Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

D-alanine--D-alanine ligase A

Gene

ddlA

Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-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

Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

Cell shape, Cell wall biogenesis/degradation, Peptidoglycan synthesis

Keywords - Ligandi

ATP-binding, Magnesium, Manganese, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

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

Complete GO annotation...

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
Contains 1 ATP-grasp domain.Curated

Phylogenomic databases

eggNOGiENOG4105CPF. Bacteria.
COG1181. LUCA.
HOGENOMiHOG000011593.
KOiK01921.
OMAiMDKIAMK.
PhylomeDBiP0A1F0.

Family and domain databases

Gene3Di3.30.1490.20. 1 hit.
3.30.470.20. 1 hit.
3.40.50.20. 1 hit.
HAMAPiMF_00047. Dala_Dala_lig. 1 hit.
InterProiIPR011761. ATP-grasp.
IPR013815. ATP_grasp_subdomain_1.
IPR013816. ATP_grasp_subdomain_2.
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.
[Graphical view]
PfamiPF07478. Dala_Dala_lig_C. 1 hit.
PF01820. Dala_Dala_lig_N. 1 hit.
[Graphical view]
PIRSFiPIRSF039102. Ddl/VanB. 1 hit.
SUPFAMiSSF52440. SSF52440. 1 hit.
TIGRFAMsiTIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITEiPS50975. ATP_GRASP. 1 hit.
PS00843. DALA_DALA_LIGASE_1. 1 hit.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view]

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_003197.1.
WP_001096588.1. NC_003197.1.

Genome annotation databases

EnsemblBacteriaiAAL19334; AAL19334; STM0380.
GeneIDi1251899.
KEGGistm:STM0380.
PATRICi32379083. VBISalEnt20916_0403.

Cross-referencesi

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_003197.1.
WP_001096588.1. NC_003197.1.

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...

Protein-protein interaction databases

STRINGi99287.STM0380.

Proteomic databases

PaxDbiP0A1F0.
PRIDEiP0A1F0.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAL19334; AAL19334; STM0380.
GeneIDi1251899.
KEGGistm:STM0380.
PATRICi32379083. VBISalEnt20916_0403.

Phylogenomic databases

eggNOGiENOG4105CPF. Bacteria.
COG1181. LUCA.
HOGENOMiHOG000011593.
KOiK01921.
OMAiMDKIAMK.
PhylomeDBiP0A1F0.

Enzyme and pathway databases

UniPathwayiUPA00219.

Miscellaneous databases

EvolutionaryTraceiP0A1F0.

Family and domain databases

Gene3Di3.30.1490.20. 1 hit.
3.30.470.20. 1 hit.
3.40.50.20. 1 hit.
HAMAPiMF_00047. Dala_Dala_lig. 1 hit.
InterProiIPR011761. ATP-grasp.
IPR013815. ATP_grasp_subdomain_1.
IPR013816. ATP_grasp_subdomain_2.
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.
[Graphical view]
PfamiPF07478. Dala_Dala_lig_C. 1 hit.
PF01820. Dala_Dala_lig_N. 1 hit.
[Graphical view]
PIRSFiPIRSF039102. Ddl/VanB. 1 hit.
SUPFAMiSSF52440. SSF52440. 1 hit.
TIGRFAMsiTIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITEiPS50975. ATP_GRASP. 1 hit.
PS00843. DALA_DALA_LIGASE_1. 1 hit.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDDLA_SALTY
AccessioniPrimary (citable) accession number: P0A1F0
Secondary accession number(s): P15051
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 1, 2005
Last sequence update: January 23, 2007
Last modified: November 2, 2016
This is version 82 of the entry and version 2 of the sequence. [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

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.