Reviewed, UniProtKB/Swiss-Prot A8HZA8 (DDL_AZOC5)

Names and origin

Protein names

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

Gene names

Name:	ddl
Ordered Locus Names:	AZC_4561

Organism

Azorhizobium caulinodans (strain ATCC 43989 / DSM 5975 / ORS 571) [Complete proteome] [HAMAP]

Taxonomic identifier

438753 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Alphaproteobacteria › Rhizobiales › Xanthobacteraceae › Azorhizobium

Protein attributes

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

General annotation (Comments)

Function	Cell wall formation By similarity. HAMAP MF_00047
Catalytic activity	ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine. HAMAP MF_00047
Cofactor	Binds 2 magnesium or manganese ions per subunit By similarity. HAMAP MF_00047
Pathway	Cell wall biogenesis; peptidoglycan biosynthesis. HAMAP MF_00047
Subcellular location	Cytoplasm By similarity HAMAP 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	cellular cell wall organization Inferred from electronic annotation. Source: UniProtKB-KW 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: UniProtKB-KW 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 HAMAP MF_00047		PRO_0000341057
Regions
	Domain	101 – 300	200	ATP-grasp
	Nucleotide binding	128 – 182	55	ATP By similarity
Sites
	Metal binding	250	1	Magnesium or manganese 1 By similarity
	Metal binding	267	1	Magnesium or manganese 1 By similarity
	Metal binding	267	1	Magnesium or manganese 2 By similarity
	Metal binding	269	1	Magnesium or manganese 2 By similarity

Sequences

	Sequence		Length	Mass (Da)
	A8HZA8-1 [UniParc]. Last modified December 4, 2007. Version 1. Checksum: 635CE58584325D3E	FASTA	306	32,913
	10 20 30 40 50 60 MAKHVAVLMG GWSPEREVSL RSGAGCAKAL EEVGYRVTRV DVDRDVAEVL ARLKPDVALN 70 80 90 100 110 120 LLHGCPGEDG TIQGILEILR IPYSHSGVLA SALAMDKARA KVVMAAAGIP VPGGHLVTRA 130 140 150 160 170 180 EAAKGHVLPP PYVLKPNTGG SSVGVFIVKE DQPHPPQELF RADWTFGESL MAEPFIKGLE 190 200 210 220 230 240 LTCGVMGDRA LDVIEVEAVH GFYDYESKYA AGGSRHILPA RVLPQIYQQV RMLALEAHRA 250 260 270 280 290 300 LGCRGISRAD FRYDDTLPDG KGLVCLEVNT QPGMTETSLV PDMAAHAGIS FGELVTWMVE DATLDR

References

[1]

"Complete genome sequence of the nitrogen-fixing bacterium Azorhizobium caulinodans ORS571." Lee K.B., Backer P.D., Aono T., Liu C.T., Suzuki S., Suzuki T., Kaneko T., Yamada M., Tabata S., Kupfer D.M., Najar F.Z., Wiley G.B., Roe B., Binnewies T., Ussery D., Vereecke D., Gevers D., Holsters M., Oyaizu H. Submitted (APR-2007) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Cross-references

Sequence databases
EMBL GenBank DDBJ	AP009384 Genomic DNA. Translation: BAF90559.1.
RefSeq	YP_001527477.1.
3D structure databases
SMR	A8HZA8. Positions 1-302.
ModBase	Search...
Genome annotation databases
GeneID	5689654.
GenomeReviews	Gene locus AZC_4561 in contig AP009384_GR.
KEGG	azc:AZC_4561.
Organism-specific databases
CMR	Search...
Phylogenomic databases
HOGENOM	HBG427092.
OMA	RSDFRWD.
Family and domain databases
HAMAP	MF_00047. Dala_Dala_lig. [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. IPR016185. PreATP-grasp-like. [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. 2 hits. [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

DDL_AZOC5

Accession

Primary (citable) accession number: A8HZA8

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 10, 2008
Last sequence update:	December 4, 2007
Last modified:	February 9, 2010
This is version 20 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)