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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Kocuria rhizophila (strain ATCC 9341 / DSM 348 / NBRC 103217 / DC2201)
Status
Reviewed-Annotation score: 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 bindingi327 – 3271Magnesium or manganese 1UniRule annotation
Metal bindingi340 – 3401Magnesium or manganese 1UniRule annotation
Metal bindingi340 – 3401Magnesium or manganese 2UniRule annotation
Metal bindingi342 – 3421Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi196 – 25156ATPUniRule 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

BioCyciKRHI378753:GJ8F-1060-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:KRH_10370
OrganismiKocuria rhizophila (strain ATCC 9341 / DSM 348 / NBRC 103217 / DC2201)
Taxonomic identifieri378753 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesMicrococcineaeMicrococcaceaeKocuria
ProteomesiUP000008838: Chromosome

Subcellular locationi

Cytoplasm 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 – 383383D-alanine--D-alanine ligasePRO_1000091188Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi378753.KRH_10370.

Structurei

3D structure databases

ProteinModelPortaliB2GFL1.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini164 – 373210ATP-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.
HOGENOMiHOG000011593.
KOiK01921.
OMAiWFPILHG.
OrthoDBiEOG64BQ73.

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. 1 hit.
[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.

B2GFL1-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSTTHETPEA TAEGDKPCIA VVFGGRSSEH SISLITARSV LRAIDRDRWD
60 70 80 90 100
VVSVGISTDG AWFLCSQEEL EALLDDQPMA QLPVGVHRVS LPLQTGDSRL
110 120 130 140 150
LIHDTSEHGA PLSRGRHIDA VFPLLHGPFG EDGTLQGMLE LADLPYVGCG
160 170 180 190 200
VAASAIGMDK HFMKLAFQAA GLEVGPYTVV HDRTWRTDPL GVREAVAELG
210 220 230 240 250
FPVFVKPARA GSSFGITRVD EPSQLDAAIA TAREHDLKLV VEAGIDGREI
260 270 280 290 300
ECAVLGGHGT DEARASLPGE IEVHGHALYD FEAKYVESDG ATLSCPARLP
310 320 330 340 350
EHVIDTLRRD AVRAFHAVDG EGLSRCDFFV TADERVLINE INTMPGFTPI
360 370 380
SMYPRMWAAS GIDYSALIDE LITLALERPV GLR
Length:383
Mass (Da):41,365
Last modified:June 10, 2008 - v1
Checksum:i06B548C65AB11521
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP009152 Genomic DNA. Translation: BAG29384.1.
RefSeqiWP_012398105.1. NC_010617.1.
YP_001854890.1. NC_010617.1.

Genome annotation databases

EnsemblBacteriaiBAG29384; BAG29384; KRH_10370.
GeneIDi6239472.
KEGGikrh:KRH_10370.
PATRICi22182290. VBIKocRhi5258_1008.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP009152 Genomic DNA. Translation: BAG29384.1.
RefSeqiWP_012398105.1. NC_010617.1.
YP_001854890.1. NC_010617.1.

3D structure databases

ProteinModelPortaliB2GFL1.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi378753.KRH_10370.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAG29384; BAG29384; KRH_10370.
GeneIDi6239472.
KEGGikrh:KRH_10370.
PATRICi22182290. VBIKocRhi5258_1008.

Phylogenomic databases

eggNOGiCOG1181.
HOGENOMiHOG000011593.
KOiK01921.
OMAiWFPILHG.
OrthoDBiEOG64BQ73.

Enzyme and pathway databases

UniPathwayiUPA00219.
BioCyciKRHI378753:GJ8F-1060-MONOMER.

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. 1 hit.
[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]
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 9341 / DSM 348 / NBRC 103217 / DC2201.

Entry informationi

Entry nameiDDL_KOCRD
AccessioniPrimary (citable) accession number: B2GFL1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: June 10, 2008
Last modified: February 4, 2015
This is version 49 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.