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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Staphylococcus aureus (strain COL)
Status
Reviewed-Annotation score: Annotation score: 3 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 bindingi293Magnesium or manganese 1UniRule annotation1
Metal bindingi306Magnesium or manganese 1UniRule annotation1
Metal bindingi306Magnesium or manganese 2UniRule annotation1
Metal bindingi308Magnesium or manganese 2UniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi167 – 222ATPUniRule 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

BioCyciMetaCyc:MONOMER-15463.
BRENDAi6.3.2.4. 3352.
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:SACOL2074
OrganismiStaphylococcus aureus (strain COL)
Taxonomic identifieri93062 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesStaphylococcaceaeStaphylococcus
Proteomesi
  • UP000000530 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_00001778741 – 356D-alanine--D-alanine ligaseAdd BLAST356

Interactioni

Protein-protein interaction databases

STRINGi93062.SACOL2074.

Structurei

Secondary structure

1356
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi4 – 11Combined sources8
Beta strandi13 – 15Combined sources3
Helixi17 – 29Combined sources13
Turni33 – 35Combined sources3
Beta strandi36 – 43Combined sources8
Beta strandi49 – 52Combined sources4
Helixi62 – 64Combined sources3
Helixi67 – 69Combined sources3
Beta strandi70 – 73Combined sources4
Helixi77 – 80Combined sources4
Beta strandi85 – 87Combined sources3
Beta strandi89 – 94Combined sources6
Beta strandi98 – 100Combined sources3
Helixi104 – 112Combined sources9
Beta strandi116 – 118Combined sources3
Helixi121 – 128Combined sources8
Helixi130 – 140Combined sources11
Beta strandi147 – 151Combined sources5
Helixi152 – 169Combined sources18
Beta strandi172 – 180Combined sources9
Beta strandi182 – 184Combined sources3
Beta strandi188 – 192Combined sources5
Helixi193 – 204Combined sources12
Beta strandi208 – 214Combined sources7
Beta strandi219 – 230Combined sources12
Beta strandi237 – 239Combined sources3
Beta strandi259 – 262Combined sources4
Helixi267 – 283Combined sources17
Beta strandi288 – 296Combined sources9
Beta strandi302 – 310Combined sources9
Helixi318 – 325Combined sources8
Helixi330 – 356Combined sources27

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2I80X-ray2.19A/B1-356[»]
2I87X-ray2.00A/B1-356[»]
2I8CX-ray2.46A/B1-356[»]
3N8DX-ray2.30A/B1-356[»]
ProteinModelPortaliQ5HEB7.
SMRiQ5HEB7.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ5HEB7.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini134 – 339ATP-graspUniRule annotationAdd BLAST206

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.

Q5HEB7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTKENICIVF GGKSAEHEVS ILTAQNVLNA IDKDKYHVDI IYITNDGDWR
60 70 80 90 100
KQNNITAEIK STDELHLENG EALEISQLLK ESSSGQPYDA VFPLLHGPNG
110 120 130 140 150
EDGTIQGLFE VLDVPYVGNG VLSAASSMDK LVMKQLFEHR GLPQLPYISF
160 170 180 190 200
LRSEYEKYEH NILKLVNDKL NYPVFVKPAN LGSSVGISKC NNEAELKEGI
210 220 230 240 250
KEAFQFDRKL VIEQGVNARE IEVAVLGNDY PEATWPGEVV KDVAFYDYKS
260 270 280 290 300
KYKDGKVQLQ IPADLDEDVQ LTLRNMALEA FKATDCSGLV RADFFVTEDN
310 320 330 340 350
QIYINETNAM PGFTAFSMYP KLWENMGLSY PELITKLIEL AKERHQDKQK

NKYKID
Length:356
Mass (Da):40,231
Last modified:February 15, 2005 - v1
Checksum:i65822883958DC645
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000046 Genomic DNA. Translation: AAW37036.1.
RefSeqiWP_000159631.1. NC_002951.2.

Genome annotation databases

EnsemblBacteriaiAAW37036; AAW37036; SACOL2074.
GeneIDi28380334.
KEGGisac:SACOL2074.
PATRICi19530419. VBIStaAur112458_2021.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000046 Genomic DNA. Translation: AAW37036.1.
RefSeqiWP_000159631.1. NC_002951.2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2I80X-ray2.19A/B1-356[»]
2I87X-ray2.00A/B1-356[»]
2I8CX-ray2.46A/B1-356[»]
3N8DX-ray2.30A/B1-356[»]
ProteinModelPortaliQ5HEB7.
SMRiQ5HEB7.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi93062.SACOL2074.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAW37036; AAW37036; SACOL2074.
GeneIDi28380334.
KEGGisac:SACOL2074.
PATRICi19530419. VBIStaAur112458_2021.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayiUPA00219.
BioCyciMetaCyc:MONOMER-15463.
BRENDAi6.3.2.4. 3352.

Miscellaneous databases

EvolutionaryTraceiQ5HEB7.

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_STAAC
AccessioniPrimary (citable) accession number: Q5HEB7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 19, 2005
Last sequence update: February 15, 2005
Last modified: November 2, 2016
This is version 90 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

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.