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B3EDF4

- DDL_CHLL2

UniProt

B3EDF4 - DDL_CHLL2

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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Chlorobium limicola (strain DSM 245 / NBRC 103803)
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 bindingi305 – 3051Magnesium or manganese 1UniRule annotation
Metal bindingi319 – 3191Magnesium or manganese 1UniRule annotation
Metal bindingi319 – 3191Magnesium or manganese 2UniRule annotation
Metal bindingi321 – 3211Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi179 – 23456ATPUniRule 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

BioCyciCLIM290315:GHUH-1567-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:Clim_1529
OrganismiChlorobium limicola (strain DSM 245 / NBRC 103803)
Taxonomic identifieri290315 [NCBI]
Taxonomic lineageiBacteriaChlorobiChlorobiaChlorobialesChlorobiaceaeChlorobium/Pelodictyon groupChlorobium
ProteomesiUP000008841: 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 – 363363D-alanine--D-alanine ligasePRO_1000091169Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi290315.Clim_1529.

Structurei

3D structure databases

ProteinModelPortaliB3EDF4.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini146 – 352207ATP-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.
HOGENOMiHOG000011593.
KOiK01921.
OMAiRSAYGIY.
OrthoDBiEOG64BQ73.

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.

B3EDF4-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSKTTIALLF GGKSTEHEIS IISARSISGA IDRERYRVVP VYITHEGAWF
60 70 80 90 100
SGDSAAEILS LDLSSIMRKS SVGNTETLLR EMIRNSAEKP FDFNFRAAGI
110 120 130 140 150
DVVFIALHGS YGEDGRVQGL LDTMGIPYTG CGVSASAIAM DKALTKLCAA
160 170 180 190 200
DAGVATAPSI TLDADSYLAD PEPVHELVDS TFGYPLFVKP ASLGSSVGIS
210 220 230 240 250
KVHLPAALPE ALKVACSYDR KILVEAAVSG KEIEVAVLGN DRPVASVPGE
260 270 280 290 300
VEPGSDFYDF QDKYIHNTAK TFIPARLPDK LLDSVRCSAI TVYKALGCRG
310 320 330 340 350
MSRVDFFVNE ENGSIVLNEI NTIPGFTDIS MYPKLFEASG IPFTALIDKL
360
LHYAQEKPEA AGR
Length:363
Mass (Da):38,980
Last modified:July 22, 2008 - v1
Checksum:i02D032C73D23E0E3
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP001097 Genomic DNA. Translation: ACD90579.1.
RefSeqiWP_012466455.1. NC_010803.1.
YP_001943558.1. NC_010803.1.

Genome annotation databases

EnsemblBacteriaiACD90579; ACD90579; Clim_1529.
GeneIDi6354634.
KEGGicli:Clim_1529.
PATRICi21375199. VBIChlLim118737_1630.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP001097 Genomic DNA. Translation: ACD90579.1 .
RefSeqi WP_012466455.1. NC_010803.1.
YP_001943558.1. NC_010803.1.

3D structure databases

ProteinModelPortali B3EDF4.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 290315.Clim_1529.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ACD90579 ; ACD90579 ; Clim_1529 .
GeneIDi 6354634.
KEGGi cli:Clim_1529.
PATRICi 21375199. VBIChlLim118737_1630.

Phylogenomic databases

eggNOGi COG1181.
HOGENOMi HOG000011593.
KOi K01921.
OMAi RSAYGIY.
OrthoDBi EOG64BQ73.

Enzyme and pathway databases

UniPathwayi UPA00219 .
BioCyci CLIM290315:GHUH-1567-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: DSM 245 / NBRC 103803.

Entry informationi

Entry nameiDDL_CHLL2
AccessioniPrimary (citable) accession number: B3EDF4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: July 22, 2008
Last modified: October 29, 2014
This is version 45 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