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Q5HEB7

- DDL_STAAC

UniProt

Q5HEB7 - DDL_STAAC

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Protein

D-alanine--D-alanine ligase

Gene
ddl, SACOL2074
Organism
Staphylococcus aureus (strain COL)
Status
Reviewed - Annotation score: 3 out of 5 - Experimental evidence at protein leveli

Functioni

Cell wall formation By similarity.UniRule annotation

Catalytic activityi

ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine.UniRule annotation

Cofactori

Binds 2 magnesium or manganese ions per subunit By similarity.

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi293 – 2931Magnesium or manganese 1 By similarity
Metal bindingi306 – 3061Magnesium or manganese 1 By similarity
Metal bindingi306 – 3061Magnesium or manganese 2 By similarity
Metal bindingi308 – 3081Magnesium or manganese 2 By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi167 – 22256ATP By similarityAdd
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. peptidoglycan biosynthetic process Source: UniProtKB-HAMAP
  2. 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

BioCyciMetaCyc:MONOMER-15463.
SAUR93062:GCEP-2068-MONOMER.
UniPathwayiUPA00219.

Names & Taxonomyi

Protein namesi
Recommended name:
D-alanine--D-alanine ligase (EC:6.3.2.4)
Alternative name(s):
D-Ala-D-Ala ligase
D-alanylalanine synthetase
Gene namesi
Name:ddl
Ordered Locus Names:SACOL2074
OrganismiStaphylococcus aureus (strain COL)
Taxonomic identifieri93062 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesStaphylococcus
ProteomesiUP000000530: Chromosome

Subcellular locationi

Cytoplasm By similarity 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 – 356356D-alanine--D-alanine ligaseUniRule annotationPRO_0000177874Add
BLAST

Proteomic databases

PRIDEiQ5HEB7.

Interactioni

Protein-protein interaction databases

STRINGi93062.SACOL2074.

Structurei

Secondary structure

1
356
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 118
Beta strandi13 – 153
Helixi17 – 2913
Turni33 – 353
Beta strandi36 – 438
Beta strandi49 – 524
Helixi62 – 643
Helixi67 – 693
Beta strandi70 – 734
Helixi77 – 804
Beta strandi85 – 873
Beta strandi89 – 946
Beta strandi98 – 1003
Helixi104 – 1129
Beta strandi116 – 1183
Helixi121 – 1288
Helixi130 – 14011
Beta strandi147 – 1515
Helixi152 – 16918
Beta strandi172 – 1809
Beta strandi182 – 1843
Beta strandi188 – 1925
Helixi193 – 20412
Beta strandi208 – 2147
Beta strandi219 – 23012
Beta strandi237 – 2393
Beta strandi259 – 2624
Helixi267 – 28317
Beta strandi288 – 2969
Beta strandi302 – 3109
Helixi318 – 3258
Helixi330 – 35627

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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. Positions 3-356.

Miscellaneous databases

EvolutionaryTraceiQ5HEB7.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini134 – 339206ATP-graspAdd
BLAST

Sequence similaritiesi

Contains 1 ATP-grasp domain.

Phylogenomic databases

eggNOGiCOG1181.
HOGENOMiHOG000011593.
KOiK01921.
OMAiQIDVIFP.
OrthoDBiEOG64BQ73.

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.
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.

Q5HEB7-1 [UniParc]FASTAAdd to Basket

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MTKENICIVF GGKSAEHEVS ILTAQNVLNA IDKDKYHVDI IYITNDGDWR    50
KQNNITAEIK STDELHLENG EALEISQLLK ESSSGQPYDA VFPLLHGPNG 100
EDGTIQGLFE VLDVPYVGNG VLSAASSMDK LVMKQLFEHR GLPQLPYISF 150
LRSEYEKYEH NILKLVNDKL NYPVFVKPAN LGSSVGISKC NNEAELKEGI 200
KEAFQFDRKL VIEQGVNARE IEVAVLGNDY PEATWPGEVV KDVAFYDYKS 250
KYKDGKVQLQ IPADLDEDVQ LTLRNMALEA FKATDCSGLV RADFFVTEDN 300
QIYINETNAM PGFTAFSMYP KLWENMGLSY PELITKLIEL AKERHQDKQK 350
NKYKID 356
Length:356
Mass (Da):40,231
Last modified:February 15, 2005 - v1
Checksum:i65822883958DC645
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000046 Genomic DNA. Translation: AAW37036.1.
RefSeqiYP_186890.1. NC_002951.2.

Genome annotation databases

EnsemblBacteriaiAAW37036; AAW37036; SACOL2074.
GeneIDi3238133.
KEGGisac:SACOL2074.
PATRICi19530419. VBIStaAur112458_2021.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000046 Genomic DNA. Translation: AAW37036.1 .
RefSeqi YP_186890.1. NC_002951.2.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2I80 X-ray 2.19 A/B 1-356 [» ]
2I87 X-ray 2.00 A/B 1-356 [» ]
2I8C X-ray 2.46 A/B 1-356 [» ]
3N8D X-ray 2.30 A/B 1-356 [» ]
ProteinModelPortali Q5HEB7.
SMRi Q5HEB7. Positions 3-356.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 93062.SACOL2074.

Proteomic databases

PRIDEi Q5HEB7.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAW37036 ; AAW37036 ; SACOL2074 .
GeneIDi 3238133.
KEGGi sac:SACOL2074.
PATRICi 19530419. VBIStaAur112458_2021.

Phylogenomic databases

eggNOGi COG1181.
HOGENOMi HOG000011593.
KOi K01921.
OMAi QIDVIFP.
OrthoDBi EOG64BQ73.

Enzyme and pathway databases

UniPathwayi UPA00219 .
BioCyci MetaCyc:MONOMER-15463.
SAUR93062:GCEP-2068-MONOMER.

Miscellaneous databases

EvolutionaryTracei Q5HEB7.
PROi Q5HEB7.

Family and domain databases

Gene3Di 3.30.1490.20. 1 hit.
3.30.470.20. 1 hit.
3.40.50.20. 1 hit.
HAMAPi MF_00047. Dala_Dala_lig.
InterProi IPR011761. 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 ]
PANTHERi PTHR23132. PTHR23132. 1 hit.
Pfami PF07478. Dala_Dala_lig_C. 1 hit.
PF01820. Dala_Dala_lig_N. 1 hit.
[Graphical view ]
SUPFAMi SSF52440. SSF52440. 1 hit.
TIGRFAMsi TIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITEi PS50975. ATP_GRASP. 1 hit.
PS00843. DALA_DALA_LIGASE_1. 1 hit.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain."
    Gill S.R., Fouts D.E., Archer G.L., Mongodin E.F., DeBoy R.T., Ravel J., Paulsen I.T., Kolonay J.F., Brinkac L.M., Beanan M.J., Dodson R.J., Daugherty S.C., Madupu R., Angiuoli S.V., Durkin A.S., Haft D.H., Vamathevan J.J., Khouri H.
    , Utterback T.R., Lee C., Dimitrov G., Jiang L., Qin H., Weidman J., Tran K., Kang K.H., Hance I.R., Nelson K.E., Fraser C.M.
    J. Bacteriol. 187:2426-2438(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: COL.

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: May 14, 2014
This is version 75 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

External Data

Dasty 3

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