Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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 bindingi270Magnesium or manganese 1UniRule annotation1
Metal bindingi282Magnesium or manganese 1UniRule annotation1
Metal bindingi282Magnesium or manganese 2UniRule annotation1
Metal bindingi284Magnesium or manganese 2UniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi147 – 198ATPUniRule annotationAdd BLAST52

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

BRENDAi6.3.2.4. 7852.
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:TTHA1587
OrganismiThermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Taxonomic identifieri300852 [NCBI]
Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus
Proteomesi
  • UP000000532 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_00003411881 – 319D-alanine--D-alanine ligaseAdd BLAST319

Interactioni

Protein-protein interaction databases

STRINGi300852.TTHA1587.

Structurei

Secondary structure

1319
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 8Combined sources6
Helixi14 – 27Combined sources14
Beta strandi32 – 37Combined sources6
Helixi46 – 55Combined sources10
Helixi71 – 73Combined sources3
Beta strandi75 – 79Combined sources5
Turni84 – 87Combined sources4
Helixi90 – 98Combined sources9
Beta strandi102 – 104Combined sources3
Helixi107 – 114Combined sources8
Helixi118 – 125Combined sources8
Beta strandi133 – 137Combined sources5
Beta strandi150 – 156Combined sources7
Turni159 – 162Combined sources4
Beta strandi164 – 168Combined sources5
Helixi169 – 171Combined sources3
Helixi172 – 180Combined sources9
Beta strandi184 – 190Combined sources7
Beta strandi196 – 207Combined sources12
Beta strandi209 – 217Combined sources9
Beta strandi219 – 222Combined sources4
Helixi225 – 229Combined sources5
Turni231 – 233Combined sources3
Beta strandi234 – 239Combined sources6
Helixi244 – 261Combined sources18
Beta strandi265 – 274Combined sources10
Beta strandi277 – 286Combined sources10
Helixi294 – 301Combined sources8
Helixi306 – 317Combined sources12

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2FB9X-ray1.90A1-319[»]
2YZGX-ray2.30A/B/C1-319[»]
2YZMX-ray2.21A/B/C1-319[»]
2YZNX-ray2.60A/B/C1-319[»]
2ZDGX-ray2.20A/B/C/D1-319[»]
2ZDHX-ray1.90A/B/C/D1-319[»]
2ZDQX-ray2.30A/B1-319[»]
ProteinModelPortaliQ5SHZ3.
SMRiQ5SHZ3.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ5SHZ3.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini120 – 315ATP-graspUniRule annotationAdd BLAST196

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.
OMAiNREIRFR.
PhylomeDBiQ5SHZ3.

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.

Q5SHZ3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRVLLIAGGV SPEHEVSLLS AEGVLRHIPF PTDLAVIAQD GRWLLGEKAL
60 70 80 90 100
TALEAKAAPE GEHPFPPPLS WERYDVVFPL LHGRFGEDGT VQGFLELLGK
110 120 130 140 150
PYVGAGVAAS ALCMDKDLSK RVLAQAGVPV VPWVAVRKGE PPVVPFDPPF
160 170 180 190 200
FVKPANTGSS VGISRVERFQ DLEAALALAF RYDEKAVVEK ALSPVRELEV
210 220 230 240 250
GVLGNVFGEA SPVGEVRYEA PFYDYETKYT PGRAELLIPA PLDPGTQETV
260 270 280 290 300
QELALKAYKV LGVRGMARVD FFLAEGELYL NELNTIPGFT PTSMYPRLFE
310
AGGVAYPELL RRLVELALT
Length:319
Mass (Da):34,666
Last modified:December 21, 2004 - v1
Checksum:i85E6F0AA367A13AF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP008226 Genomic DNA. Translation: BAD71410.1.
RefSeqiWP_011228789.1. NC_006461.1.
YP_144853.1. NC_006461.1.

Genome annotation databases

EnsemblBacteriaiBAD71410; BAD71410; BAD71410.
GeneIDi3168507.
KEGGittj:TTHA1587.
PATRICi23958129. VBITheThe93045_1557.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP008226 Genomic DNA. Translation: BAD71410.1.
RefSeqiWP_011228789.1. NC_006461.1.
YP_144853.1. NC_006461.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2FB9X-ray1.90A1-319[»]
2YZGX-ray2.30A/B/C1-319[»]
2YZMX-ray2.21A/B/C1-319[»]
2YZNX-ray2.60A/B/C1-319[»]
2ZDGX-ray2.20A/B/C/D1-319[»]
2ZDHX-ray1.90A/B/C/D1-319[»]
2ZDQX-ray2.30A/B1-319[»]
ProteinModelPortaliQ5SHZ3.
SMRiQ5SHZ3.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi300852.TTHA1587.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAD71410; BAD71410; BAD71410.
GeneIDi3168507.
KEGGittj:TTHA1587.
PATRICi23958129. VBITheThe93045_1557.

Phylogenomic databases

eggNOGiENOG4105CPF. Bacteria.
COG1181. LUCA.
HOGENOMiHOG000011593.
KOiK01921.
OMAiNREIRFR.
PhylomeDBiQ5SHZ3.

Enzyme and pathway databases

UniPathwayiUPA00219.
BRENDAi6.3.2.4. 7852.

Miscellaneous databases

EvolutionaryTraceiQ5SHZ3.

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_THET8
AccessioniPrimary (citable) accession number: Q5SHZ3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 10, 2008
Last sequence update: December 21, 2004
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. 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.