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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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi270 – 2701Magnesium or manganese 1UniRule annotation
Metal bindingi282 – 2821Magnesium or manganese 1UniRule annotation
Metal bindingi282 – 2821Magnesium or manganese 2UniRule annotation
Metal bindingi284 – 2841Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi147 – 19852ATPUniRule annotationAdd
BLAST

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-HAMAP
  2. D-alanine-D-alanine ligase activity Source: UniProtKB-HAMAP
  3. magnesium ion binding Source: UniProtKB-HAMAP
  4. manganese ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. cell wall organization Source: UniProtKB-KW
  2. peptidoglycan biosynthetic process Source: UniProtKB-HAMAP
  3. regulation of cell shape Source: UniProtKB-KW
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

BioCyciTTHE300852:GH8R-1626-MONOMER.
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
ProteomesiUP000000532: Chromosome

Subcellular locationi

Cytoplasm UniRule annotation

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 319319D-alanine--D-alanine ligasePRO_0000341188Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi300852.TTHA1587.

Structurei

Secondary structure

1
319
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 86Combined sources
Helixi14 – 2714Combined sources
Beta strandi32 – 376Combined sources
Helixi46 – 5510Combined sources
Helixi71 – 733Combined sources
Beta strandi75 – 795Combined sources
Turni84 – 874Combined sources
Helixi90 – 989Combined sources
Beta strandi102 – 1043Combined sources
Helixi107 – 1148Combined sources
Helixi118 – 1258Combined sources
Beta strandi133 – 1375Combined sources
Beta strandi150 – 1567Combined sources
Turni159 – 1624Combined sources
Beta strandi164 – 1685Combined sources
Helixi169 – 1713Combined sources
Helixi172 – 1809Combined sources
Beta strandi184 – 1907Combined sources
Beta strandi196 – 20712Combined sources
Beta strandi209 – 2179Combined sources
Beta strandi219 – 2224Combined sources
Helixi225 – 2295Combined sources
Turni231 – 2333Combined sources
Beta strandi234 – 2396Combined sources
Helixi244 – 26118Combined sources
Beta strandi265 – 27410Combined sources
Beta strandi277 – 28610Combined sources
Helixi294 – 3018Combined sources
Helixi306 – 31712Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 1-319.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ5SHZ3.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini120 – 315196ATP-graspUniRule annotationAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG1181.
HOGENOMiHOG000011593.
KOiK01921.
OMAiVAAYEID.
OrthoDBiEOG64BQ73.
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.
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]
PANTHERiPTHR23132. PTHR23132. 1 hit.
PfamiPF07478. Dala_Dala_lig_C. 1 hit.
PF01820. Dala_Dala_lig_N. 1 hit.
[Graphical view]
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.
RefSeqiYP_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.
RefSeqiYP_144853.1. NC_006461.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 1-319.
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

eggNOGiCOG1181.
HOGENOMiHOG000011593.
KOiK01921.
OMAiVAAYEID.
OrthoDBiEOG64BQ73.
PhylomeDBiQ5SHZ3.

Enzyme and pathway databases

UniPathwayiUPA00219.
BioCyciTTHE300852:GH8R-1626-MONOMER.

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.
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]
PANTHERiPTHR23132. PTHR23132. 1 hit.
PfamiPF07478. Dala_Dala_lig_C. 1 hit.
PF01820. Dala_Dala_lig_N. 1 hit.
[Graphical view]
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...

Publicationsi

  1. "Complete genome sequence of Thermus thermophilus HB8."
    Masui R., Kurokawa K., Nakagawa N., Tokunaga F., Koyama Y., Shibata T., Oshima T., Yokoyama S., Yasunaga T., Kuramitsu S.
    Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: HB8 / ATCC 27634 / DSM 579.

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: January 7, 2015
This is version 78 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

External Data

Dasty 3

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 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.