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C4XRH9

- DDL_DESMR

UniProt

C4XRH9 - DDL_DESMR

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Protein

D-alanine--D-alanine ligase

Gene

ddl

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.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 bindingi249 – 2491Magnesium or manganese 1UniRule annotation
Metal bindingi261 – 2611Magnesium or manganese 1UniRule annotation
Metal bindingi261 – 2611Magnesium or manganese 2UniRule annotation
Metal bindingi263 – 2631Magnesium or manganese 2UniRule annotation

Regions

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

BioCyciDMAG573370:GHJL-2055-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:DMR_20330
OrganismiDesulfovibrio magneticus (strain ATCC 700980 / DSM 13731 / RS-1)
Taxonomic identifieri573370 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfovibrionaceaeDesulfovibrio
ProteomesiUP000009071: 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 – 304304D-alanine--D-alanine ligasePRO_1000202198Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi573370.DMR_20330.

Structurei

3D structure databases

ProteinModelPortaliC4XRH9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

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

        10         20         30         40         50
MKILLVAGGW SSERAVSLSG AVQIEKALTS LGHEVVPYDL SHDFPGFVRR
60 70 80 90 100
AKACDFVFLS LHGAPGEDGL PQALLDAAGV PYQGSGPAGS FLALNKAASK
110 120 130 140 150
QLFLEACLPT PRWTFVPRDA GTSARPDFPL PWFVKPNLGG SSIHMTLVRR
160 170 180 190 200
AEELPAALEK VFAHGDDALI EEGLSGPELT CAVLGDEALP PILIRPKAGE
210 220 230 240 250
FFDYASKYEP DAADEICPAP VEPAVTEELS RLSLAAHRVL GLCGYSRADF
260 270 280 290 300
ILAPEGLRLL EVNTLPGMTP TSLLPRAAAT AGLSFADLIA RLIELGLAQQ

AKRP
Length:304
Mass (Da):32,255
Last modified:July 28, 2009 - v1
Checksum:i285C53A06A55A506
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP010904 Genomic DNA. Translation: BAH75524.1.
RefSeqiYP_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:
EMBLi
GenBanki
DDBJi
Links Updated
AP010904 Genomic DNA. Translation: BAH75524.1 .
RefSeqi 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: November 26, 2014
This is version 42 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