Reviewed, UniProtKB/Swiss-Prot Q83MF7 (DDLB_SHIFL)

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:	SF0089, S0091

Organism

Shigella flexneri [Complete proteome] [HAMAP]

Taxonomic identifier

623 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Shigella

Protein attributes

Sequence length	306 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 – 306	306	D-alanine--D-alanine ligase B		PRO_0000177873
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
Experimental info
	Sequence conflict	65	1	R → P in AAP15635. Ref.2

Sequences

	Sequence		Length	Mass (Da)
	Q83MF7-1 [UniParc]. Last modified June 1, 2003. Version 1. Checksum: A07A81804D4AADB6	FASTA	306	32,822
	10 20 30 40 50 60 MTDKIAVLLG GTSAEREVSL NSGAAVLAGL REGGIDAYPV DPKEVDVTQL KSMGFQKVFI 70 80 90 100 110 120 ALHGRGGEDG TLQGMLELMG LPYTGSGVMA SALSIDKLRS KLLWQGAGLP VAPWVALTRA 130 140 150 160 170 180 EFEKGLSDKQ LAEISALGLP VIVKPSREGS SVGMSKVVAE NALQDALRLA FQHDEEVLIE 190 200 210 220 230 240 KWLSGPEFTV AILGEEILPS IRIQPSGTFY DYEAKYLSDE TQYFCPAGLE ASQEANLQAL 250 260 270 280 290 300 VLKAWTTLGC KGWGRIDVML DSDGQFYLLE ANTSPGMTSH SLVPMAARQA GMSFSQLVVR ILELAD

References

[1]

"Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157." Jin Q., Yuan Z., Xu J., Wang Y., Shen Y., Lu W., Wang J., Liu H., Yang J., Yang F., Zhang X., Zhang J., Yang G., Wu H., Qu D., Dong J., Sun L., Xue Y. , Zhao A., Gao Y., Zhu J., Kan B., Ding K., Chen S., Cheng H., Yao Z., He B., Chen R., Ma D., Qiang B., Wen Y., Hou Y., Yu J. Nucleic Acids Res. 30:4432-4441(2002) [PubMed: 12384590] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: 301 / Serotype 2a.

[2]

"Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T." Wei J., Goldberg M.B., Burland V., Venkatesan M.M., Deng W., Fournier G., Mayhew G.F., Plunkett G. III, Rose D.J., Darling A., Mau B., Perna N.T., Payne S.M., Runyen-Janecky L.J., Zhou S., Schwartz D.C., Blattner F.R. Infect. Immun. 71:2775-2786(2003) [PubMed: 12704152] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 700930 / 2457T / Serotype 2a.

Cross-references

Sequence databases
EMBLGenBankDDBJ	AE005674 Genomic DNA. Translation: AAN41754.1. AE014073 Genomic DNA. Translation: AAP15635.1.
RefSeq	NP_706047.1. NP_835830.1.
3D structure databases
HSSP	HSSP built from PDB template 1IOV based on UniProtKB P07862.
SMR	Q83MF7. Positions 1-306.
ModBase	Search...
Genome annotation databases
GeneID	1024534. 1076520.
GenomeReviews	Gene locus S0091 in contig AE014073_GR. Gene locus SF0089 in contig AE005674_GR.
KEGG	sfl:SF0089. sfx:S0091.
Organism-specific databases
CMR	Search...
Phylogenomic databases
HOGENOM	Q83MF7.
Enzyme and pathway databases
BioCyc	SFLE198214:AAN41754.1-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_SHIFL

Accession

Primary (citable) accession number: Q83MF7
Secondary accession number(s): Q7UDS4

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 15, 2003
Last sequence update:	June 1, 2003
Last modified:	November 25, 2008
This is version 48 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)