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A1RK54

- DDL_SHESW

UniProt

A1RK54 - DDL_SHESW

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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Shewanella sp. (strain W3-18-1)
Status
Reviewed - 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

Binds 2 magnesium or manganese ions per subunit.By similarity

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi284 – 2841Magnesium or manganese 1UniRule annotation
Metal bindingi297 – 2971Magnesium or manganese 1UniRule annotation
Metal bindingi297 – 2971Magnesium or manganese 2UniRule annotation
Metal bindingi299 – 2991Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi154 – 20956ATPUniRule 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

BioCyciSSP351745:GCOY-2300-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:Sputw3181_2224
OrganismiShewanella sp. (strain W3-18-1)
Taxonomic identifieri351745 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaAlteromonadalesShewanellaceaeShewanella
ProteomesiUP000002597: Chromosome

Subcellular locationi

Cytoplasm UniRule annotation

GO - Cellular componenti

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

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 337337D-alanine--D-alanine ligasePRO_1000074796Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi351745.Sputw3181_2224.

Structurei

3D structure databases

ProteinModelPortaliA1RK54.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini124 – 330207ATP-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.
OMAiQIDVIFP.
OrthoDBiEOG6ND0KB.

Family and domain databases

Gene3Di3.30.1490.20. 1 hit.
3.30.470.20. 1 hit.
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.

A1RK54-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSRINLLLLC GGGSAEHDIS LMSANYFESS LAKSDQFSVL RVELDKLGQY
60 70 80 90 100
RTAAGDECEL TNNREIRFRD ETKAPWPVDY VIPCIHGYPG ETGDIQSYFN
110 120 130 140 150
LIQLPYFGCE SEASSNCFNK ITAKMWFSAL GIPNTPYIFL HQYDDEAISQ
160 170 180 190 200
AQTALANWGS IFIKAASQGS SVGCYKVDDS SKVAQVLKDA FGYAPYVVVE
210 220 230 240 250
KTIKARELEV AVYEYNGEIV ATLPGEIICD TNTFYTFDEK YAKSSKARTD
260 270 280 290 300
VVAKDVSVEL SEQIRAYAIK AFKGMKLRHL SRIDFFLTAE NEILLNEINT
310 320 330
FPGSTPISMF PKMLQNHGHD FTEYLSLVIN NQLSAKD
Length:337
Mass (Da):37,699
Last modified:February 6, 2007 - v1
Checksum:iDDFDF5D66C245D98
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000503 Genomic DNA. Translation: ABM25049.1.
RefSeqiWP_011789515.1. NC_008750.1.
YP_963603.1. NC_008750.1.

Genome annotation databases

EnsemblBacteriaiABM25049; ABM25049; Sputw3181_2224.
GeneIDi4661547.
KEGGishw:Sputw3181_2224.
PATRICi23598159. VBISheSp103602_2325.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000503 Genomic DNA. Translation: ABM25049.1 .
RefSeqi WP_011789515.1. NC_008750.1.
YP_963603.1. NC_008750.1.

3D structure databases

ProteinModelPortali A1RK54.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 351745.Sputw3181_2224.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ABM25049 ; ABM25049 ; Sputw3181_2224 .
GeneIDi 4661547.
KEGGi shw:Sputw3181_2224.
PATRICi 23598159. VBISheSp103602_2325.

Phylogenomic databases

eggNOGi COG1181.
HOGENOMi HOG000011592.
KOi K01921.
OMAi QIDVIFP.
OrthoDBi EOG6ND0KB.

Enzyme and pathway databases

UniPathwayi UPA00219 .
BioCyci SSP351745:GCOY-2300-MONOMER.

Family and domain databases

Gene3Di 3.30.1490.20. 1 hit.
3.30.470.20. 1 hit.
3.40.50.20. 1 hit.
HAMAPi MF_00047. Dala_Dala_lig.
InterProi 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 ]
PANTHERi PTHR23132. PTHR23132. 1 hit.
Pfami PF07478. Dala_Dala_lig_C. 1 hit.
PF01820. Dala_Dala_lig_N. 1 hit.
[Graphical view ]
SUPFAMi SSF52440. SSF52440. 1 hit.
TIGRFAMsi TIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITEi PS50975. ATP_GRASP. 1 hit.
PS00843. DALA_DALA_LIGASE_1. 1 hit.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: W3-18-1.

Entry informationi

Entry nameiDDL_SHESW
AccessioniPrimary (citable) accession number: A1RK54
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 20, 2008
Last sequence update: February 6, 2007
Last modified: October 29, 2014
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

Documents

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

External Data

Dasty 3