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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Coxiella burnetii (strain RSA 493 / Nine Mile phase I)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

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: peptidoglycan biosynthesis

This protein is involved in the pathway peptidoglycan biosynthesis, which is part of Cell wall biogenesis.UniRule annotation
View all proteins of this organism that are known to be involved in the pathway peptidoglycan biosynthesis and in Cell wall biogenesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi303Magnesium or manganese 1UniRule annotation1
Metal bindingi316Magnesium or manganese 1UniRule annotation1
Metal bindingi316Magnesium or manganese 2UniRule annotation1
Metal bindingi318Magnesium or manganese 2UniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi176 – 231ATPUniRule annotationAdd BLAST56

GO - Molecular functioni

GO - Biological processi

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

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:CBU_1338
OrganismiCoxiella burnetii (strain RSA 493 / Nine Mile phase I)
Taxonomic identifieri227377 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaLegionellalesCoxiellaceaeCoxiella
Proteomesi
  • UP000002671 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001778131 – 372D-alanine--D-alanine ligaseAdd BLAST372

Interactioni

Protein-protein interaction databases

STRINGi227377.CBU_1338.

Structurei

Secondary structure

1372
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi4 – 12Combined sources9
Helixi18 – 31Combined sources14
Turni34 – 36Combined sources3
Beta strandi37 – 44Combined sources8
Beta strandi50 – 53Combined sources4
Helixi56 – 61Combined sources6
Helixi64 – 70Combined sources7
Beta strandi73 – 78Combined sources6
Beta strandi87 – 89Combined sources3
Beta strandi100 – 104Combined sources5
Turni109 – 112Combined sources4
Helixi115 – 122Combined sources8
Beta strandi127 – 129Combined sources3
Helixi132 – 139Combined sources8
Helixi141 – 150Combined sources10
Beta strandi159 – 161Combined sources3
Helixi170 – 177Combined sources8
Beta strandi183 – 189Combined sources7
Helixi193 – 195Combined sources3
Beta strandi196 – 199Combined sources4
Helixi202 – 212Combined sources11
Turni213 – 215Combined sources3
Beta strandi219 – 223Combined sources5
Beta strandi227 – 239Combined sources13
Beta strandi246 – 249Combined sources4
Beta strandi268 – 271Combined sources4
Helixi277 – 293Combined sources17
Beta strandi298 – 306Combined sources9
Beta strandi312 – 320Combined sources9
Helixi328 – 335Combined sources8
Helixi340 – 370Combined sources31

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3TQTX-ray1.88A/B1-372[»]
ProteinModelPortaliQ83BZ9.
SMRiQ83BZ9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini145 – 349ATP-graspUniRule annotationAdd BLAST205

Sequence similaritiesi

Belongs to the D-alanine--D-alanine ligase family.UniRule annotation
Contains 1 ATP-grasp domain.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105CPF. Bacteria.
COG1181. LUCA.
HOGENOMiHOG000011593.
KOiK01921.
OMAiMDKIAMK.

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. 1 hit.
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]
PfamiPF07478. Dala_Dala_lig_C. 1 hit.
PF01820. Dala_Dala_lig_N. 1 hit.
[Graphical view]
PIRSFiPIRSF039102. Ddl/VanB. 1 hit.
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.

Q83BZ9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAEKLHISVL CGGQSTEHEI SIQSAKNIVN TLDAAKYLIS VIFIDHVGRW
60 70 80 90 100
YLIDQPEMFL AHSPDHLVKE GSARPITIAF GDAAKPWQSL NGDGRRYSAD
110 120 130 140 150
CVFPMVHGTQ GEDGALQGLL ELLNLPYVGA NVQSSAVCME KDLTKTVLRA
160 170 180 190 200
GGIPVVDWHT LSPRDATEGV YQRLLDRWGT SELFVKAVSL GSSVATLPVK
210 220 230 240 250
TETEFTKAVK EVFRYDDRLM VEPRIRGREI ECAVLGNGAP KASLPGEIIP
260 270 280 290 300
HHDYYSYDAK YLDPNGATTT TSVDLSESVT KQIQQIAIDA FKMVHCSGMA
310 320 330 340 350
RVDFFVTPNN KVLVNEINTI PGFTNISMYP KMWEASGLPC PNLLDQLIEL
360 370
AIDRHQEQQK LIRCYEVKAR SL
Length:372
Mass (Da):41,218
Last modified:June 1, 2003 - v1
Checksum:iC983B28F92B519EC
GO

Sequence cautioni

The sequence AAO90841 differs from that shown. Reason: Erroneous initiation.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE016828 Genomic DNA. Translation: AAO90841.2. Different initiation.
RefSeqiNP_820327.2. NC_002971.3.

Genome annotation databases

EnsemblBacteriaiAAO90841; AAO90841; CBU_1338.
GeneIDi1209244.
KEGGicbu:CBU_1338.
PATRICi17931413. VBICoxBur82552_1330.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE016828 Genomic DNA. Translation: AAO90841.2. Different initiation.
RefSeqiNP_820327.2. NC_002971.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3TQTX-ray1.88A/B1-372[»]
ProteinModelPortaliQ83BZ9.
SMRiQ83BZ9.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi227377.CBU_1338.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAO90841; AAO90841; CBU_1338.
GeneIDi1209244.
KEGGicbu:CBU_1338.
PATRICi17931413. VBICoxBur82552_1330.

Phylogenomic databases

eggNOGiENOG4105CPF. Bacteria.
COG1181. LUCA.
HOGENOMiHOG000011593.
KOiK01921.
OMAiMDKIAMK.

Enzyme and pathway databases

UniPathwayiUPA00219.

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. 1 hit.
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]
PfamiPF07478. Dala_Dala_lig_C. 1 hit.
PF01820. Dala_Dala_lig_N. 1 hit.
[Graphical view]
PIRSFiPIRSF039102. Ddl/VanB. 1 hit.
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...

Entry informationi

Entry nameiDDL_COXBU
AccessioniPrimary (citable) accession number: Q83BZ9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 2003
Last sequence update: June 1, 2003
Last modified: November 2, 2016
This is version 88 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. Coxiella burnetii
    Coxiella burnetii (strain RSA 493): entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

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 one 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.