ddl

Functionⁱ

Cell wall formation.UniRule annotation

Catalytic activityⁱ

ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine.UniRule annotation

Cofactorⁱ

Mg²⁺By similarity, Mn²⁺By similarityNote: Binds 2 magnesium or manganese ions per subunit.By similarity

Pathwayⁱ: peptidoglycan biosynthesis

This protein is involved in the pathway peptidoglycan biosynthesis, which is part of Cell wall biogenesis.UniRule annotation
View all proteins of this organism that are known to be involved in the pathway peptidoglycan biosynthesis and in Cell wall biogenesis.

Sites

Feature key	Position(s)	DescriptionActions	Length
Metal bindingⁱ	238	Magnesium or manganese 1UniRule annotation	1
Metal bindingⁱ	250	Magnesium or manganese 1UniRule annotation	1
Metal bindingⁱ	250	Magnesium or manganese 2UniRule annotation	1
Metal bindingⁱ	252	Magnesium or manganese 2UniRule annotation	1

Regions

Feature key	Position(s)	DescriptionActions	Graphical view	Length
Nucleotide bindingⁱ	124 – 169	ATPUniRule annotationAdd BLAST		46

GO - Molecular functionⁱ

ATP binding Source: UniProtKB-KW
D-alanine-D-alanine ligase activity Source: UniProtKB-EC
metal ion binding Source: UniProtKB-KW

Complete GO annotation...

GO - Biological processⁱ

cell wall organization Source: UniProtKB-KW
peptidoglycan biosynthetic process Source: UniProtKB-UniPathway
regulation of cell shape Source: UniProtKB-KW

Complete GO annotation...

Keywordsⁱ

Molecular function	Ligase
Biological process	Cell shape, Cell wall biogenesis/degradation, Peptidoglycan synthesis
Ligand	ATP-binding, Magnesium, Manganese, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

UniPathwayⁱ	UPA00219.

UniPathwayⁱ

UPA00219.

Names & Taxonomyⁱ

Protein namesⁱ	Recommended name: D-alanine--D-alanine ligaseUniRule annotation (EC:6.3.2.4UniRule annotation) Alternative name(s): D-Ala-D-Ala ligaseUniRule annotation D-alanylalanine synthetaseUniRule annotation
Gene namesⁱ	Name:ddlUniRule annotation Ordered Locus Names:FN1454
Organismⁱ	Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / CIP 101130 / JCM 8532 / LMG 13131)
Taxonomic identifierⁱ	190304 [NCBI]
Taxonomic lineageⁱ	cellular organisms › Bacteria › Fusobacteria › Fusobacteriia › Fusobacteriales › Fusobacteriaceae › Fusobacterium › Fusobacterium nucleatum ›
Proteomesⁱ	UP000002521 Componentⁱ: Chromosome

Subcellular locationⁱ

Cytoplasm
UniRule annotation
Manual assertion according to rulesⁱ
- HAMAP-Rule:MF_00047

GO - Cellular componentⁱ

cytoplasm Source: UniProtKB-SubCell

Complete GO annotation...

Keywords - Cellular componentⁱ

Cytoplasm

PTM / Processingⁱ

Molecule processing

Feature key	Position(s)	DescriptionActions	Graphical view	Length
ChainⁱPRO_0000177824	1 – 287	D-alanine--D-alanine ligaseAdd BLAST		287

Interactionⁱ

Protein-protein interaction databases

STRINGⁱ	190304.FN1454.

STRINGⁱ

190304.FN1454.

Structureⁱ

3D structure databases

ProteinModelPortalⁱ	Q8RDQ4.
SMRⁱ	Q8RDQ4.
ModBaseⁱ	Search...
MobiDBⁱ	Search...

Family & Domainsⁱ

Domains and Repeats

Feature key	Position(s)	DescriptionActions	Graphical view	Length
Domainⁱ	98 – 283	ATP-graspUniRule annotationAdd BLAST		186

Sequence similaritiesⁱ

Belongs to the D-alanine--D-alanine ligase family.UniRule annotation

Phylogenomic databases

eggNOGⁱ	ENOG4105CPF. Bacteria. COG1181. LUCA.
HOGENOMⁱ	HOG000011592.
InParanoidⁱ	Q8RDQ4.
KEGG Orthology (KO) More...KOⁱ	K01921.
OMAⁱ	YETKYTE.

Family and domain databases

Gene3Dⁱ	3.30.1490.20. 1 hit.
HAMAPⁱ	MF_00047. Dala_Dala_lig. 1 hit.
InterProⁱ	View protein in InterPro IPR011761. ATP-grasp. IPR013815. ATP_grasp_subdomain_1. 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.
Pfam protein domain database More...Pfamⁱ	View protein in Pfam PF07478. Dala_Dala_lig_C. 1 hit. PF01820. Dala_Dala_lig_N. 1 hit.
PIRSFⁱ	PIRSF039102. Ddl/VanB. 2 hits.
SUPFAMⁱ	SSF52440. SSF52440. 1 hit.
TIGRFAMsⁱ	TIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITEⁱ	View protein in PROSITE PS50975. ATP_GRASP. 1 hit. PS00843. DALA_DALA_LIGASE_1. 1 hit. PS00844. DALA_DALA_LIGASE_2. 1 hit.

Sequenceⁱ

Sequence statusⁱ: Complete.

Q8RDQ4-1 [UniParc]FASTA Add to basket

« Hide

        10         20         30         40         50
MRIAVFMGGT SSEKEISLKS GEAVLESLQK QGYDAYGVIL DERNQVSAFV 
        60         70         80         90        100
DNDYDLAYLV LHGGNGENGK IQAVLDILGK KYTGSGVLAS AITMDKDKTK 
       110        120        130        140        150
QIAQSVGIKT PKSYRPVEEI ERFPVIIKPV DEGSSKGLFL CNNKEEAEEA 
       160        170        180        190        200
VKKLAKPIIE DYIIGEELTV GVLNGEALGV LKIIPQADVL YDYDSKYAKG 
       210        220        230        240        250
GSVHEFPAKI ENKSYKEAMK IAEKIHSEFG MKGISRSDFI LSEGELYFLE 
       260        270        280 
VNSSPGMTKT SLIPDLATLK GYSFDDVVRI TVETFLE

Length:287

Mass (Da):31,483

Last modified:June 1, 2002 - v1

Checksum:ⁱ213241D408D247DE

GO

Sequence databases

Select the link destinations: EMBLⁱ GenBankⁱ DDBJⁱ Links Updated	AE009951 Genomic DNA. Translation: AAL95647.1.
NCBI Reference Sequences More...RefSeqⁱ	NP_604348.1. NC_003454.1. WP_011017163.1. NC_003454.1.

Genome annotation databases

EnsemblBacteriaⁱ	AAL95647; AAL95647; FN1454.
GeneIDⁱ	992375.
KEGGⁱ	fnu:FN1454.
PATRICⁱ	fig\|190304.8.peg.2014.

Similar proteinsⁱ

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:

100%	UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%	UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%	UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.

Cross-referencesⁱ

Sequence databases

Select the link destinations: EMBLⁱ GenBankⁱ DDBJⁱ Links Updated	AE009951 Genomic DNA. Translation: AAL95647.1.
NCBI Reference Sequences More...RefSeqⁱ	NP_604348.1. NC_003454.1. WP_011017163.1. NC_003454.1.

3D structure databases

ProteinModelPortalⁱ	Q8RDQ4.
SMRⁱ	Q8RDQ4.
ModBaseⁱ	Search...
MobiDBⁱ	Search...

Protein-protein interaction databases

STRINGⁱ	190304.FN1454.

STRINGⁱ

190304.FN1454.

Protocols and materials databases

Structural Biology Knowledgebase	Search...

Structural Biology Knowledgebase

Search...

Genome annotation databases

EnsemblBacteriaⁱ	AAL95647; AAL95647; FN1454.
GeneIDⁱ	992375.
KEGGⁱ	fnu:FN1454.
PATRICⁱ	fig\|190304.8.peg.2014.

Phylogenomic databases

eggNOGⁱ	ENOG4105CPF. Bacteria. COG1181. LUCA.
HOGENOMⁱ	HOG000011592.
InParanoidⁱ	Q8RDQ4.
KEGG Orthology (KO) More...KOⁱ	K01921.
OMAⁱ	YETKYTE.

Enzyme and pathway databases

UniPathwayⁱ	UPA00219.

UniPathwayⁱ

UPA00219.

Family and domain databases

Gene3Dⁱ	3.30.1490.20. 1 hit.
HAMAPⁱ	MF_00047. Dala_Dala_lig. 1 hit.
InterProⁱ	View protein in InterPro IPR011761. ATP-grasp. IPR013815. ATP_grasp_subdomain_1. 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.
Pfam protein domain database More...Pfamⁱ	View protein in Pfam PF07478. Dala_Dala_lig_C. 1 hit. PF01820. Dala_Dala_lig_N. 1 hit.
PIRSFⁱ	PIRSF039102. Ddl/VanB. 2 hits.
SUPFAMⁱ	SSF52440. SSF52440. 1 hit.
TIGRFAMsⁱ	TIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITEⁱ	View protein in PROSITE PS50975. ATP_GRASP. 1 hit. PS00843. DALA_DALA_LIGASE_1. 1 hit. PS00844. DALA_DALA_LIGASE_2. 1 hit.
ProtoNetⁱ	Search...

Entry informationⁱ

Entry nameⁱ	DDL_FUSNN
Accessionⁱ	Q8RDQ4Primary (citable) accession number: Q8RDQ4
Entry historyⁱ	Integrated into UniProtKB/Swiss-Prot:	December 15, 2003
	Last sequence update:	June 1, 2002
	Last modified:	July 5, 2017
	This is version 100 of the entry and version 1 of the sequence. See complete history.
Entry statusⁱ	Reviewed (UniProtKB/Swiss-Prot)
Annotation program	Prokaryotic Protein Annotation Program

UniProtKB

UniParc

Help

UniRef

Proteomes

Annotation systems

Supporting data

UniProtKB - Q8RDQ4 (DDL_FUSNN)

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D-alanine--D-alanine ligase

Select a section on the left to see content.

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">‘Function’</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>Pathwayi: peptidoglycan biosynthesis

Sites

Regions

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Biological processi

Enzyme and pathway databases

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Cellular componenti

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

Protein-protein interaction databases

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

3D structure databases

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Phylogenomic databases

Family and domain databases

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including length and molecular weight.<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

Sequence databases

Genome annotation databases

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

3D structure databases

Protein-protein interaction databases

Protocols and materials databases

Genome annotation databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Documents

Functionⁱ

Pathwayⁱ: peptidoglycan biosynthesis

GO - Molecular functionⁱ

GO - Biological processⁱ

Names & Taxonomyⁱ

Subcellular locationⁱ

GO - Cellular componentⁱ

PTM / Processingⁱ

Interactionⁱ

Structureⁱ

Family & Domainsⁱ

Sequence similaritiesⁱ

Sequenceⁱ

Cross-referencesⁱ

Entry informationⁱ

Miscellaneousⁱ