Reviewed, UniProtKB/Swiss-Prot A5FUL3 (DDL_ACICJ)

Names and origin

Protein names

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

Gene names

Name:	ddl
Ordered Locus Names:	Acry_0066

Organism

Acidiphilium cryptum (strain JF-5) [Complete proteome] [HAMAP]

Taxonomic identifier

349163 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Alphaproteobacteria › Rhodospirillales › Acetobacteraceae › Acidiphilium

Protein attributes

Sequence length	301 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Inferred from homology.

General annotation (Comments)

Function	Cell wall formation By similarity.
Catalytic activity	ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine.
Cofactor	Binds 2 magnesium or manganese ions per subunit By similarity.
Pathway	Cell wall biogenesis; peptidoglycan biosynthesis.
Subcellular location	CytoplasmBy 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: HAMAP
Molecular function	ATP binding Inferred from electronic annotation. Source: InterPro 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 – 301	301	D-alanine--D-alanine ligase		PRO_0000341043
Regions
	Domain	102 – 295	194	ATP-grasp
	Nucleotide binding	128 – 181	54	ATP By similarity
Sites
	Metal binding	248	1	Magnesium or manganese 1 By similarity
	Metal binding	262	1	Magnesium or manganese 1 By similarity
	Metal binding	262	1	Magnesium or manganese 2 By similarity
	Metal binding	264	1	Magnesium or manganese 2 By similarity

Sequences

	Sequence		Length	Mass (Da)
	A5FUL3-1 [UniParc]. Last modified June 12, 2007. Version 1. Checksum: F822B442B250D7E6	FASTA	301	32,139
	10 20 30 40 50 60 MKRVAVLLGG ISEEREVSLA SGRQVAAALR KAGYDVFEIE VGADLGAVIA ALTPAPDAVF 70 80 90 100 110 120 NALHGRFGED GTIQGVLDYM GIPYTHSGVR ASSMAMDKGA AKAVFAAAGL PLAQHRIVPL 130 140 150 160 170 180 DELAEADPLP RPYVIKPVNE GSSVGVFILR EGDNRRADIA RAWRHGSVAM TEEYVPGREL 190 200 210 220 230 240 TVSVLEDRAL AVTEIRAEGF YDYTAKYAAG ASRHEIPADV PPSVSARARD VAVAAHRALG 250 260 270 280 290 300 CRGATRSDFR YDDETDRLVL LEVNTQPGMT PTSLLPEQAA HCGIDFPALC AWMVENAACR V

References

[1]

"Complete sequence of chromosome of Acidiphilium cryptum JF-5." Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S., Sims D., Brettin T., Bruce D., Han C., Schmutz J., Larimer F., Land M. , Hauser L., Kyrpides N., Kim E., Magnuson T., Richardson P. Submitted (MAY-2007) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Cross-references

Sequence databases
EMBLGenBankDDBJ	CP000697 Genomic DNA. Translation: ABQ29295.1.
RefSeq	YP_001233214.1.
3D structure databases
ModBase	Search...
Genome annotation databases
GeneID	5162594.
GenomeReviews	Gene locus Acry_0066 in contig CP000697_GR.
KEGG	acr:Acry_0066.
Organism-specific databases
CMR	Search...
Family and domain databases
HAMAP	MF_00047. [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. [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

DDL_ACICJ

Accession

Primary (citable) accession number: A5FUL3

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 10, 2008
Last sequence update:	June 12, 2007
Last modified:	November 25, 2008
This is version 17 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)