Reviewed, UniProtKB/Swiss-Prot Q8ZRU1 (DDLB_SALTY)

Names and origin

Protein names

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

Gene names

Name:	ddlB
Ordered Locus Names:	STM0130

Organism

Salmonella typhimurium [Complete proteome] [HAMAP]

Taxonomic identifier

602 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Salmonella

Protein attributes

Sequence length	306 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
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.
Subunit structure	Monomer By similarity.
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
	Initiator methionine	1	1	Removed By similarity
	Chain	2 – 306	305	D-alanine--D-alanine ligase B		PRO_0000177870
Regions
	Domain	101 – 303	203	ATP-grasp
	Nucleotide binding	134 – 189	56	ATP By similarity
Sites
	Metal binding	257	1	Magnesium or manganese 1 By similarity
	Metal binding	270	1	Magnesium or manganese 1 By similarity
	Metal binding	270	1	Magnesium or manganese 2 By similarity
	Metal binding	272	1	Magnesium or manganese 2 By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q8ZRU1-1 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: AE590226C6D957B6	FASTA	306	32,635
	10 20 30 40 50 60 MADKIAVLLG GTSAERDVSL NSGAAVLAGL REGGINAHPV DPQEVDVAQL KAMGFQKVFI 70 80 90 100 110 120 ALHGRGGEDG TLQGMLELLG LPYTGSGVMA SALSMDKLRS KLLWQGAGLP VAPWVALTRA 130 140 150 160 170 180 EFEKGLSEEQ KARISALGLP LIVKPSREGS SVGMTKVVEE NALQGALSLA FQHDDEILIE 190 200 210 220 230 240 KWLCGPEFTV AIVGEEILPS IRIQPAGTFY DYEAKYLSDE TQYFCPAGLD ASQEAALQSL 250 260 270 280 290 300 VLQAWKALGC TGWGRIDVML DSDGQFYLLE ANTSPGMTSH SLVPMAARQA GMSFSQLVVR ILELAD

References

[1]

"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.

Cross-references

Sequence databases
EMBLGenBankDDBJ	AE008700 Genomic DNA. Translation: AAL19094.1.
RefSeq	NP_459135.1.
3D structure databases
HSSP	HSSP built from PDB template 1IOV based on UniProtKB P07862.
SMR	Q8ZRU1. Positions 1-306.
ModBase	Search...
Genome annotation databases
GeneID	1251648.
GenomeReviews	Gene locus STM0130 in contig AE006468_GR.
KEGG	stm:STM0130.
NMPDR	fig|99287.1.peg.128.
Organism-specific databases
StyGene	ddlB. SG?????.
CMR	Search...
Phylogenomic databases
HOGENOM	Q8ZRU1.
Enzyme and pathway databases
BioCyc	STYP99287:STM0130-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

DDLB_SALTY

Accession

Primary (citable) accession number: Q8ZRU1

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 2, 2002
Last sequence update:	January 23, 2007
Last modified:	November 25, 2008
This is version 50 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

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