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C4XRH9

- DDL_DESMR

UniProt

C4XRH9 - DDL_DESMR

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Protein

D-alanine--D-alanine ligase

Gene
ddl, DMR_20330
Organism
Desulfovibrio magneticus (strain ATCC 700980 / DSM 13731 / RS-1)
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 bindingi249 – 2491Magnesium or manganese 1 By similarity
Metal bindingi261 – 2611Magnesium or manganese 1 By similarity
Metal bindingi261 – 2611Magnesium or manganese 2 By similarity
Metal bindingi263 – 2631Magnesium or manganese 2 By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi126 – 18055ATP 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

BioCyciDMAG573370:GHJL-2055-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:DMR_20330
OrganismiDesulfovibrio magneticus (strain ATCC 700980 / DSM 13731 / RS-1)
Taxonomic identifieri573370 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfovibrionaceaeDesulfovibrio
ProteomesiUP000009071: 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 – 304304D-alanine--D-alanine ligaseUniRule annotationPRO_1000202198Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi573370.DMR_20330.

Structurei

3D structure databases

ProteinModelPortaliC4XRH9.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini100 – 294195ATP-graspAdd
BLAST

Sequence similaritiesi

Contains 1 ATP-grasp domain.

Phylogenomic databases

eggNOGiCOG1181.
HOGENOMiHOG000011592.
KOiK01921.
OMAiGCDARSS.
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. 2 hits.
[Graphical view]
SUPFAMiSSF52440. SSF52440. 1 hit.
PROSITEiPS50975. ATP_GRASP. 1 hit.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

C4XRH9-1 [UniParc]FASTAAdd to Basket

« Hide

MKILLVAGGW SSERAVSLSG AVQIEKALTS LGHEVVPYDL SHDFPGFVRR    50
AKACDFVFLS LHGAPGEDGL PQALLDAAGV PYQGSGPAGS FLALNKAASK 100
QLFLEACLPT PRWTFVPRDA GTSARPDFPL PWFVKPNLGG SSIHMTLVRR 150
AEELPAALEK VFAHGDDALI EEGLSGPELT CAVLGDEALP PILIRPKAGE 200
FFDYASKYEP DAADEICPAP VEPAVTEELS RLSLAAHRVL GLCGYSRADF 250
ILAPEGLRLL EVNTLPGMTP TSLLPRAAAT AGLSFADLIA RLIELGLAQQ 300
AKRP 304
Length:304
Mass (Da):32,255
Last modified:July 28, 2009 - v1
Checksum:i285C53A06A55A506
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AP010904 Genomic DNA. Translation: BAH75524.1.
RefSeqiWP_015860715.1. NC_012796.1.
YP_002953410.1. NC_012796.1.

Genome annotation databases

EnsemblBacteriaiBAH75524; BAH75524; DMR_20330.
GeneIDi7983730.
KEGGidma:DMR_20330.
PATRICi21750329. VBIDesMag26496_1935.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AP010904 Genomic DNA. Translation: BAH75524.1 .
RefSeqi WP_015860715.1. NC_012796.1.
YP_002953410.1. NC_012796.1.

3D structure databases

ProteinModelPortali C4XRH9.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 573370.DMR_20330.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai BAH75524 ; BAH75524 ; DMR_20330 .
GeneIDi 7983730.
KEGGi dma:DMR_20330.
PATRICi 21750329. VBIDesMag26496_1935.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayi UPA00219 .
BioCyci DMAG573370:GHJL-2055-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. 2 hits.
[Graphical view ]
SUPFAMi SSF52440. SSF52440. 1 hit.
PROSITEi PS50975. ATP_GRASP. 1 hit.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "Whole genome sequence of Desulfovibrio magneticus strain RS-1 revealed common gene clusters in magnetotactic bacteria."
    Nakazawa H., Arakaki A., Narita-Yamada S., Yashiro I., Jinno K., Aoki N., Tsuruyama A., Okamura Y., Tanikawa S., Fujita N., Takeyama H., Matsunaga T.
    Genome Res. 19:1801-1808(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700980 / DSM 13731 / RS-1.

Entry informationi

Entry nameiDDL_DESMR
AccessioniPrimary (citable) accession number: C4XRH9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 22, 2009
Last sequence update: July 28, 2009
Last modified: September 3, 2014
This is version 39 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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