C3PMU6 (DDL_RICAE) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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

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

Gene names

Name:	ddl
Ordered Locus Names:	RAF_ORF0310

Organism

Rickettsia africae (strain ESF-5) [Complete proteome] [HAMAP]

Taxonomic identifier

347255 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Alphaproteobacteria › Rickettsiales › Rickettsiaceae › Rickettsieae › Rickettsia › spotted fever group › Rickettsia africae

Protein attributes

Sequence length	321 AA.
Sequence status	Complete.
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. 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.
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: 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 – 321	321	D-alanine--D-alanine ligase HAMAP-Rule MF_00047		PRO_1000202204
Regions
	Domain	121 – 315	195	ATP-grasp
	Nucleotide binding	147 – 199	53	ATP By similarity
Sites
	Metal binding	268	1	Magnesium or manganese 1 By similarity
	Metal binding	282	1	Magnesium or manganese 1 By similarity
	Metal binding	282	1	Magnesium or manganese 2 By similarity
	Metal binding	284	1	Magnesium or manganese 2 By similarity

Sequences

	Sequence		Length	Mass (Da)
	C3PMU6 [UniParc]. Last modified June 16, 2009. Version 1. Checksum: 90C75F677CD30BBC	FASTA	321	36,022
	10 20 30 40 50 60 MHKYQTHWVE HSIVKILSST GKKHIALMVG GMSAEREVSL VSSEGVSKAL IELGYRVTFI 70 80 90 100 110 120 DMGADIAVRL QEIKPDIVFN CLHGTYGEDG CLPGLLNIMR IPYTHSGMLS SALAFDKIHS 130 140 150 160 170 180 RIWFLTNNIN MAESIVVNKS DNIKNDPMKR PYVIKPLTQG SSIGVEVIFA EDDFNFADYD 190 200 210 220 230 240 FPYGDQVIIE QYIKGRELQV AVLNGKALGA LEIKLLKNRF YDYETKYTEG FADHLCPAPL 250 260 270 280 290 300 PANLYEKLLI ESEKIYKTMN CKGPARAEFI LEEQTNKLYA LEINTHPGMT PLSIVPEIAA 310 320 YAGINFTNLI EEIIKMASFE S

References

[1]

"Analysis of the Rickettsia africae genome reveals that virulence acquisition in Rickettsia species may be explained by genome reduction." Fournier P.-E., El Karkouri K., Leroy Q., Robert C., Giumelli B., Renesto P., Socolovschi C., Parola P., Audic S., Raoult D. BMC Genomics 10:166-166(2009) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ESF-5.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP001612 Genomic DNA. Translation: ACP53256.1.
RefSeq	YP_002844999.1. NC_012633.1.
3D structure databases
ProteinModelPortal	C3PMU6.
ModBase	Search...
Protein-protein interaction databases
STRING	347255.RAF_ORF0310.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	ACP53256; ACP53256; RAF_ORF0310.
GeneID	7815310.
KEGG	raf:RAF_ORF0310.
PATRIC	17872465. VBIRicAfr6986_0372.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG1181.
HOGENOM	HOG000011592.
KO	K01921.
OMA	KYTEGFA.
ProtClustDB	PRK01372.
Enzyme and pathway databases
BioCyc	RAFR347255:GJCT-294-MONOMER.
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

DDL_RICAE

Accession

Primary (citable) accession number: C3PMU6

Entry history

Integrated into UniProtKB/Swiss-Prot:	September 22, 2009
Last sequence update:	June 16, 2009
Last modified:	May 1, 2013
This is version 36 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program