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P0A1F0

- DDLA_SALTY

UniProt

P0A1F0 - DDLA_SALTY

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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: 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

Binds 2 magnesium or manganese ions per subunit.By similarity

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi302 – 3021Magnesium or manganese 1By similarity
Metal bindingi315 – 3151Magnesium or manganese 1By similarity
Metal bindingi315 – 3151Magnesium or manganese 2By similarity
Metal bindingi317 – 3171Magnesium or manganese 2By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi175 – 23056ATPBy similarityAdd
BLAST

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-HAMAP
  2. D-alanine-D-alanine ligase activity Source: UniProtKB-HAMAP
  3. magnesium ion binding Source: UniProtKB-HAMAP
  4. manganese ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. cell wall organization Source: UniProtKB-KW
  2. peptidoglycan biosynthetic process Source: UniProtKB-HAMAP
  3. regulation of cell shape Source: UniProtKB-KW
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

BioCyciSENT99287:GCTI-381-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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeSalmonella
ProteomesiUP000001014: Chromosome

Subcellular locationi

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 364363D-alanine--D-alanine ligase APRO_0000177868Add
BLAST

Proteomic databases

PaxDbiP0A1F0.
PRIDEiP0A1F0.

Interactioni

Protein-protein interaction databases

STRINGi99287.STM0380.

Structurei

Secondary structure

1
364
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 118
Helixi17 – 3014
Turni33 – 353
Beta strandi36 – 438
Beta strandi49 – 524
Beta strandi54 – 607
Turni64 – 663
Beta strandi75 – 784
Beta strandi83 – 853
Beta strandi87 – 893
Turni90 – 923
Beta strandi100 – 1045
Turni109 – 1124
Helixi115 – 1228
Beta strandi127 – 1293
Helixi132 – 1398
Helixi141 – 15010
Beta strandi158 – 1625
Turni163 – 1653
Helixi166 – 1683
Helixi171 – 1788
Beta strandi180 – 1867
Turni191 – 1944
Beta strandi196 – 2005
Helixi201 – 21414
Beta strandi216 – 2227
Beta strandi226 – 23813
Beta strandi240 – 2489
Turni257 – 2604
Helixi262 – 2654
Beta strandi267 – 2715
Helixi276 – 29217
Beta strandi297 – 3059
Beta strandi311 – 3199
Helixi327 – 3337
Turni334 – 3363
Helixi339 – 35921

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP0A1F0.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini145 – 348204ATP-graspAdd
BLAST

Sequence similaritiesi

Belongs to the D-alanine--D-alanine ligase family.Curated
Contains 1 ATP-grasp domain.Curated

Phylogenomic databases

eggNOGiCOG1181.
HOGENOMiHOG000011593.
KOiK01921.
OMAiQIDVIFP.
OrthoDBiEOG64BQ73.
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.
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]
PANTHERiPTHR23132. PTHR23132. 1 hit.
PfamiPF07478. Dala_Dala_lig_C. 1 hit.
PF01820. Dala_Dala_lig_N. 1 hit.
[Graphical view]
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)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti17 – 171H → A.

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M20793 Genomic DNA. Translation: AAA27056.1.
AE006468 Genomic DNA. Translation: AAL19334.1.
PIRiA28642. CEEBDT.
RefSeqiNP_459375.1. NC_003197.1.

Genome annotation databases

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

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M20793 Genomic DNA. Translation: AAA27056.1 .
AE006468 Genomic DNA. Translation: AAL19334.1 .
PIRi A28642. CEEBDT.
RefSeqi NP_459375.1. NC_003197.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
3I12 X-ray 2.20 A/B/C/D 1-364 [» ]
3Q1K X-ray 2.20 A/B/C/D 1-364 [» ]
ProteinModelPortali P0A1F0.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 99287.STM0380.

Proteomic databases

PaxDbi P0A1F0.
PRIDEi P0A1F0.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAL19334 ; AAL19334 ; STM0380 .
GeneIDi 1251899.
KEGGi stm:STM0380.
PATRICi 32379083. VBISalEnt20916_0403.

Phylogenomic databases

eggNOGi COG1181.
HOGENOMi HOG000011593.
KOi K01921.
OMAi QIDVIFP.
OrthoDBi EOG64BQ73.
PhylomeDBi P0A1F0.

Enzyme and pathway databases

UniPathwayi UPA00219 .
BioCyci SENT99287:GCTI-381-MONOMER.

Miscellaneous databases

EvolutionaryTracei P0A1F0.

Family and domain databases

Gene3Di 3.30.1490.20. 1 hit.
3.30.470.20. 1 hit.
3.40.50.20. 1 hit.
HAMAPi MF_00047. Dala_Dala_lig.
InterProi IPR011761. 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 ]
PANTHERi PTHR23132. PTHR23132. 1 hit.
Pfami PF07478. Dala_Dala_lig_C. 1 hit.
PF01820. Dala_Dala_lig_N. 1 hit.
[Graphical view ]
SUPFAMi SSF52440. SSF52440. 1 hit.
TIGRFAMsi TIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITEi PS50975. ATP_GRASP. 1 hit.
PS00843. DALA_DALA_LIGASE_1. 1 hit.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Isolation, cloning, and sequencing of the Salmonella typhimurium ddlA gene with purification and characterization of its product, D-alanine:D-alanine ligase (ADP forming)."
    Daub E., Zawadzke L.E., Botstein D., Walsh C.T.
    Biochemistry 27:3701-3708(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-36.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: LT2 / SGSC1412 / ATCC 700720.

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: October 29, 2014
This is version 74 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

External Data

Dasty 3