Q83MF7 (DDLB_SHIFL) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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

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

Gene names

Name:	ddlB
Ordered Locus Names:	SF0089, S0091

Organism

Shigella flexneri [Complete proteome] [HAMAP]

Taxonomic identifier

623 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Shigella

Protein attributes

Sequence length	306 AA.
Sequence status	Complete.
Protein existence	Inferred from homology

General annotation (Comments)

Function	Cell wall formation By similarity. HAMAP-Rule MF_00047
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 HAMAP-Rule MF_00047.
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	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 – 306	306	D-alanine--D-alanine ligase B HAMAP-Rule MF_00047		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 [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] [Europe PMC] [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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 700930 / 2457T / Serotype 2a.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AE005674 Genomic DNA. Translation: AAN41754.1. AE014073 Genomic DNA. Translation: AAP15635.1.
RefSeq	NP_706047.1. NC_004337.2. NP_835830.1. NC_004741.1.
3D structure databases
ProteinModelPortal	Q83MF7.
SMR	Q83MF7. Positions 1-306.
ModBase	Search...
Protein-protein interaction databases
STRING	198214.SF0089.
Proteomic databases
PaxDb	Q83MF7.
PRIDE	Q83MF7.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAN41754; AAN41754; SF0089. AAP15635; AAP15635; S0091.
GeneID	1024534. 1076520.
KEGG	sfl:SF0089. sfx:S0091.
PATRIC	18701122. VBIShiFle31049_0103.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG1181.
HOGENOM	HOG000011592.
KO	K01921.
OMA	WREAARY.
ProtClustDB	PRK01372.
Enzyme and pathway databases
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

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:	May 29, 2013
This is version 81 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program