C4XRH9 (DDL_DESMR) 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:	DMR_20330

Organism

Desulfovibrio magneticus (strain ATCC 700980 / DSM 13731 / RS-1) [Complete proteome] [HAMAP]

Taxonomic identifier

573370 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › delta/epsilon subdivisions › Deltaproteobacteria › Desulfovibrionales › Desulfovibrionaceae › Desulfovibrio › Desulfovibrio magneticus

Protein attributes

Sequence length	304 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 – 304	304	D-alanine--D-alanine ligase HAMAP-Rule MF_00047		PRO_1000202198
Regions
	Domain	100 – 294	195	ATP-grasp
	Nucleotide binding	126 – 180	55	ATP By similarity
Sites
	Metal binding	249	1	Magnesium or manganese 1 By similarity
	Metal binding	261	1	Magnesium or manganese 1 By similarity
	Metal binding	261	1	Magnesium or manganese 2 By similarity
	Metal binding	263	1	Magnesium or manganese 2 By similarity

Sequences

	Sequence		Length	Mass (Da)
	C4XRH9 [UniParc]. Last modified July 28, 2009. Version 1. Checksum: 285C53A06A55A506	FASTA	304	32,255
	10 20 30 40 50 60 MKILLVAGGW SSERAVSLSG AVQIEKALTS LGHEVVPYDL SHDFPGFVRR AKACDFVFLS 70 80 90 100 110 120 LHGAPGEDGL PQALLDAAGV PYQGSGPAGS FLALNKAASK QLFLEACLPT PRWTFVPRDA 130 140 150 160 170 180 GTSARPDFPL PWFVKPNLGG SSIHMTLVRR AEELPAALEK VFAHGDDALI EEGLSGPELT 190 200 210 220 230 240 CAVLGDEALP PILIRPKAGE FFDYASKYEP DAADEICPAP VEPAVTEELS RLSLAAHRVL 250 260 270 280 290 300 GLCGYSRADF ILAPEGLRLL EVNTLPGMTP TSLLPRAAAT AGLSFADLIA RLIELGLAQQ AKRP

References

[1]

"Whole genome sequence of Desulfovibrio magneticus strain RS-1 revealed common gene clusters in magnetotactic bacteria." Nakazawa H., Arakaki A., Narita-Yamada S., Yashiro I., Jinno K., Aoki N., Tsuruyama A., Okamura Y., Tanikawa S., Fujita N., Takeyama H., Matsunaga T. Genome Res. 19:1801-1808(2009) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 700980 / DSM 13731 / RS-1.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AP010904 Genomic DNA. Translation: BAH75524.1.
RefSeq	YP_002953410.1. NC_012796.1.
3D structure databases
ProteinModelPortal	C4XRH9.
ModBase	Search...
Protein-protein interaction databases
STRING	573370.DMR_20330.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	BAH75524; BAH75524; DMR_20330.
GeneID	7983730.
KEGG	dma:DMR_20330.
PATRIC	21750329. VBIDesMag26496_1935.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG1181.
HOGENOM	HOG000011592.
KO	K01921.
OMA	GELQAMC.
ProtClustDB	CLSK704556.
Enzyme and pathway databases
BioCyc	DMAG573370:GHJL-4035-MONOMER.
UniPathway	UPA00219.
Family and domain databases
Gene3D	3.30.1490.20. 1 hit. 3.30.470.20. 1 hit. 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.
PROSITE	PS50975. ATP_GRASP. 1 hit. PS00843. DALA_DALA_LIGASE_1. False negative. PS00844. DALA_DALA_LIGASE_2. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

DDL_DESMR

Accession

Primary (citable) accession number: C4XRH9

Entry history

Integrated into UniProtKB/Swiss-Prot:	September 22, 2009
Last sequence update:	July 28, 2009
Last modified:	May 1, 2013
This is version 33 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program