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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Rhodoferax ferrireducens (strain ATCC BAA-621 / DSM 15236 / T118) (Albidiferax ferrireducens)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

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

Pathway: 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 keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi278 – 2781Magnesium or manganese 1UniRule annotation
Metal bindingi292 – 2921Magnesium or manganese 1UniRule annotation
Metal bindingi292 – 2921Magnesium or manganese 2UniRule annotation
Metal bindingi294 – 2941Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi151 – 20656ATPUniRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

Cell shape, Cell wall biogenesis/degradation, Peptidoglycan synthesis

Keywords - Ligandi

ATP-binding, Magnesium, Manganese, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciAFER338969:GHU9-3465-MONOMER.
UniPathwayiUPA00219.

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:Rfer_3423
OrganismiRhodoferax ferrireducens (strain ATCC BAA-621 / DSM 15236 / T118) (Albidiferax ferrireducens)
Taxonomic identifieri338969 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesComamonadaceaeRhodoferax
ProteomesiUP000008332 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 346346D-alanine--D-alanine ligasePRO_0000341165Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi338969.Rfer_3423.

Structurei

3D structure databases

ProteinModelPortaliQ21SX1.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini125 – 325201ATP-graspUniRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the D-alanine--D-alanine ligase family.UniRule annotation
Contains 1 ATP-grasp domain.UniRule annotation

Phylogenomic databases

eggNOGiCOG1181.
HOGENOMiHOG000011592.
KOiK01921.
OMAiPFLLEMN.
OrthoDBiEOG6ND0KB.

Family and domain databases

Gene3Di3.30.1490.20. 1 hit.
3.30.470.20. 2 hits.
3.40.50.20. 1 hit.
HAMAPiMF_00047. Dala_Dala_lig.
InterProiIPR011761. 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]
PANTHERiPTHR23132. PTHR23132. 1 hit.
PfamiPF07478. Dala_Dala_lig_C. 1 hit.
PF01820. Dala_Dala_lig_N. 2 hits.
[Graphical view]
SUPFAMiSSF52440. SSF52440. 1 hit.
TIGRFAMsiTIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITEiPS50975. ATP_GRASP. 1 hit.
PS00843. DALA_DALA_LIGASE_1. 1 hit.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q21SX1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSQIGINDGA SQQPAGTTLG GVAARLGKVA VLMGGASAER EVSLMSGQGV
60 70 80 90 100
LQALISQGVD AHAFDPAERD LAELKVEGFS HCFIALHGRF GEDGTVQGAL
110 120 130 140 150
ELLGIPYTGS GVMASSIAID KVMTKRIWRS EGLPTPEWRQ VDSAAATSEA
160 170 180 190 200
FAALGSPMIV KPDREGSTIG LTKVTQIEQC GAAYALAARH DAMVLCEQFV
210 220 230 240 250
KGDEVTIPLL GSGAGAHALP VIRIVAPDGN YDYQNKYFTD TTQYLVPANL
260 270 280 290 300
PAGEEAHIQQ LALKAYQVLG CRGWARVDVM IDARTRAPFL LEINTSPGMT
310 320 330 340
PHSLVPMAAK AAGVSYPALC LEVLRHATLD YAAAGGDAQQ PSTEPA
Length:346
Mass (Da):36,268
Last modified:April 18, 2006 - v1
Checksum:i58D8C494A9A7B3C2
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000267 Genomic DNA. Translation: ABD71132.1.
RefSeqiWP_011465695.1. NC_007908.1.
YP_524663.1. NC_007908.1.

Genome annotation databases

EnsemblBacteriaiABD71132; ABD71132; Rfer_3423.
KEGGirfr:Rfer_3423.
PATRICi23239635. VBIRhoFer131161_3812.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000267 Genomic DNA. Translation: ABD71132.1.
RefSeqiWP_011465695.1. NC_007908.1.
YP_524663.1. NC_007908.1.

3D structure databases

ProteinModelPortaliQ21SX1.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi338969.Rfer_3423.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABD71132; ABD71132; Rfer_3423.
KEGGirfr:Rfer_3423.
PATRICi23239635. VBIRhoFer131161_3812.

Phylogenomic databases

eggNOGiCOG1181.
HOGENOMiHOG000011592.
KOiK01921.
OMAiPFLLEMN.
OrthoDBiEOG6ND0KB.

Enzyme and pathway databases

UniPathwayiUPA00219.
BioCyciAFER338969:GHU9-3465-MONOMER.

Family and domain databases

Gene3Di3.30.1490.20. 1 hit.
3.30.470.20. 2 hits.
3.40.50.20. 1 hit.
HAMAPiMF_00047. Dala_Dala_lig.
InterProiIPR011761. 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]
PANTHERiPTHR23132. PTHR23132. 1 hit.
PfamiPF07478. Dala_Dala_lig_C. 1 hit.
PF01820. Dala_Dala_lig_N. 2 hits.
[Graphical view]
SUPFAMiSSF52440. SSF52440. 1 hit.
TIGRFAMsiTIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITEiPS50975. ATP_GRASP. 1 hit.
PS00843. DALA_DALA_LIGASE_1. 1 hit.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Complete sequence of chromosome of Rhodoferax ferrireducens DSM 15236."
    Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T., Hammon N., Israni S., Pitluck S., Brettin T., Bruce D., Han C., Tapia R., Gilna P., Kiss H., Schmutz J., Larimer F., Land M.
    , Kyrpides N., Ivanova N., Richardson P.
    Submitted (FEB-2006) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC BAA-621 / DSM 15236 / T118.

Entry informationi

Entry nameiDDL_RHOFT
AccessioniPrimary (citable) accession number: Q21SX1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 10, 2008
Last sequence update: April 18, 2006
Last modified: May 27, 2015
This is version 72 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.