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Protein

D-alanine--D-alanine ligase A

Gene

ddlA

Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Cell wall formation.

Catalytic activityi

ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine.

Cofactori

Mg2+By similarity, Mn2+By similarityNote: Binds 2 magnesium or manganese ions per subunit.By similarity

Pathwayi: peptidoglycan biosynthesis

This protein is involved in the pathway peptidoglycan biosynthesis, which is part of Cell wall biogenesis.
View all proteins of this organism that are known to be involved in the pathway peptidoglycan biosynthesis and in Cell wall biogenesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi302Magnesium or manganese 1By similarity1
Metal bindingi315Magnesium or manganese 1By similarity1
Metal bindingi315Magnesium or manganese 2By similarity1
Metal bindingi317Magnesium or manganese 2By similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi175 – 230ATPBy similarityAdd BLAST56

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionLigase
Biological processCell shape, Cell wall biogenesis/degradation, Peptidoglycan synthesis
LigandATP-binding, Magnesium, Manganese, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciSENT99287:G1FZD-385-MONOMER
UniPathwayiUPA00219

Names & Taxonomyi

Protein namesi
Recommended name:
D-alanine--D-alanine ligase A (EC:6.3.2.4)
Alternative name(s):
D-Ala-D-Ala ligase A
D-alanylalanine synthetase A
Gene namesi
Name:ddlA
Ordered Locus Names:STM0380
OrganismiSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Taxonomic identifieri99287 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeSalmonella
Proteomesi
  • UP000001014 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00001778682 – 364D-alanine--D-alanine ligase AAdd BLAST363

Proteomic databases

PaxDbiP0A1F0
PRIDEiP0A1F0

Interactioni

Protein-protein interaction databases

STRINGi99287.STM0380

Structurei

Secondary structure

1364
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi4 – 11Combined sources8
Helixi17 – 30Combined sources14
Turni33 – 35Combined sources3
Beta strandi36 – 43Combined sources8
Beta strandi49 – 52Combined sources4
Beta strandi54 – 60Combined sources7
Turni64 – 66Combined sources3
Beta strandi75 – 78Combined sources4
Beta strandi83 – 85Combined sources3
Beta strandi87 – 89Combined sources3
Turni90 – 92Combined sources3
Beta strandi100 – 104Combined sources5
Turni109 – 112Combined sources4
Helixi115 – 122Combined sources8
Beta strandi127 – 129Combined sources3
Helixi132 – 139Combined sources8
Helixi141 – 150Combined sources10
Beta strandi158 – 162Combined sources5
Turni163 – 165Combined sources3
Helixi166 – 168Combined sources3
Helixi171 – 178Combined sources8
Beta strandi180 – 186Combined sources7
Turni191 – 194Combined sources4
Beta strandi196 – 200Combined sources5
Helixi201 – 214Combined sources14
Beta strandi216 – 222Combined sources7
Beta strandi226 – 238Combined sources13
Beta strandi240 – 248Combined sources9
Turni257 – 260Combined sources4
Helixi262 – 265Combined sources4
Beta strandi267 – 271Combined sources5
Helixi276 – 292Combined sources17
Beta strandi297 – 305Combined sources9
Beta strandi311 – 319Combined sources9
Helixi327 – 333Combined sources7
Turni334 – 336Combined sources3
Helixi339 – 359Combined sources21

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3I12X-ray2.20A/B/C/D1-364[»]
3Q1KX-ray2.20A/B/C/D1-364[»]
ProteinModelPortaliP0A1F0
SMRiP0A1F0
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A1F0

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini145 – 348ATP-graspAdd BLAST204

Sequence similaritiesi

Belongs to the D-alanine--D-alanine ligase family.Curated

Phylogenomic databases

eggNOGiENOG4105CPF Bacteria
COG1181 LUCA
HOGENOMiHOG000011593
KOiK01921
OMAiRCDFFVI
PhylomeDBiP0A1F0

Family and domain databases

Gene3Di3.30.1490.20, 1 hit
HAMAPiMF_00047 Dala_Dala_lig, 1 hit
InterProiView protein in InterPro
IPR011761 ATP-grasp
IPR013815 ATP_grasp_subdomain_1
IPR000291 D-Ala_lig_Van_CS
IPR005905 D_ala_D_ala
IPR011095 Dala_Dala_lig_C
IPR011127 Dala_Dala_lig_N
IPR016185 PreATP-grasp_dom_sf
PfamiView protein in Pfam
PF07478 Dala_Dala_lig_C, 1 hit
PF01820 Dala_Dala_lig_N, 1 hit
PIRSFiPIRSF039102 Ddl/VanB, 1 hit
SUPFAMiSSF52440 SSF52440, 1 hit
TIGRFAMsiTIGR01205 D_ala_D_alaTIGR, 1 hit
PROSITEiView protein in PROSITE
PS50975 ATP_GRASP, 1 hit
PS00843 DALA_DALA_LIGASE_1, 1 hit
PS00844 DALA_DALA_LIGASE_2, 1 hit

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P0A1F0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAKLRVGIVF GGKSAEHEVS LQSAKNIVDA IDKTRFDVVL LGIDKAGQWH
60 70 80 90 100
VNDAENYLQN ADDPAHIALR PSAISLAQVP GKHQHQLINA QNGQPLPTVD
110 120 130 140 150
VIFPIVHGTL GEDGSLQGML RVANLPFVGS DVLSSAACMD KDVAKRLLRD
160 170 180 190 200
AGLNIAPFIT LTRTNRHAFS FAEVESRLGL PLFVKPANQG SSVGVSKVAN
210 220 230 240 250
EAQYQQAVAL AFEFDHKVVV EQGIKGREIE CAVLGNDNPQ ASTCGEIVLN
260 270 280 290 300
SEFYAYDTKY IDDNGAQVVV PAQIPSEVND KIRAIAIQAY QTLGCAGMAR
310 320 330 340 350
VDVFLTADNE VVINEINTLP GFTNISMYPK LWQASGLGYT DLISRLIELA
360
LERHTANNAL KTTM
Length:364
Mass (Da):39,357
Last modified:January 23, 2007 - v2
Checksum:i00AB43A06746E276
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural varianti17H → A. 1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M20793 Genomic DNA Translation: AAA27056.1
AE006468 Genomic DNA Translation: AAL19334.1
PIRiA28642 CEEBDT
RefSeqiNP_459375.1, NC_003197.2
WP_001096588.1, NC_003197.2

Genome annotation databases

EnsemblBacteriaiAAL19334; AAL19334; STM0380
GeneIDi1251899
KEGGistm:STM0380
PATRICifig|99287.12.peg.403

Similar proteinsi

Entry informationi

Entry nameiDDLA_SALTY
AccessioniPrimary (citable) accession number: P0A1F0
Secondary accession number(s): P15051
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 1, 2005
Last sequence update: January 23, 2007
Last modified: March 28, 2018
This is version 90 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families
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