Q8RDQ4 (DDL_FUSNN) 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:	FN1454

Organism

Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / CIP 101130 / JCM 8532 / LMG 13131) [Reference proteome] [HAMAP]

Taxonomic identifier

190304 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Fusobacteria › Fusobacteriia › Fusobacteriales › Fusobacteriaceae › Fusobacterium › Fusobacterium nucleatum › Fusobacterium nucleatum subsp. nucleatum

Protein attributes

Sequence length	287 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 Reference 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 – 287	287	D-alanine--D-alanine ligase HAMAP-Rule MF_00047		PRO_0000177824
Regions
	Domain	98 – 283	186	ATP-grasp
	Nucleotide binding	124 – 169	46	ATP By similarity
Sites
	Metal binding	238	1	Magnesium or manganese 1 By similarity
	Metal binding	250	1	Magnesium or manganese 1 By similarity
	Metal binding	250	1	Magnesium or manganese 2 By similarity
	Metal binding	252	1	Magnesium or manganese 2 By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q8RDQ4 [UniParc]. Last modified June 1, 2002. Version 1. Checksum: 213241D408D247DE	FASTA	287	31,483
	10 20 30 40 50 60 MRIAVFMGGT SSEKEISLKS GEAVLESLQK QGYDAYGVIL DERNQVSAFV DNDYDLAYLV 70 80 90 100 110 120 LHGGNGENGK IQAVLDILGK KYTGSGVLAS AITMDKDKTK QIAQSVGIKT PKSYRPVEEI 130 140 150 160 170 180 ERFPVIIKPV DEGSSKGLFL CNNKEEAEEA VKKLAKPIIE DYIIGEELTV GVLNGEALGV 190 200 210 220 230 240 LKIIPQADVL YDYDSKYAKG GSVHEFPAKI ENKSYKEAMK IAEKIHSEFG MKGISRSDFI 250 260 270 280 LSEGELYFLE VNSSPGMTKT SLIPDLATLK GYSFDDVVRI TVETFLE

References

[1]

"Genome sequence and analysis of the oral bacterium Fusobacterium nucleatum strain ATCC 25586." Kapatral V., Anderson I., Ivanova N., Reznik G., Los T., Lykidis A., Bhattacharyya A., Bartman A., Gardner W., Grechkin G., Zhu L., Vasieva O., Chu L., Kogan Y., Chaga O., Goltsman E., Bernal A., Larsen N. , D'Souza M., Walunas T., Pusch G., Haselkorn R., Fonstein M., Kyrpides N.C., Overbeek R. J. Bacteriol. 184:2005-2018(2002) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 25586 / CIP 101130 / JCM 8532 / LMG 13131.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AE009951 Genomic DNA. Translation: AAL95647.1.
RefSeq	NP_604348.1. NC_003454.1.
3D structure databases
ProteinModelPortal	Q8RDQ4.
ModBase	Search...
Protein-protein interaction databases
STRING	190304.FN1454.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAL95647; AAL95647; FN1454.
GeneID	992375.
KEGG	fnu:FN1454.
PATRIC	21952669. VBIFusNuc122357_2014.
Phylogenomic databases
eggNOG	COG1181.
HOGENOM	HOG000011592.
KO	K01921.
OMA	GMTENSL.
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_FUSNN

Accession

Primary (citable) accession number: Q8RDQ4

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 15, 2003
Last sequence update:	June 1, 2002
Last modified:	May 1, 2013
This is version 78 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program