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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Yersinia pestis
Status
Reviewed-Annotation score: -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

Keywordsi

Molecular functionLigase
Biological processCell shape, Cell wall biogenesis/degradation, Peptidoglycan synthesis
LigandATP-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

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001779121 – 306D-alanine--D-alanine ligaseAdd BLAST306

Proteomic databases

PaxDbiQ8ZIE7

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

Phylogenomic databases

eggNOGiENOG4105CPF Bacteria
COG1181 LUCA
HOGENOMiHOG000011592
KOiK01921
OMAiYETKYTE

Family and domain databases

Gene3Di3.30.1490.20, 1 hit
HAMAPiMF_00047 Dala_Dala_lig, 1 hit
InterProiView protein in InterPro
IPR011761 ATP-grasp
IPR013815 ATP_grasp_subdomain_1
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_sf
PfamiView protein in Pfam
PF07478 Dala_Dala_lig_C, 1 hit
PF01820 Dala_Dala_lig_N, 1 hit
PIRSFiPIRSF039102 Ddl/VanB, 1 hit
SUPFAMiSSF52440 SSF52440, 1 hit
TIGRFAMsiTIGR01205 D_ala_D_alaTIGR, 1 hit
PROSITEiView protein in PROSITE
PS50975 ATP_GRASP, 1 hit
PS00843 DALA_DALA_LIGASE_1, 1 hit
PS00844 DALA_DALA_LIGASE_2, 1 hit

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_PDBR01000066.1
YP_002345628.1, NC_003143.1

Genome annotation databases

EnsemblBacteriaiAAM87172; AAM87172; y3624
AAS63775; AAS63775; YP_3627
GeneIDi1173401
KEGGiype:YPO0557
ypk:y3624
ypm:YP_3627
PATRICifig|214092.21.peg.810

Similar proteinsi

Entry informationi

Entry nameiDDL_YERPE
AccessioniPrimary (citable) accession number: Q8ZIE7
Secondary accession number(s): Q0WJB0
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 2, 2002
Last sequence update: March 1, 2002
Last modified: May 23, 2018
This is version 129 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

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