxonomyi

Protein namesi
Recommended name:
Diaminopropionate ammonia-lyase (EC:4.3.1.15)
Short name:
DAPAL
Alternative name(s):
2,3-diaminopropionate ammonia-lyase
Alpha,beta-diaminopropionate ammonia-lyase
Diaminopropionatase
Gene namesi
Name:ygeX
Ordered Locus Names:b2871, JW2839
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13054. ygeX.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Pathology & Biotechi

Disruption phenotypei

No growth on minimal medium plus DL-DAP; growth can be restored by a mix of 8 amino acids (Arg, Asn, Cys, Glu, Ile, Leu, Met and Thr).1 Publication

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi77 – 771K → H or R: No longer binds cofactor, loss of enzymatic activity. 1 Publication
Mutagenesisi120 – 1201D → N: No activity on D-DAP, 150-fold reduced catalytic efficiency for L-DAP; alters substrate stereospecificity. 1 Publication
Mutagenesisi189 – 1891D → N: 10000-fold reduced catalytic efficiency for both D- and L-DAP. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 398398Diaminopropionate ammonia-lyasePRO_0000185590Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei77 – 771N6-(pyridoxal phosphate)lysine
Disulfide bondi265 ↔ 2911 Publication

Keywords - PTMi

Disulfide bond

Proteomic databases

PaxDbiP66899.
PRIDEiP66899.

Expressioni

Inductioni

Slightly induced by DL-DAP.1 Publication

Interactioni

Subunit structurei

Homodimer.3 Publications

Protein-protein interaction databases

BioGridi4262322. 13 interactions.
IntActiP66899. 1 interaction.
STRINGi511145.b2871.

Structurei

Secondary structure

1
398
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi8 – 125Combined sources
Helixi22 – 243Combined sources
Helixi26 – 3611Combined sources
Beta strandi47 – 493Combined sources
Helixi51 – 577Combined sources
Beta strandi59 – 668Combined sources
Helixi67 – 693Combined sources
Turni71 – 744Combined sources
Helixi78 – 9316Combined sources
Helixi97 – 993Combined sources
Helixi102 – 1076Combined sources
Beta strandi114 – 1185Combined sources
Helixi122 – 13413Combined sources
Beta strandi137 – 1426Combined sources
Helixi148 – 1558Combined sources
Turni156 – 1583Combined sources
Beta strandi160 – 1634Combined sources
Helixi168 – 18215Combined sources
Helixi197 – 21923Combined sources
Beta strandi225 – 2306Combined sources
Beta strandi232 – 2343Combined sources
Helixi235 – 24814Combined sources
Helixi250 – 2523Combined sources
Beta strandi254 – 2607Combined sources
Helixi261 – 2633Combined sources
Helixi265 – 2728Combined sources
Helixi296 – 30510Combined sources
Beta strandi308 – 3125Combined sources
Helixi315 – 32511Combined sources
Helixi338 – 35215Combined sources
Helixi356 – 3627Combined sources
Beta strandi370 – 3756Combined sources
Beta strandi379 – 3813Combined sources
Helixi382 – 3898Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4D9GX-ray2.45A/B1-398[»]
4D9IX-ray2.00A/B1-398[»]
4D9KX-ray2.19A/B/C/D1-398[»]
4D9MX-ray2.50A/B1-398[»]
4D9NX-ray2.50A/B1-398[»]
ProteinModelPortaliP66899.
SMRiP66899. Positions 2-397.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4107RCH. Bacteria.
COG1171. LUCA.
HOGENOMiHOG000220594.
InParanoidiP66899.
KOiK01751.
OMAiSVVYMPK.
OrthoDBiEOG6GTZFV.
PhylomeDBiP66899.

Family and domain databases

InterProiIPR010081. DiNH2opropionate_NH3_lyase.
IPR019871. DiNH2propionate_NH3-lyase_sub.
IPR001926. TrpB-like_PLP-dep.
[Graphical view]
PfamiPF00291. PALP. 1 hit.
[Graphical view]
SUPFAMiSSF53686. SSF53686. 1 hit.
TIGRFAMsiTIGR03528. 2_3_DAP_am_ly. 1 hit.
TIGR01747. diampropi_NH3ly. 1 hit.

Sequencei

Sequence statusi: Complete.

P66899-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSVFSLKIDI ADNKFFNGET SPLFSQSQAK LARQFHQKIA GYRPTPLCAL
60 70 80 90 100
DDLANLFGVK KILVKDESKR FGLNAFKMLG GAYAIAQLLC EKYHLDIETL
110 120 130 140 150
SFEHLKNAIG EKMTFATTTD GNHGRGVAWA AQQLGQNAVI YMPKGSAQER
160 170 180 190 200
VDAILNLGAE CIVTDMNYDD TVRLTMQHAQ QHGWEVVQDT AWEGYTKIPT
210 220 230 240 250
WIMQGYATLA DEAVEQMREM GVTPTHVLLQ AGVGAMAGGV LGYLVDVYSP
260 270 280 290 300
QNLHSIIVEP DKADCIYRSG VKGDIVNVGG DMATIMAGLA CGEPNPLGWE
310 320 330 340 350
ILRNCATQFI SCQDSVAALG MRVLGNPYGN DPRIISGESG AVGLGVLAAV
360 370 380 390
HYHPQRQSLM EKLALNKDAV VLVISTEGDT DVKHYREVVW EGKHAVAP
Length:398
Mass (Da):43,328
Last modified:October 11, 2004 - v1
Checksum:iFAF1277E86D60232
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U28375 Genomic DNA. Translation: AAA83052.1.
U00096 Genomic DNA. Translation: AAC75909.1.
AP009048 Genomic DNA. Translation: BAE76937.1.
PIRiG65070.
RefSeqiNP_417347.1. NC_000913.3.
WP_000110493.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75909; AAC75909; b2871.
BAE76937; BAE76937; BAE76937.
GeneIDi947012.
KEGGiecj:JW2839.
eco:b2871.
PATRICi32121152. VBIEscCol129921_2964.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U28375 Genomic DNA. Translation: AAA83052.1.
U00096 Genomic DNA. Translation: AAC75909.1.
AP009048 Genomic DNA. Translation: BAE76937.1.
PIRiG65070.
RefSeqiNP_417347.1. NC_000913.3.
WP_000110493.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4D9GX-ray2.45A/B1-398[»]
4D9IX-ray2.00A/B1-398[»]
4D9KX-ray2.19A/B/C/D1-398[»]
4D9MX-ray2.50A/B1-398[»]
4D9NX-ray2.50A/B1-398[»]
ProteinModelPortaliP66899.
SMRiP66899. Positions 2-397.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262322. 13 interactions.
IntActiP66899. 1 interaction.
STRINGi511145.b2871.

Proteomic databases

PaxDbiP66899.
PRIDEiP66899.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75909; AAC75909; b2871.
BAE76937; BAE76937; BAE76937.
GeneIDi947012.
KEGGiecj:JW2839.
eco:b2871.
PATRICi32121152. VBIEscCol129921_2964.

Organism-specific databases

EchoBASEiEB2866.
EcoGeneiEG13054. ygeX.

Phylogenomic databases

eggNOGiENOG4107RCH. Bacteria.
COG1171. LUCA.
HOGENOMiHOG000220594.
InParanoidiP66899.
KOiK01751.
OMAiSVVYMPK.
OrthoDBiEOG6GTZFV.
PhylomeDBiP66899.

Enzyme and pathway databases

BioCyciEcoCyc:G7490-MONOMER.
ECOL316407:JW2839-MONOMER.
MetaCyc:G7490-MONOMER.
SABIO-RKP66899.

Miscellaneous databases

PROiP66899.

Family and domain databases

InterProiIPR010081. DiNH2opropionate_NH3_lyase.
IPR019871. DiNH2propionate_NH3-lyase_sub.
IPR001926. TrpB-like_PLP-dep.
[Graphical view]
PfamiPF00291. PALP. 1 hit.
[Graphical view]
SUPFAMiSSF53686. SSF53686. 1 hit.
TIGRFAMsiTIGR03528. 2_3_DAP_am_ly. 1 hit.
TIGR01747. diampropi_NH3ly. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  2. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. "Gene cloning, purification, and characterization of 2,3-diaminopropionate ammonia-lyase from Escherichia coli."
    Uo T., Yoshimura T., Nishiyama T., Esaki N.
    Biosci. Biotechnol. Biochem. 66:2639-2644(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, ACTIVE SITE, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATES, SUBUNIT.
  4. "Characterization of recombinant diaminopropionate ammonia-lyase from Escherichia coli and Salmonella typhimurium."
    Khan F., Jala V.R., Rao N.A., Savithri H.S.
    Biochem. Biophys. Res. Commun. 306:1083-1088(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, COFACTOR, SUBUNIT.
  5. "Functional analysis of the genes encoding diaminopropionate ammonia lyase in Escherichia coli and Salmonella enterica serovar Typhimurium."
    Kalyani J.N., Ramachandra N., Kachroo A.H., Mahadevan S., Savithri H.S.
    J. Bacteriol. 194:5604-5612(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INDUCTION, DISRUPTION PHENOTYPE.
    Strain: K12.
  6. "Crystal structure of Escherichia coli diaminopropionate ammonia-lyase reveals mechanism of enzyme activation and catalysis."
    Bisht S., Rajaram V., Bharath S.R., Kalyani J.N., Khan F., Rao A.N., Savithri H.S., Murthy M.R.
    J. Biol. Chem. 287:20369-20381(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) ALONE AND IN COMPLEX WITH SUBSTRATE, FUNCTION, REACTION MECHANISM, COFACTOR, ACTIVE SITE, SUBUNIT, DISULFIDE BOND, MUTAGENESIS OF LYS-77; ASP-120 AND ASP-189.

Entry informationi

Entry nameiDPAL_ECOLI
AccessioniPrimary (citable) accession number: P66899
Secondary accession number(s): Q2M9W9, Q46804
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 11, 2004
Last sequence update: October 11, 2004
Last modified: June 8, 2016
This is version 85 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.