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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Psychrobacter cryohalolentis (strain K5)
Status
Unreviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Cell wall formation.UniRule annotationSAAS annotation

Catalytic activityi

ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine.UniRule annotationSAAS annotation

Cofactori

Protein has several cofactor binding sites:
  • Mg2+UniRule annotationSAAS annotation, Mn2+UniRule annotationSAAS annotationNote: Binds 2 magnesium or manganese ions per subunit.UniRule annotationSAAS annotation
  • Mg2+, Mn2+Note: Binds 2 magnesium or manganese ions per subunit.

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi330 – 3301Magnesium or manganese 1UniRule annotation
Metal bindingi343 – 3431Magnesium or manganese 1UniRule annotation
Metal bindingi343 – 3431Magnesium or manganese 2UniRule annotation
Metal bindingi345 – 3451Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi205 – 26056ATPUniRule 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

LigaseUniRule annotationSAAS annotation

Keywords - Biological processi

Cell shape, Cell wall biogenesis/degradationUniRule annotationSAAS annotation, Peptidoglycan synthesisUniRule annotationSAAS annotation

Keywords - Ligandi

ATP-bindingUniRule annotationSAAS annotation, MagnesiumUniRule annotationSAAS annotation, ManganeseUniRule annotationSAAS annotation, Metal-bindingUniRule annotationSAAS annotation, Nucleotide-binding

Enzyme and pathway databases

BioCyciPCRY335284:GHE9-2072-MONOMER.
UniPathwayiUPA00219.

Names & Taxonomyi

Protein namesi
Recommended name:
D-alanine--D-alanine ligaseUniRule annotationSAAS annotation (EC:6.3.2.4UniRule annotationSAAS annotation)
Alternative name(s):
D-Ala-D-Ala ligaseUniRule annotation
D-alanylalanine synthetaseUniRule annotation
Gene namesi
Name:ddlUniRule annotation
Ordered Locus Names:Pcryo_2030Imported
OrganismiPsychrobacter cryohalolentis (strain K5)Imported
Taxonomic identifieri335284 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesMoraxellaceaePsychrobacter
ProteomesiUP000002425: Chromosome

Subcellular locationi

Cytoplasm UniRule annotationSAAS annotation

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

CytoplasmUniRule annotationSAAS annotation

Interactioni

Protein-protein interaction databases

STRINGi335284.Pcryo_2030.

Structurei

3D structure databases

ProteinModelPortaliQ1Q946.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini179 – 376198ATP-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.
OMAiPFLLEMN.
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.

Q1Q946-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNNTKENNNI DEDGVNVEQN ATDNSNNNIK GNVQNNTAPI INPETALAAA
60 70 80 90 100
AQAEQDKVNN NSQSANTLPA IKESKVKEGN EFGRVAVIYG GNSNERSVSL
110 120 130 140 150
DSGAAVLQAL QNQGVDATHF DPKHQDITEL RQYDRVFNVL HGRGGEDGLL
160 170 180 190 200
QGVLQWFDIP QTGSGILASA LGMDKVRTKQ LWQGCGLSTA PFSLLTADTD
210 220 230 240 250
WQQVVNMLGL PLIIKPVHEG SSIGMTKVNN LDELPAAYAT AVQCGDVVMA
260 270 280 290 300
ERWITGREFT IVIIDDEAYP VIRLEPADIT NFYDFEAKYN RNDTSYYIPC
310 320 330 340 350
GLSAADEKHL QDLSLSAFRA VDAKGWGRID AMQDEAGNFW LLEINTVPGM
360 370
TSHSLVPMAA KARGMDFESL CWHILAQTV
Length:379
Mass (Da):41,383
Last modified:May 16, 2006 - v1
Checksum:iDA17D68F493E8BA6
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000323 Genomic DNA. Translation: ABE75807.1.
RefSeqiYP_581291.1. NC_007969.1.

Genome annotation databases

EnsemblBacteriaiABE75807; ABE75807; Pcryo_2030.
GeneIDi4035403.
KEGGipcr:Pcryo_2030.
PATRICi23063679. VBIPsyCry128170_2154.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000323 Genomic DNA. Translation: ABE75807.1.
RefSeqiYP_581291.1. NC_007969.1.

3D structure databases

ProteinModelPortaliQ1Q946.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi335284.Pcryo_2030.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABE75807; ABE75807; Pcryo_2030.
GeneIDi4035403.
KEGGipcr:Pcryo_2030.
PATRICi23063679. VBIPsyCry128170_2154.

Phylogenomic databases

eggNOGiCOG1181.
HOGENOMiHOG000011592.
KOiK01921.
OMAiPFLLEMN.
OrthoDBiEOG6ND0KB.

Enzyme and pathway databases

UniPathwayiUPA00219.
BioCyciPCRY335284:GHE9-2072-MONOMER.

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]
ProtoNetiSearch...

Publicationsi

  1. "Complete sequence of chromosome of Psychrobacter cryohalolentis K5."
    US DOE Joint Genome Institute
    Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S., Brettin T., Bruce D., Han C., Tapia R., Sims D.R., Gilna P., Schmutz J.
    , Larimer F., Land M., Hauser L., Kyrpides N., Kim E., Richardson P.
    Submitted (MAR-2006) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K5Imported.

Entry informationi

Entry nameiQ1Q946_PSYCK
AccessioniPrimary (citable) accession number: Q1Q946
Entry historyi
Integrated into UniProtKB/TrEMBL: May 16, 2006
Last sequence update: May 16, 2006
Last modified: March 4, 2015
This is version 74 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteomeImported

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.