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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)DescriptionActionsGraphical viewLength
Active sitei77Proton acceptor; for D-DAP ammonia-lyase activityCurated1
Active sitei120Proton acceptor; for L-DAP ammonia-lyase activityCurated1

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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
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)DescriptionActionsGraphical viewLength
Mutagenesisi77K → H or R: No longer binds cofactor, loss of enzymatic activity. 1 Publication1
Mutagenesisi120D → N: No activity on D-DAP, 150-fold reduced catalytic efficiency for L-DAP; alters substrate stereospecificity. 1 Publication1
Mutagenesisi189D → N: 10000-fold reduced catalytic efficiency for both D- and L-DAP. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001855901 – 398Diaminopropionate ammonia-lyaseAdd BLAST398

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei77N6-(pyridoxal phosphate)lysine1
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 interactors.
IntActiP66899. 1 interactor.
STRINGi511145.b2871.

Structurei

Secondary structure

1398
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi8 – 12Combined sources5
Helixi22 – 24Combined sources3
Helixi26 – 36Combined sources11
Beta strandi47 – 49Combined sources3
Helixi51 – 57Combined sources7
Beta strandi59 – 66Combined sources8
Helixi67 – 69Combined sources3
Turni71 – 74Combined sources4
Helixi78 – 93Combined sources16
Helixi97 – 99Combined sources3
Helixi102 – 107Combined sources6
Beta strandi114 – 118Combined sources5
Helixi122 – 134Combined sources13
Beta strandi137 – 142Combined sources6
Helixi148 – 155Combined sources8
Turni156 – 158Combined sources3
Beta strandi160 – 163Combined sources4
Helixi168 – 182Combined sources15
Helixi197 – 219Combined sources23
Beta strandi225 – 230Combined sources6
Beta strandi232 – 234Combined sources3
Helixi235 – 248Combined sources14
Helixi250 – 252Combined sources3
Beta strandi254 – 260Combined sources7
Helixi261 – 263Combined sources3
Helixi265 – 272Combined sources8
Helixi296 – 305Combined sources10
Beta strandi308 – 312Combined sources5
Helixi315 – 325Combined sources11
Helixi338 – 352Combined sources15
Helixi356 – 362Combined sources7
Beta strandi370 – 375Combined sources6
Beta strandi379 – 381Combined sources3
Helixi382 – 389Combined sources8

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4107RCH. Bacteria.
COG1171. LUCA.
HOGENOMiHOG000220594.
InParanoidiP66899.
KOiK01751.
OMAiSVVYMPK.
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
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262322. 13 interactors.
IntActiP66899. 1 interactor.
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.
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...

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: November 2, 2016
This is version 88 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.