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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Pseudomonas stutzeri (strain A1501)
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

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi261 – 2611Magnesium or manganese 1UniRule annotation
Metal bindingi274 – 2741Magnesium or manganese 1UniRule annotation
Metal bindingi274 – 2741Magnesium or manganese 2UniRule annotation
Metal bindingi276 – 2761Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi138 – 19356ATPUniRule annotationAdd
BLAST

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-HAMAP
  2. D-alanine-D-alanine ligase activity Source: UniProtKB-HAMAP
  3. magnesium ion binding Source: UniProtKB-HAMAP
  4. manganese ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. cell wall organization Source: UniProtKB-KW
  2. peptidoglycan biosynthetic process Source: UniProtKB-HAMAP
  3. regulation of cell shape Source: UniProtKB-KW
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

BioCyciPSTU379731:GJER-1085-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:PST_1084
OrganismiPseudomonas stutzeri (strain A1501)
Taxonomic identifieri379731 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas
ProteomesiUP000000233 Componenti: Chromosome

Subcellular locationi

Cytoplasm UniRule annotation

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 314314D-alanine--D-alanine ligasePRO_0000341156Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi379731.PST_1084.

Structurei

3D structure databases

ProteinModelPortaliA4VII0.
SMRiA4VII0. Positions 14-307.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini112 – 307196ATP-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. 1 hit.
[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.

A4VII0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MMALQSTRDP KEFGRVAVLF GGKSAEREVS LKSGAAVLAA LQAAGVDAFG
60 70 80 90 100
IDAGDDLLQR LSSERIDRAF IVLHGRGGED GSMQGLLECA GIPYTGSGIL
110 120 130 140 150
ASALAMDKLR TKQVWQSLGL PTPRHAVLAS EVDCQAAAQM LGFPLIVKPA
160 170 180 190 200
HEGSSIGMAK VGDVAELIAA WRAASAYDAQ VLVEQWIQGP EFTVAVLHGE
210 220 230 240 250
VLPPIGLGTP HTFYDYDAKY LASDTQYRIP CGLDAAREEA LKVLSARACE
260 270 280 290 300
AVGIRGWARV DVMQDAEGNF WLLEVNTVPG MTDHSLVPMA ARAAGLDFQQ
310
LVLSILDDSL EAGN
Length:314
Mass (Da):33,316
Last modified:May 28, 2007 - v1
Checksum:i1436C0AE352581AD
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000304 Genomic DNA. Translation: ABP78781.1.
RefSeqiWP_011912271.1. NC_009434.1.
YP_001171623.1. NC_009434.1.

Genome annotation databases

EnsemblBacteriaiABP78781; ABP78781; PST_1084.
KEGGipsa:PST_1084.
PATRICi19962587. VBIPseStu31643_1080.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000304 Genomic DNA. Translation: ABP78781.1.
RefSeqiWP_011912271.1. NC_009434.1.
YP_001171623.1. NC_009434.1.

3D structure databases

ProteinModelPortaliA4VII0.
SMRiA4VII0. Positions 14-307.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi379731.PST_1084.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABP78781; ABP78781; PST_1084.
KEGGipsa:PST_1084.
PATRICi19962587. VBIPseStu31643_1080.

Phylogenomic databases

eggNOGiCOG1181.
HOGENOMiHOG000011592.
KOiK01921.
OMAiPFLLEMN.
OrthoDBiEOG6ND0KB.

Enzyme and pathway databases

UniPathwayiUPA00219.
BioCyciPSTU379731:GJER-1085-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. 1 hit.
[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 genome sequence of the metabolically versatile and root-associated nitrogen-fixing bacterium Pseudomonas stutzeri A1501."
    Yan Y., Yang J., Dou Y., Ping S., Chen M., Yao Z., Li H., Lu W., Zhang W., Peng J., Liu W., He S., Geng L., Zhang X., Yang F., Li D., Lin Z., Wang Y.
    , Elmerich C., Lin M., Jin Q.
    Submitted (MAR-2006) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: A1501.

Entry informationi

Entry nameiDDL_PSEU5
AccessioniPrimary (citable) accession number: A4VII0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 9, 2008
Last sequence update: May 28, 2007
Last modified: March 31, 2015
This is version 61 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.