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B5EBQ4

- DDL_GEOBB

UniProt

B5EBQ4 - DDL_GEOBB

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Protein

D-alanine--D-alanine ligase

Gene
ddl, Gbem_0494
Organism
Geobacter bemidjiensis (strain Bem / ATCC BAA-1014 / DSM 16622)
Status
Reviewed - Annotation score: 3 out of 5 - Protein inferred from homologyi

Functioni

Cell wall formation By similarity.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 bindingi253 – 2531Magnesium or manganese 1 By similarity
Metal bindingi266 – 2661Magnesium or manganese 1 By similarity
Metal bindingi266 – 2661Magnesium or manganese 2 By similarity
Metal bindingi268 – 2681Magnesium or manganese 2 By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi134 – 18552ATP By similarityAdd
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. peptidoglycan biosynthetic process Source: UniProtKB-HAMAP
  2. 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

BioCyciGBEM404380:GHFR-498-MONOMER.
UniPathwayiUPA00219.

Names & Taxonomyi

Protein namesi
Recommended name:
D-alanine--D-alanine ligase (EC:6.3.2.4)
Alternative name(s):
D-Ala-D-Ala ligase
D-alanylalanine synthetase
Gene namesi
Name:ddl
Ordered Locus Names:Gbem_0494
OrganismiGeobacter bemidjiensis (strain Bem / ATCC BAA-1014 / DSM 16622)
Taxonomic identifieri404380 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfuromonadalesGeobacteraceaeGeobacter
ProteomesiUP000008825: Chromosome

Subcellular locationi

Cytoplasm By similarity 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 – 305305D-alanine--D-alanine ligaseUniRule annotationPRO_1000091183Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi404380.Gbem_0494.

Structurei

3D structure databases

ProteinModelPortaliB5EBQ4.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini107 – 299193ATP-graspAdd
BLAST

Sequence similaritiesi

Contains 1 ATP-grasp domain.

Phylogenomic databases

eggNOGiCOG1181.
HOGENOMiHOG000011592.
KOiK01921.
OMAiCSGYSRV.
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. 2 hits.
[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.
[Graphical view]

Sequencei

Sequence statusi: Complete.

B5EBQ4-1 [UniParc]FASTAAdd to Basket

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MTVEELKKKK IAVLMGGLSA EREVSLNSGK AVLASLVKQG FRAVGIDVGR    50
DLPQRLAEEQ VELAFIALHG RFGEDGSVQG LLELMGIPYT GSGVLASALA 100
IDKIASKVIF ASAGLKLAPY QVLRRGEELK LANPLPVVVK PSREGSSVGV 150
GIVRDPSRMQ AALDEAFRYD SEILIEGFID GREVQVGILN GKALGAIEII 200
PKGEFYDYEA KYTDGGAQHI LPARLPEAVY AEVLRQGEKA HAALGCDCYS 250
RVDFLVTETG DCFLLEVNTL PGMTDLSLLP EIAGGAGIAF GELVLRILQA 300
ASLKI 305
Length:305
Mass (Da):32,505
Last modified:October 14, 2008 - v1
Checksum:iADF7975E890CCF3C
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP001124 Genomic DNA. Translation: ACH37523.1.
RefSeqiYP_002137319.1. NC_011146.1.

Genome annotation databases

EnsemblBacteriaiACH37523; ACH37523; Gbem_0494.
GeneIDi6783323.
KEGGigbm:Gbem_0494.
PATRICi21984645. VBIGeoBem56306_0485.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP001124 Genomic DNA. Translation: ACH37523.1 .
RefSeqi YP_002137319.1. NC_011146.1.

3D structure databases

ProteinModelPortali B5EBQ4.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 404380.Gbem_0494.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ACH37523 ; ACH37523 ; Gbem_0494 .
GeneIDi 6783323.
KEGGi gbm:Gbem_0494.
PATRICi 21984645. VBIGeoBem56306_0485.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayi UPA00219 .
BioCyci GBEM404380:GHFR-498-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. 2 hits.
[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.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Bem / ATCC BAA-1014 / DSM 16622.

Entry informationi

Entry nameiDDL_GEOBB
AccessioniPrimary (citable) accession number: B5EBQ4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: October 14, 2008
Last modified: May 14, 2014
This is version 43 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

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