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Q12LP2

- DDL_SHEDO

UniProt

Q12LP2 - DDL_SHEDO

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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Shewanella denitrificans (strain OS217 / ATCC BAA-1090 / DSM 15013)
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

BioCyciSDEN318161:GHKQ-2432-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:Sden_2354
OrganismiShewanella denitrificans (strain OS217 / ATCC BAA-1090 / DSM 15013)
Taxonomic identifieri318161 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaAlteromonadalesShewanellaceaeShewanella
ProteomesiUP000001982: 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 – 335335D-alanine--D-alanine ligasePRO_1000074786Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi318161.Sden_2354.

Structurei

3D structure databases

ProteinModelPortaliQ12LP2.
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. 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.

Q12LP2-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MAKINVLLLC GGGGAEHDIS LMSARFFETS LAKSDQFSVL TLTLDKQGRY
60 70 80 90 100
HTQDGNLCSL TNRREIRFED PSIAPWAVDY VIPCIHGFPG ETGDIQSYFN
110 120 130 140 150
LIQLPYFGCE SEASSNCFNK ITAKMWFSAL GVPNTPYIFL HQFDQEAIAQ
160 170 180 190 200
TQAAFDTWGS VFIKAASQGS SVGCYKVDVR DNIAKVLEEA FGYAPYVVVE
210 220 230 240 250
KTIKARELEV AVYEYQGDII ATLPGEIICD TNKFYSFDEK YAKDSKARTD
260 270 280 290 300
VVASNLSPKL CLQIQDYAIK AFKGMKLRHL SRIDFFLTQD DEILLNEINT
310 320 330
FPGLTPISMF PKMLQNHGHD FTEYLSDVIS QQLGR
Length:335
Mass (Da):37,585
Last modified:August 22, 2006 - v1
Checksum:i112BC8E7C0123B8D
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000302 Genomic DNA. Translation: ABE55634.1.
RefSeqiWP_011496785.1. NC_007954.1.
YP_563357.1. NC_007954.1.

Genome annotation databases

EnsemblBacteriaiABE55634; ABE55634; Sden_2354.
GeneIDi4018848.
KEGGisdn:Sden_2354.
PATRICi23490633. VBISheDen79529_2475.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000302 Genomic DNA. Translation: ABE55634.1 .
RefSeqi WP_011496785.1. NC_007954.1.
YP_563357.1. NC_007954.1.

3D structure databases

ProteinModelPortali Q12LP2.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 318161.Sden_2354.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ABE55634 ; ABE55634 ; Sden_2354 .
GeneIDi 4018848.
KEGGi sdn:Sden_2354.
PATRICi 23490633. VBISheDen79529_2475.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayi UPA00219 .
BioCyci SDEN318161:GHKQ-2432-MONOMER.

Family and domain databases

Gene3Di 3.30.1490.20. 1 hit.
3.30.470.20. 2 hits.
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: OS217 / ATCC BAA-1090 / DSM 15013.

Entry informationi

Entry nameiDDL_SHEDO
AccessioniPrimary (citable) accession number: Q12LP2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 20, 2008
Last sequence update: August 22, 2006
Last modified: October 29, 2014
This is version 65 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