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A1VST4

- DDL_POLNA

UniProt

A1VST4 - DDL_POLNA

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Protein

D-alanine--D-alanine ligase

Gene
ddl, Pnap_3415
Organism
Polaromonas naphthalenivorans (strain CJ2)
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 bindingi264 – 2641Magnesium or manganese 1 By similarity
Metal bindingi278 – 2781Magnesium or manganese 1 By similarity
Metal bindingi278 – 2781Magnesium or manganese 2 By similarity
Metal bindingi280 – 2801Magnesium or manganese 2 By similarity

Regions

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

BioCyciPNAP365044:GJ8X-3464-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:Pnap_3415
OrganismiPolaromonas naphthalenivorans (strain CJ2)
Taxonomic identifieri365044 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesComamonadaceaePolaromonas
ProteomesiUP000000644: 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 – 325325D-alanine--D-alanine ligaseUniRule annotationPRO_0000341150Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi365044.Pnap_3415.

Structurei

3D structure databases

ProteinModelPortaliA1VST4.
SMRiA1VST4. Positions 9-313.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini107 – 311205ATP-graspAdd
BLAST

Sequence similaritiesi

Contains 1 ATP-grasp domain.

Phylogenomic databases

eggNOGiCOG1181.
HOGENOMiHOG000011592.
KOiK01921.
OMAiDRIQAND.
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.

A1VST4-1 [UniParc]FASTAAdd to Basket

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MSPNPSSFGK VAVLMGGRSA EREISLMSGS GVVQALRSQG IDAHAFDPAE    50
RDLGELKTGG FARCFIALHG RFGEDGTVQG ALELLGIPYT GSGVMASSMA 100
IDKVMTKRLL LSESLPTPRY VLLRRGGYSP AQVDAIVDTL GLPLIVKPAR 150
EGSSLGLSKV TERAAMAAAV ALAEKMDADI LCEQFISGDE VTCPVLGTGE 200
QARALPVIRI VAPEGNYDYQ NKYFTDTTQY LVPCGLPAGE EAAIQQLVLQ 250
AFRTLNCRGW ARADVMIDQA TRKPYLLEIN TSPGMTGHSL VPMSARAAGI 300
SYEALCVEVL KTALLDHQPR DGSLP 325
Length:325
Mass (Da):34,584
Last modified:February 6, 2007 - v1
Checksum:iA75A4DD1D3D691F3
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000529 Genomic DNA. Translation: ABM38712.1.
RefSeqiYP_983633.1. NC_008781.1.

Genome annotation databases

EnsemblBacteriaiABM38712; ABM38712; Pnap_3415.
GeneIDi4688839.
KEGGipna:Pnap_3415.
PATRICi22951551. VBIPolNap76733_4296.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000529 Genomic DNA. Translation: ABM38712.1 .
RefSeqi YP_983633.1. NC_008781.1.

3D structure databases

ProteinModelPortali A1VST4.
SMRi A1VST4. Positions 9-313.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 365044.Pnap_3415.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ABM38712 ; ABM38712 ; Pnap_3415 .
GeneIDi 4688839.
KEGGi pna:Pnap_3415.
PATRICi 22951551. VBIPolNap76733_4296.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayi UPA00219 .
BioCyci PNAP365044:GJ8X-3464-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: CJ2.

Entry informationi

Entry nameiDDL_POLNA
AccessioniPrimary (citable) accession number: A1VST4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 10, 2008
Last sequence update: February 6, 2007
Last modified: May 14, 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

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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