P0A1F0 (DDLA_SALTY) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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 names

Name:	ddlA
Ordered Locus Names:	STM0380

Organism

Salmonella typhimurium

Taxonomic identifier

90371 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Salmonella

Protein attributes

Sequence length	364 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Cell wall formation. HAMAP MF_00047
Catalytic activity	ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine. HAMAP MF_00047
Cofactor	Binds 2 magnesium or manganese ions per subunit By similarity.
Pathway	Cell wall biogenesis; peptidoglycan biosynthesis. HAMAP MF_00047
Subcellular location	Cytoplasm HAMAP MF_00047.
Sequence similarities	Belongs to the D-alanine--D-alanine ligase family. Contains 1 ATP-grasp domain.

Ontologies

Keywords
Biological process	Cell shape Cell wall biogenesis/degradation Peptidoglycan synthesis
Cellular component	Cytoplasm
Ligand	ATP-binding Magnesium Manganese Metal-binding Nucleotide-binding
Molecular function	Ligase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological process	cellular cell wall organization Inferred from electronic annotation. Source: UniProtKB-KW peptidoglycan biosynthetic process Inferred from electronic annotation. Source: UniProtKB-KW regulation of cell shape Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	cell wall Inferred from electronic annotation. Source: InterPro cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW D-alanine-D-alanine ligase activity Inferred from electronic annotation. Source: EC metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.1

Chain

2 – 364

363

D-alanine--D-alanine ligase A HAMAP MF_00047

PRO_0000177868

Regions

Domain

145 – 348

204

ATP-grasp

Nucleotide binding

175 – 230

56

ATP By similarity

Sites

Metal binding

302

1

Magnesium or manganese 1 By similarity

Metal binding

315

1

Magnesium or manganese 1 By similarity

Metal binding

315

1

Magnesium or manganese 2 By similarity

Metal binding

317

1

Magnesium or manganese 2 By similarity

Natural variations

Natural variant

17

1

H → A.

Secondary structure

1

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364

Helix Strand Turn

Details...

Beta strand

4 – 6

3

Helix

17 – 30

14

Turn

33 – 35

3

Beta strand

36 – 41

6

Beta strand

54 – 60

7

Turn

64 – 66

3

Beta strand

75 – 78

4

Beta strand

84 – 90

7

Turn

120 – 124

5

Helix

132 – 139

8

Helix

141 – 150

10

Beta strand

158 – 162

5

Turn

163 – 165

3

Helix

166 – 168

3

Helix

171 – 177

7

Beta strand

182 – 186

5

Beta strand

196 – 200

5

Helix

201 – 214

14

Beta strand

216 – 221

6

Beta strand

228 – 234

7

Turn

257 – 260

4

Helix

276 – 292

17

Beta strand

299 – 305

7

Beta strand

311 – 318

8

Helix

327 – 333

7

Helix

340 – 359

20

Sequences

	Sequence		Length	Mass (Da)
	P0A1F0 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: 00AB43A06746E276	FASTA	364	39,357
	10 20 30 40 50 60 MAKLRVGIVF GGKSAEHEVS LQSAKNIVDA IDKTRFDVVL LGIDKAGQWH VNDAENYLQN 70 80 90 100 110 120 ADDPAHIALR PSAISLAQVP GKHQHQLINA QNGQPLPTVD VIFPIVHGTL GEDGSLQGML 130 140 150 160 170 180 RVANLPFVGS DVLSSAACMD KDVAKRLLRD AGLNIAPFIT LTRTNRHAFS FAEVESRLGL 190 200 210 220 230 240 PLFVKPANQG SSVGVSKVAN EAQYQQAVAL AFEFDHKVVV EQGIKGREIE CAVLGNDNPQ 250 260 270 280 290 300 ASTCGEIVLN SEFYAYDTKY IDDNGAQVVV PAQIPSEVND KIRAIAIQAY QTLGCAGMAR 310 320 330 340 350 360 VDVFLTADNE VVINEINTLP GFTNISMYPK LWQASGLGYT DLISRLIELA LERHTANNAL KTTM

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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: 2841972] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-36.
[2]	"Complete genome sequence of Salmonella enterica serovar Typhimurium LT2." McClelland M., Sanderson K.E., Spieth J., Clifton S.W., Latreille P., Courtney L., Porwollik S., Ali J., Dante M., Du F., Hou S., Layman D., Leonard S., Nguyen C., Scott K., Holmes A., Grewal N., Mulvaney E. , Ryan E., Sun H., Florea L., Miller W., Stoneking T., Nhan M., Waterston R., Wilson R.K. Nature 413:852-856(2001) [PubMed: 11677609] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: LT2 / SGSC1412 / ATCC 700720.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M20793 Genomic DNA. Translation: AAA27056.1.
AE006468 Genomic DNA. Translation: AAL19334.1.

PIR

CEEBDT. A28642.

RefSeq

NP_459375.1. NC_003197.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

P0A1F0.

ModBase

Search...

Proteomic databases

PRIDE

P0A1F0.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

1251899.

GenomeReviews

Gene locus STM0380 in contig AE006468_GR.

KEGG

stm:STM0380.

PATRIC

32379083. VBISalEnt20916_0403.

Phylogenomic databases

HOGENOM

HBG427092.

OMA

LLHGPFG.

ProtClustDB

PRK01966.

Enzyme and pathway databases

BioCyc

STYP99287:STM0380-MONOMER.

Family and domain databases

HAMAP

MF_00047. Dala_Dala_lig.
[Tree]

InterPro

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.
IPR013817. Pre-ATP_grasp.
IPR016185. PreATP-grasp-like.
[Graphical view]

Gene3D

G3DSA:3.30.1490.20. ATP_grasp_subdomain_1. 1 hit.
G3DSA:3.30.470.20. ATP_grasp_subdomain_2. 1 hit.
G3DSA:3.40.50.20. Pre-ATP_grasp. 1 hit.

KO

K01921.

PANTHER

PTHR23132. PTHR23132. 1 hit.

Pfam

PF07478. Dala_Dala_lig_C. 1 hit.
PF01820. Dala_Dala_lig_N. 1 hit.
[Graphical view]

SUPFAM

SSF52440. PreATP-grasp-like. 1 hit.

TIGRFAMs

TIGR01205. D_ala_D_alaTIGR. 1 hit.

PROSITE

PS50975. ATP_GRASP. 1 hit.
PS00843. DALA_DALA_LIGASE_1. 1 hit.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

DDLA_SALTY

Accession

Primary (citable) accession number: P0A1F0
Secondary accession number(s): P15051

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 1, 2005
Last sequence update:	January 23, 2007
Last modified:	January 25, 2012
This is version 54 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program