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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Nitratiruptor sp. (strain SB155-2)
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 bindingi282 – 2821Magnesium or manganese 1UniRule annotation
Metal bindingi294 – 2941Magnesium or manganese 1UniRule annotation
Metal bindingi294 – 2941Magnesium or manganese 2UniRule annotation
Metal bindingi296 – 2961Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi159 – 21052ATPUniRule 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

BioCyciNSP387092:GHA5-1136-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:NIS_1097
OrganismiNitratiruptor sp. (strain SB155-2)
Taxonomic identifieri387092 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaEpsilonproteobacteriaNitratiruptor
ProteomesiUP000001118 Componenti: Chromosome

Subcellular locationi

  1. 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 – 342342D-alanine--D-alanine ligasePRO_1000074779Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi387092.NIS_1097.

Structurei

3D structure databases

ProteinModelPortaliA6Q3Z7.
SMRiA6Q3Z7. Positions 1-322.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini132 – 326195ATP-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.
HOGENOMiHOG000102494.
KOiK01921.
OMAiYRIAFIG.
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.

A6Q3Z7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQYAVVFGGK SYEHEISIVS TIAIKDIIPG AIFIFLDGNR DFYLIEKADL
60 70 80 90 100
KSNYFSSGNY KKSPKLELKK GGFYQKSLLK EKKIPADVVI NLVHGADGED
110 120 130 140 150
GKLASLLEFF EIDYIGPRIE GSVISYSKLL TKLYAKECGI EVLPYQLLRK
160 170 180 190 200
QDKKIIDFEY PVIIKPNHLG SSIGVSVVYD SSELEYALDV AFEFDDEVLI
210 220 230 240 250
EPFIEGIEEY NLAGAKGQTF HFSKIEAVKK EKLLDFEKKY LDFGRSGEVK
260 270 280 290 300
DASLNETLRL HIRNAFEKIY DPLFSGAIIR IDFFVRDGKL YLNEINPVPG
310 320 330 340
SLANYLFGDF RAVLEDVAKH LPKSKNIVID YRYINSIQSA KK
Length:342
Mass (Da):38,808
Last modified:August 21, 2007 - v1
Checksum:i8C442237BE583032
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP009178 Genomic DNA. Translation: BAF70206.1.
RefSeqiWP_012082469.1. NC_009662.1.
YP_001356563.1. NC_009662.1.

Genome annotation databases

EnsemblBacteriaiBAF70206; BAF70206; NIS_1097.
KEGGinis:NIS_1097.
PATRICi22684290. VBINitSp82229_1149.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP009178 Genomic DNA. Translation: BAF70206.1.
RefSeqiWP_012082469.1. NC_009662.1.
YP_001356563.1. NC_009662.1.

3D structure databases

ProteinModelPortaliA6Q3Z7.
SMRiA6Q3Z7. Positions 1-322.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi387092.NIS_1097.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAF70206; BAF70206; NIS_1097.
KEGGinis:NIS_1097.
PATRICi22684290. VBINitSp82229_1149.

Phylogenomic databases

eggNOGiCOG1181.
HOGENOMiHOG000102494.
KOiK01921.
OMAiYRIAFIG.
OrthoDBiEOG6ND0KB.

Enzyme and pathway databases

UniPathwayiUPA00219.
BioCyciNSP387092:GHA5-1136-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. "Deep-sea vent epsilon-proteobacterial genomes provide insights into emergence of pathogens."
    Nakagawa S., Takaki Y., Shimamura S., Reysenbach A.-L., Takai K., Horikoshi K.
    Proc. Natl. Acad. Sci. U.S.A. 104:12146-12150(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: SB155-2.

Entry informationi

Entry nameiDDL_NITSB
AccessioniPrimary (citable) accession number: A6Q3Z7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 20, 2008
Last sequence update: August 21, 2007
Last modified: April 1, 2015
This is version 60 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.