Q8PPA6 (DDL_XANAC) 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
Synonyms:	ddlB
Ordered Locus Names:	XAC0781

Organism

Xanthomonas axonopodis pv. citri (strain 306) [Complete proteome] [HAMAP]

Taxonomic identifier

190486 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Xanthomonadales › Xanthomonadaceae › Xanthomonas › Xanthomonas citri group › Xanthomonas campestris pv. citri › Xanthomonas citri pv. citri

Protein attributes

Sequence length	318 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 – 318	318	D-alanine--D-alanine ligase HAMAP-Rule MF_00047		PRO_0000177907
Regions
	Domain	117 – 315	199	ATP-grasp
	Nucleotide binding	146 – 201	56	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)
	Q8PPA6 [UniParc]. Last modified October 1, 2002. Version 1. Checksum: CDD9278939E537DE	FASTA	318	33,687
	10 20 30 40 50 60 MSALVGNART SDPAAFGRVA VLLGGTSSER EVSLNSGGNV LDALRARGVD AQPVDGIPAL 70 80 90 100 110 120 AKALVAQQFD RVFNVLHGHN GGGEDGIVQG LMEAFGVPYT GSDVLGSALS MDKIRTKQVW 130 140 150 160 170 180 LSLGLSTPRY ARLAAGASAE DIHAAARQIG LPIIVKPANE GSSVGVSRVF DQAQLEEAVT 190 200 210 220 230 240 LAARYDGALL MEQLIEGDEL TVAVLGDTAL PSIRIVPKGQ WYDYNAKYIA DDTQYLCPGL 250 260 270 280 290 300 EGEAEAQIRQ LALDAFRAAG CRGWGRVDVM RDGSSGQLYL LEVNTAPGMT SHSLVPKAAR 310 QLGIDFETLV WRVLEQTL

References

[1]

"Comparison of the genomes of two Xanthomonas pathogens with differing host specificities." da Silva A.C.R., Ferro J.A., Reinach F.C., Farah C.S., Furlan L.R., Quaggio R.B., Monteiro-Vitorello C.B., Van Sluys M.A., Almeida N.F. Jr., Alves L.M.C., do Amaral A.M., Bertolini M.C., Camargo L.E.A., Camarotte G., Cannavan F., Cardozo J., Chambergo F., Ciapina L.P. , Cicarelli R.M.B., Coutinho L.L., Cursino-Santos J.R., El-Dorry H., Faria J.B., Ferreira A.J.S., Ferreira R.C.C., Ferro M.I.T., Formighieri E.F., Franco M.C., Greggio C.C., Gruber A., Katsuyama A.M., Kishi L.T., Leite R.P., Lemos E.G.M., Lemos M.V.F., Locali E.C., Machado M.A., Madeira A.M.B.N., Martinez-Rossi N.M., Martins E.C., Meidanis J., Menck C.F.M., Miyaki C.Y., Moon D.H., Moreira L.M., Novo M.T.M., Okura V.K., Oliveira M.C., Oliveira V.R., Pereira H.A., Rossi A., Sena J.A.D., Silva C., de Souza R.F., Spinola L.A.F., Takita M.A., Tamura R.E., Teixeira E.C., Tezza R.I.D., Trindade dos Santos M., Truffi D., Tsai S.M., White F.F., Setubal J.C., Kitajima J.P. Nature 417:459-463(2002) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: 306.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AE008923 Genomic DNA. Translation: AAM35669.1.
RefSeq	NP_641133.1. NC_003919.1.
3D structure databases
ProteinModelPortal	Q8PPA6.
SMR	Q8PPA6. Positions 17-316.
ModBase	Search...
Protein-protein interaction databases
STRING	190486.XAC0781.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAM35669; AAM35669; XAC0781.
GeneID	1154852.
KEGG	xac:XAC0781.
PATRIC	24053482. VBIXanAxo33670_0840.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG1181.
HOGENOM	HOG000011592.
KO	K01921.
OMA	EVLVEKW.
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

DDL_XANAC

Accession

Primary (citable) accession number: Q8PPA6

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 15, 2003
Last sequence update:	October 1, 2002
Last modified:	May 1, 2013
This is version 75 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program