Reviewed, UniProtKB/Swiss-Prot Q88EV6 (DDLA_PSEPK)

Names and origin

Protein names

Recommended name:
    D-alanine--D-alanine ligase A
    EC=6.3.2.4
Alternative name(s):
    D-alanylalanine synthetase A
    D-Ala-D-Ala ligase A

Gene names

Name:	ddlA
Ordered Locus Names:	PP_4346

Organism

Pseudomonas putida (strain KT2440) [Complete proteome] [HAMAP]

Taxonomic identifier

160488 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Pseudomonadales › Pseudomonadaceae › Pseudomonas

Protein attributes

Sequence length	352 AA.
Sequence status	Complete.
Protein existence	Inferred from homology.

General annotation (Comments)

Function	Cell wall formation By similarity. 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. HAMAP MF_00047
Pathway	Cell wall biogenesis; peptidoglycan biosynthesis. HAMAP MF_00047
Subcellular location	Cytoplasm By similarity 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	Complete 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: HAMAP 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: HAMAP magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW manganese 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
	Chain	1 – 352	352	D-alanine--D-alanine ligase A HAMAP MF_00047		PRO_0000177857
Regions
	Domain	138 – 341	204	ATP-grasp
	Nucleotide binding	165 – 220	56	ATP By similarity
Sites
	Metal binding	295	1	Magnesium or manganese 1 By similarity
	Metal binding	308	1	Magnesium or manganese 1 By similarity
	Metal binding	308	1	Magnesium or manganese 2 By similarity
	Metal binding	310	1	Magnesium or manganese 2 By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q88EV6-1 [UniParc]. Last modified June 1, 2003. Version 1. Checksum: 51FA8522FD896BB1	FASTA	352	37,805
	10 20 30 40 50 60 MKQNVIALVF GGRSSEHSVA LRSAATIHAA LMALGHRVHC VGIDREGNWR YQGEPCQFPG 70 80 90 100 110 120 AVDRSAPLIS IRPGHRSLSY TTQESGTVEI GIDLLFPALH GRWGEDGTIQ GLAAMCGLPC 130 140 150 160 170 180 VGSGVLGSAM AMDKDVTKRM VQSAGLVVVP WLAMNSMRPW EELVECLGSS TLFVKPATSG 190 200 210 220 230 240 SSIGVSRVSN ALEYAAAFAI AAREDTKVLV EAAVCGREIE CGVLELEEGL MASVVGEIIK 250 260 270 280 290 300 KEGHAYYDYQ AKYDSNSVTG LRVPSLLPPD IVARIQALSV QAFRCLELKG YARVDFFLTE 310 320 330 340 350 EGEIILNEIN TLPGFTSASM YPKMFECSGY PPPKLVGALV EYGLSSASKE RL

References

[1]

"Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440." Nelson K.E., Weinel C., Paulsen I.T., Dodson R.J., Hilbert H., Martins dos Santos V.A.P., Fouts D.E., Gill S.R., Pop M., Holmes M., Brinkac L.M., Beanan M.J., DeBoy R.T., Daugherty S.C., Kolonay J.F., Madupu R., Nelson W.C., White O. , Peterson J.D., Khouri H.M., Hance I., Chris Lee P., Holtzapple E.K., Scanlan D., Tran K., Moazzez A., Utterback T.R., Rizzo M., Lee K., Kosack D., Moestl D., Wedler H., Lauber J., Stjepandic D., Hoheisel J., Straetz M., Heim S., Kiewitz C., Eisen J.A., Timmis K.N., Duesterhoeft A., Tuemmler B., Fraser C.M. Environ. Microbiol. 4:799-808(2002) [PubMed: 12534463] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Cross-references

Sequence databases
EMBL GenBank DDBJ	AE015451 Genomic DNA. Translation: AAN69925.1.
RefSeq	NP_746461.1.
3D structure databases
SMR	Q88EV6. Positions 1-345.
ModBase	Search...
Protein-protein interaction databases
STRING	Q88EV6.
Genome annotation databases
GeneID	1042642.
GenomeReviews	Gene locus PP_4346 in contig AE015451_GR.
KEGG	ppu:PP_4346.
NMPDR	fig|160488.1.peg.4291.
TIGR	PP_4346.
Phylogenomic databases
eggNOG	COG1181.
HOGENOM	HBG427092.
OMA	FTDISMY.
PhylomeDB	Q88EV6.
Family and domain databases
HAMAP	MF_00047. Dala_Dala_lig. [Tree]
InterPro	IPR011761. ATP-grasp. 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:3.30.470.20. ATP_grasp_subdomain_2. 1 hit. G3DSA:3.40.50.20. Pre-ATP_grasp. 1 hit.
Pfam	PF07478. Dala_Dala_lig_C. 1 hit. PF01820. Dala_Dala_lig_N. 1 hit. [Graphical view]
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_PSEPK

Accession

Primary (citable) accession number: Q88EV6

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 15, 2003
Last sequence update:	June 1, 2003
Last modified:	February 9, 2010
This is version 50 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)