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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Yersinia pestis
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 bindingi257Magnesium or manganese 1UniRule annotation1
Metal bindingi270Magnesium or manganese 1UniRule annotation1
Metal bindingi270Magnesium or manganese 2UniRule annotation1
Metal bindingi272Magnesium or manganese 2UniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi134 – 189ATPUniRule 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
Synonyms:ddlB
Ordered Locus Names:YPO0557, y3624, YP_3627
OrganismiYersinia pestis
Taxonomic identifieri632 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesYersiniaceaeYersinia
Proteomesi
  • UP000000815 Componenti: Chromosome
  • UP000001019 Componenti: Chromosome
  • UP000002490 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_00001779121 – 306D-alanine--D-alanine ligaseAdd BLAST306

Proteomic databases

PRIDEiQ8ZIE7.

Interactioni

Protein-protein interaction databases

IntActiQ8ZIE7. 3 interactors.
STRINGi187410.y3624.

Structurei

Secondary structure

1306
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi4 – 9Combined sources6
Helixi16 – 32Combined sources17
Beta strandi36 – 41Combined sources6
Turni42 – 44Combined sources3
Helixi47 – 49Combined sources3
Turni50 – 54Combined sources5
Beta strandi57 – 60Combined sources4
Turni65 – 67Combined sources3
Beta strandi68 – 70Combined sources3
Helixi71 – 79Combined sources9
Beta strandi83 – 85Combined sources3
Helixi88 – 93Combined sources6
Helixi97 – 106Combined sources10
Beta strandi114 – 118Combined sources5
Helixi119 – 124Combined sources6
Helixi127 – 134Combined sources8
Helixi135 – 137Combined sources3
Beta strandi139 – 147Combined sources9
Turni150 – 153Combined sources4
Beta strandi155 – 157Combined sources3
Helixi160 – 162Combined sources3
Helixi163 – 171Combined sources9
Beta strandi175 – 181Combined sources7
Beta strandi187 – 193Combined sources7
Beta strandi201 – 204Combined sources4
Beta strandi206 – 209Combined sources4
Helixi212 – 216Combined sources5
Beta strandi222 – 226Combined sources5
Helixi231 – 247Combined sources17
Beta strandi252 – 260Combined sources9
Beta strandi266 – 274Combined sources9
Beta strandi278 – 281Combined sources4
Helixi282 – 290Combined sources9
Helixi294 – 303Combined sources10

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3V4ZX-ray2.69A/B1-306[»]
4ZQIX-ray2.30A/B/C/D1-306[»]
5BPFX-ray2.28A/B/C/D1-306[»]
5BPHX-ray1.70A/B/C/D1-306[»]
5C1OX-ray2.50A/B/C/D1-306[»]
5C1PX-ray2.40A/B/C/D1-306[»]
ProteinModelPortaliQ8ZIE7.
SMRiQ8ZIE7.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini101 – 303ATP-graspUniRule annotationAdd BLAST203

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.
HOGENOMiHOG000011592.
KOiK01921.
OMAiFQHDDEV.

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. 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.

Q8ZIE7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAEKVAVLLG GTSAEREVSL LSGQAVLAGL KEAGIDAYGV DTKDFPVTQL
60 70 80 90 100
KEQGFDKVFI ALHGRGGEDG TLQGVLEFLQ LPYTGSGVMA SALTMDKLRT
110 120 130 140 150
KLVWQALGLP ISPYVALNRQ QFETLSPEEL VACVAKLGLP LIVKPSHEGS
160 170 180 190 200
SVGMSKVDHA SELQKALVEA FQHDSDVLIE KWLSGPEFTV AILGDEVLPS
210 220 230 240 250
IRIQPPGVFY DYDAKYLSDK TQYFCPSGLS DESEQQLAAL ALQAYHALDC
260 270 280 290 300
SGWGRVDVMQ DRDGHFYLLE VNTSPGMTSH SLVPMAARQY GLSFSQLVAR

ILMLAD
Length:306
Mass (Da):33,150
Last modified:March 1, 2002 - v1
Checksum:iC78CFF3D2E11F846
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL590842 Genomic DNA. Translation: CAL19236.1.
AE009952 Genomic DNA. Translation: AAM87172.1.
AE017042 Genomic DNA. Translation: AAS63775.1.
PIRiAB0069.
RefSeqiWP_002210432.1. NZ_LQBA01000066.1.
YP_002345628.1. NC_003143.1.

Genome annotation databases

EnsemblBacteriaiAAM87172; AAM87172; y3624.
AAS63775; AAS63775; YP_3627.
GeneIDi1173401.
KEGGiype:YPO0557.
ypk:y3624.
ypm:YP_3627.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL590842 Genomic DNA. Translation: CAL19236.1.
AE009952 Genomic DNA. Translation: AAM87172.1.
AE017042 Genomic DNA. Translation: AAS63775.1.
PIRiAB0069.
RefSeqiWP_002210432.1. NZ_LQBA01000066.1.
YP_002345628.1. NC_003143.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3V4ZX-ray2.69A/B1-306[»]
4ZQIX-ray2.30A/B/C/D1-306[»]
5BPFX-ray2.28A/B/C/D1-306[»]
5BPHX-ray1.70A/B/C/D1-306[»]
5C1OX-ray2.50A/B/C/D1-306[»]
5C1PX-ray2.40A/B/C/D1-306[»]
ProteinModelPortaliQ8ZIE7.
SMRiQ8ZIE7.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiQ8ZIE7. 3 interactors.
STRINGi187410.y3624.

Proteomic databases

PRIDEiQ8ZIE7.

Protocols and materials databases

DNASUi1148571.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAM87172; AAM87172; y3624.
AAS63775; AAS63775; YP_3627.
GeneIDi1173401.
KEGGiype:YPO0557.
ypk:y3624.
ypm:YP_3627.

Phylogenomic databases

eggNOGiENOG4105CPF. Bacteria.
COG1181. LUCA.
HOGENOMiHOG000011592.
KOiK01921.
OMAiFQHDDEV.

Enzyme and pathway databases

UniPathwayiUPA00219.

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. 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_YERPE
AccessioniPrimary (citable) accession number: Q8ZIE7
Secondary accession number(s): Q0WJB0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 2, 2002
Last sequence update: March 1, 2002
Last modified: November 2, 2016
This is version 118 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. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.