Reviewed, UniProtKB/Swiss-Prot Q5LI31 (DDL_BACFN)

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:	BF0435

Organism

Bacteroides fragilis (strain ATCC 25285 / NCTC 9343) [Complete proteome] [HAMAP]

Taxonomic identifier

272559 [NCBI]

Taxonomic lineage

Bacteria › Bacteroidetes › Bacteroidia › Bacteroidales › Bacteroidaceae › Bacteroides

Protein attributes

Sequence length	324 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 – 324	324	D-alanine--D-alanine ligase		PRO_1000030424
Regions
	Domain	121 – 321	201	ATP-grasp
	Nucleotide binding	149 – 204	56	ATP By similarity
Sites
	Metal binding	275	1	Magnesium or manganese 1 By similarity
	Metal binding	288	1	Magnesium or manganese 1 By similarity
	Metal binding	288	1	Magnesium or manganese 2 By similarity
	Metal binding	290	1	Magnesium or manganese 2 By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q5LI31-1 [UniParc]. Last modified June 21, 2005. Version 1. Checksum: 514769F1E9649728	FASTA	324	36,076
	10 20 30 40 50 60 MKRNIAIVAG GDTSEIVVSL RSAQGIYSFI DKEKYNLYIV EMEGRRWEVQ LQDGSKTPVD 70 80 90 100 110 120 RNDFSFMNGA EKVVFDFAYI TIHGTPGEDG RLQGYFDMIR IPYSCCGVLA AAITYDKFVC 130 140 150 160 170 180 NQYLKAFGVR ISESLLLRQG QAVSDEDVVE KIGLPCFIKP NLGGSSFGVT KVKTREQIQP 190 200 210 220 230 240 AIAKAFSEAE EVMIEAFMGG TELTCGCYKT KEKSVVFPLT EVVTHNEFFD YDAKYNGQVD 250 260 270 280 290 300 EITPARISEE LTRRVQTLTS AIYDILGCSG IIRVDYIITE GEKINLLEVN TTPGMTATSF 310 320 IPQQVRAAGL DIKDVMTDII ENKF

References

[1]

"Extensive DNA inversions in the B. fragilis genome control variable gene expression." Cerdeno-Tarraga A.-M., Patrick S., Crossman L.C., Blakely G., Abratt V., Lennard N., Poxton I., Duerden B., Harris B., Quail M.A., Barron A., Clark L., Corton C., Doggett J., Holden M.T.G., Larke N., Line A., Lord A. , Norbertczak H., Ormond D., Price C., Rabbinowitsch E., Woodward J., Barrell B.G., Parkhill J. Science 307:1463-1465(2005) [PubMed: 15746427] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Cross-references

Sequence databases
EMBLGenBankDDBJ	CR626927 Genomic DNA. Translation: CAH06197.1.
RefSeq	YP_210157.1.
3D structure databases
ModBase	Search...
Genome annotation databases
GeneID	3285190.
GenomeReviews	Gene locus BF0435 in contig CR626927_GR.
KEGG	bfs:BF0435.
Organism-specific databases
CMR	Search...
Phylogenomic databases
HOGENOM	Q5LI31.
Enzyme and pathway databases
BioCyc	BFRA272559:BF0435-MON.
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_BACFN

Accession

Primary (citable) accession number: Q5LI31

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 15, 2008
Last sequence update:	June 21, 2005
Last modified:	November 25, 2008
This is version 32 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)