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A4XQS6

- DDL_PSEMY

UniProt

A4XQS6 - DDL_PSEMY

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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Pseudomonas mendocina (strain ymp)
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 bindingi260 – 2601Magnesium or manganese 1UniRule annotation
Metal bindingi273 – 2731Magnesium or manganese 1UniRule annotation
Metal bindingi273 – 2731Magnesium or manganese 2UniRule annotation
Metal bindingi275 – 2751Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi137 – 19256ATPUniRule 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

BioCyciPMEN399739:GHR6-929-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:Pmen_0924
OrganismiPseudomonas mendocina (strain ymp)
Taxonomic identifieri399739 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas
ProteomesiUP000000229: 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 – 313313D-alanine--D-alanine ligasePRO_0000341155Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi399739.Pmen_0924.

Structurei

3D structure databases

ProteinModelPortaliA4XQS6.
SMRiA4XQS6. Positions 13-306.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini111 – 306196ATP-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.
OMAiANDTQYR.
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.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

A4XQS6-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSLHSSLDPK AFGRVAVLFG GKSAEREVSL KSGNAVLSAL QAAGVDAFGI
60 70 80 90 100
DVGDDFLQRL ASEKIDRAFI VLHGRGGEDG SMQGLLECAG IPYTGSGILA
110 120 130 140 150
SALAMDKLRT KQVWHSLGLP TPRHAVLTSQ ADCEAAAAEL GFPLIVKPAH
160 170 180 190 200
EGSSIGMAKV ESVEALIAAW QDAARYDSQV LVEQWIAGPE YTVAVLRGEV
210 220 230 240 250
LPPIGLGTPH SFYDYDAKYL ADDTQYRIPC GLSAEKEAEL KELTARACEA
260 270 280 290 300
VGTQGWARAD VMQDASGQFW LLEVNTVPGM TDHSLVPMAA RAAGLDFQQL
310
VLAILADSVE ARG
Length:313
Mass (Da):33,179
Last modified:May 29, 2007 - v1
Checksum:iA047906A8C20E8D5
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000680 Genomic DNA. Translation: ABP83692.1.
RefSeqiYP_001186424.1. NC_009439.1.

Genome annotation databases

EnsemblBacteriaiABP83692; ABP83692; Pmen_0924.
GeneIDi5108782.
KEGGipmy:Pmen_0924.
PATRICi19908280. VBIPseMen131592_0933.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000680 Genomic DNA. Translation: ABP83692.1 .
RefSeqi YP_001186424.1. NC_009439.1.

3D structure databases

ProteinModelPortali A4XQS6.
SMRi A4XQS6. Positions 13-306.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 399739.Pmen_0924.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ABP83692 ; ABP83692 ; Pmen_0924 .
GeneIDi 5108782.
KEGGi pmy:Pmen_0924.
PATRICi 19908280. VBIPseMen131592_0933.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayi UPA00219 .
BioCyci PMEN399739:GHR6-929-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.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ymp.

Entry informationi

Entry nameiDDL_PSEMY
AccessioniPrimary (citable) accession number: A4XQS6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 10, 2008
Last sequence update: May 29, 2007
Last modified: October 29, 2014
This is version 57 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