D-alanine--D-alanine ligase - Staphylococcus aureus (strain COL)

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Reviewed, UniProtKB/Swiss-Prot Q5HEB7 (DDL_STAAC)

Last modified February 9, 2010. Version 44. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein names

Recommended name:
    D-alanine--D-alanine ligase
    EC=6.3.2.4
Alternative name(s):
    D-alanylalanine synthetase
    D-Ala-D-Ala ligase

Gene names

Name:	ddl
Ordered Locus Names:	SACOL2074

Organism

Staphylococcus aureus (strain COL) [Complete proteome] [HAMAP]

Taxonomic identifier

93062 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Bacillales › Staphylococcus

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Protein attributes

Sequence length	356 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level.

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General annotation (Comments)

Function	Cell wall formation By similarity. HAMAP MF_00047
Catalytic activity	ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine. HAMAP MF_00047
Cofactor	Binds 2 magnesium or manganese ions per subunit By similarity. HAMAP MF_00047
Pathway	Cell wall biogenesis; peptidoglycan biosynthesis. HAMAP MF_00047
Subcellular location	Cytoplasm By similarity HAMAP MF_00047.
Sequence similarities	Belongs to the D-alanine--D-alanine ligase family. Contains 1 ATP-grasp domain.

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Ontologies

Keywords
Biological process	Cell shape Cell wall biogenesis/degradation Peptidoglycan synthesis
Cellular component	Cytoplasm
Ligand	ATP-binding Magnesium Manganese Metal-binding Nucleotide-binding
Molecular function	Ligase
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	cellular cell wall organization Inferred from electronic annotation. Source: UniProtKB-KW peptidoglycan biosynthetic process Inferred from electronic annotation. Source: HAMAP regulation of cell shape Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	cell wall Inferred from electronic annotation. Source: InterPro cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW D-alanine-D-alanine ligase activity Inferred from electronic annotation. Source: HAMAP magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW manganese ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 356

356

D-alanine--D-alanine ligase HAMAP MF_00047

PRO_0000177874

Regions

Domain

134 – 339

206

ATP-grasp

Nucleotide binding

167 – 222

ATP By similarity

Sites

Metal binding

293

Magnesium or manganese 1 By similarity

Metal binding

306

Magnesium or manganese 1 By similarity

Metal binding

306

Magnesium or manganese 2 By similarity

Metal binding

308

Magnesium or manganese 2 By similarity

Secondary structure

356

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

Q5HEB7-1 [UniParc].

Last modified February 15, 2005. Version 1.
Checksum: 65822883958DC645
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FASTA

356

40,231

        10         20         30         40         50         60 
MTKENICIVF GGKSAEHEVS ILTAQNVLNA IDKDKYHVDI IYITNDGDWR KQNNITAEIK 

        70         80         90        100        110        120 
STDELHLENG EALEISQLLK ESSSGQPYDA VFPLLHGPNG EDGTIQGLFE VLDVPYVGNG 

       130        140        150        160        170        180 
VLSAASSMDK LVMKQLFEHR GLPQLPYISF LRSEYEKYEH NILKLVNDKL NYPVFVKPAN 

       190        200        210        220        230        240 
LGSSVGISKC NNEAELKEGI KEAFQFDRKL VIEQGVNARE IEVAVLGNDY PEATWPGEVV 

       250        260        270        280        290        300 
KDVAFYDYKS KYKDGKVQLQ IPADLDEDVQ LTLRNMALEA FKATDCSGLV RADFFVTEDN 

       310        320        330        340        350 
QIYINETNAM PGFTAFSMYP KLWENMGLSY PELITKLIEL AKERHQDKQK NKYKID

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References

[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.

Fraser C.M.
J. Bacteriol. 187:2426-2438(2005) [PubMed: 15774886] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Additional computationally mapped references.

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Cross-references

Sequence databases

EMBL
GenBank
DDBJ

CP000046 Genomic DNA. Translation: AAW37036.1.

RefSeq

YP_186890.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ModBase

Search...

Protein-protein interaction databases

STRING

Q5HEB7.

Genome annotation databases

GeneID

3238133.

GenomeReviews

Gene locus SACOL2074 in contig CP000046_GR.

KEGG

sac:SACOL2074.

TIGR

SACOL2074.

Phylogenomic databases

eggNOG

COG1181.

HOGENOM

HBG427092.

OMA

FTDISMY.

Enzyme and pathway databases

BioCyc

SAUR93062:SACOL2074-MONOMER.

Family and domain databases

HAMAP

MF_00047. Dala_Dala_lig.
[Tree]

InterPro

IPR011761. ATP-grasp.
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.
IPR013817. Pre-ATP_grasp.
IPR016185. PreATP-grasp-like.
[Graphical view]

Gene3D

G3DSA:3.30.470.20. ATP_grasp_subdomain_2. 1 hit.
G3DSA:3.40.50.20. Pre-ATP_grasp. 1 hit.

Pfam

PF07478. Dala_Dala_lig_C. 1 hit.
PF01820. Dala_Dala_lig_N. 1 hit.
[Graphical view]

TIGRFAMs

TIGR01205. D_ala_D_alaTIGR. 1 hit.

PROSITE

PS50975. ATP_GRASP. 1 hit.
PS00843. DALA_DALA_LIGASE_1. 1 hit.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view]

ProtoNet

Search...

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Entry information

Entry name

DDL_STAAC

Accession

Primary (citable) accession number: Q5HEB7

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 19, 2005
Last sequence update:	February 15, 2005
Last modified:	February 9, 2010
This is version 44 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)

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