Q3K746 (DDL_PSEPF) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
D-alanine--D-alanine ligase
EC=6.3.2.4

Alternative name(s):
D-Ala-D-Ala ligase
D-alanylalanine synthetase

Gene names

Name:	ddl
Ordered Locus Names:	Pfl01_4671

Organism

Pseudomonas fluorescens (strain Pf0-1) [Complete proteome] [HAMAP]

Taxonomic identifier

205922 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Pseudomonadales › Pseudomonadaceae › Pseudomonas › Pseudomonas fluorescens group › Pseudomonas fluorescens

Protein attributes

Sequence length	324 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Cell wall formation By similarity.
Catalytic activity	ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine. HAMAP-Rule MF_00047
Cofactor	Binds 2 magnesium or manganese ions per subunit By similarity.
Pathway	Cell wall biogenesis; peptidoglycan biosynthesis. HAMAP-Rule MF_00047
Subcellular location	Cytoplasm By similarity.
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	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: HAMAP D-alanine-D-alanine ligase activity Inferred from electronic annotation. Source: HAMAP magnesium ion binding Inferred from electronic annotation. Source: HAMAP manganese ion binding Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 324	324	D-alanine--D-alanine ligase HAMAP-Rule MF_00047		PRO_1000030486
Regions
	Domain	116 – 311	196	ATP-grasp
	Nucleotide binding	142 – 197	56	ATP By similarity
Sites
	Metal binding	265	1	Magnesium or manganese 1 By similarity
	Metal binding	278	1	Magnesium or manganese 1 By similarity
	Metal binding	278	1	Magnesium or manganese 2 By similarity
	Metal binding	280	1	Magnesium or manganese 2 By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q3K746 [UniParc]. Last modified November 8, 2005. Version 1. Checksum: B86436D8182D1BC3	FASTA	324	34,373
	10 20 30 40 50 60 MTAAYANLFS TIAPKDFGRV AVLFGGLSAE REVSLKSGNA VLTALQSAGV DAFGIDVGAD 70 80 90 100 110 120 ILQRLLSEKI DRAFIILHGR GGEDGSMQGL LEVAGIPYTG SGILASALAM DKLRTKQVWH 130 140 150 160 170 180 TLGIPTPRHA VLRSEADCIS AATELGFPLI VKPAHEGSSI GMAKVSSASE LIDAWKAAST 190 200 210 220 230 240 YDSQVLVEQW IHGPEFTIAT LRDQVLPPIA LGTPHTFYDY DAKYIANDTQ YRIPCGLDAA 250 260 270 280 290 300 KEKELMDLTA QACEALGIAG WGRADVMQDA DGKFWFLEVN TAPGMTDHSL VPMAAKAAGL 310 320 DFQQLVLAIL AASVDADGKK EARG

References

[1]

"Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens." Silby M.W., Cerdeno-Tarraga A.M., Vernikos G.S., Giddens S.R., Jackson R.W., Preston G.M., Zhang X.-X., Moon C.D., Gehrig S.M., Godfrey S.A.C., Knight C.G., Malone J.G., Robinson Z., Spiers A.J., Harris S., Challis G.L., Yaxley A.M., Harris D. , Seeger K., Murphy L., Rutter S., Squares R., Quail M.A., Saunders E., Mavromatis K., Brettin T.S., Bentley S.D., Hothersall J., Stephens E., Thomas C.M., Parkhill J., Levy S.B., Rainey P.B., Thomson N.R. Genome Biol. 10:R51.1-R51.16(2009) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: Pf0-1.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP000094 Genomic DNA. Translation: ABA76408.1.
RefSeq	YP_350399.1. NC_007492.2.
3D structure databases
ProteinModelPortal	Q3K746.
SMR	Q3K746. Positions 18-311.
ModBase	Search...
Protein-protein interaction databases
STRING	205922.Pfl01_4671.
2D gel databases
World-2DPAGE	0008:Q3K746.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	ABA76408; ABA76408; Pfl01_4671.
GeneID	3714571.
KEGG	pfo:Pfl01_4671.
PATRIC	19891502. VBIPseFlu44242_4677.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG1181.
HOGENOM	HOG000011592.
KO	K01921.
OMA	WREAARY.
ProtClustDB	PRK01372.
Enzyme and pathway databases
BioCyc	PFLU205922:GJBD-4738-MONOMER.
UniPathway	UPA00219.
Family and domain databases
Gene3D	3.30.1490.20. 1 hit. 3.30.470.20. 2 hits. 3.40.50.20. 1 hit.
HAMAP	MF_00047. Dala_Dala_lig.
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. IPR016185. PreATP-grasp_dom. [Graphical view]
PANTHER	PTHR23132. PTHR23132. 1 hit.
Pfam	PF07478. Dala_Dala_lig_C. 1 hit. PF01820. Dala_Dala_lig_N. 2 hits. [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

DDL_PSEPF

Accession

Primary (citable) accession number: Q3K746

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 15, 2008
Last sequence update:	November 8, 2005
Last modified:	May 1, 2013
This is version 67 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program