Q5HEB7 (DDL_STAAC) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
D-alanine--D-alanine ligase
EC=6.3.2.4

Alternative name(s):
D-Ala-D-Ala ligase
D-alanylalanine synthetase

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

Protein attributes

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

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.
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.

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: UniProtKB-KW 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: EC metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

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

56

ATP By similarity

Sites

Metal binding

293

1

Magnesium or manganese 1 By similarity

Metal binding

306

1

Magnesium or manganese 1 By similarity

Metal binding

306

1

Magnesium or manganese 2 By similarity

Metal binding

308

1

Magnesium or manganese 2 By similarity

Secondary structure

1

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356

Helix Strand Turn

Details...

Beta strand

4 – 11

8

Helix

17 – 29

13

Turn

33 – 35

3

Beta strand

36 – 43

8

Beta strand

49 – 52

4

Helix

62 – 64

3

Helix

67 – 69

3

Beta strand

70 – 73

4

Helix

77 – 80

4

Beta strand

85 – 87

3

Beta strand

89 – 95

7

Beta strand

98 – 103

6

Helix

104 – 111

8

Beta strand

116 – 118

3

Helix

121 – 127

7

Helix

130 – 139

10

Beta strand

147 – 151

5

Helix

152 – 169

18

Beta strand

172 – 183

12

Beta strand

188 – 192

5

Helix

193 – 203

11

Turn

204 – 206

3

Beta strand

208 – 214

7

Beta strand

219 – 230

12

Beta strand

237 – 239

3

Beta strand

259 – 262

4

Helix

267 – 283

17

Beta strand

287 – 296

10

Beta strand

302 – 310

9

Helix

318 – 324

7

Turn

325 – 327

3

Sequences

	Sequence		Length	Mass (Da)
	Q5HEB7 [UniParc]. Last modified February 15, 2005. Version 1. Checksum: 65822883958DC645	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

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. , 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: 15774886] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: COL.

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Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

CP000046 Genomic DNA. Translation: AAW37036.1.

RefSeq

YP_186890.1. NC_002951.2.

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	[»]
3N8D	X-ray	2.30	A/B	1-356	[»]

ProteinModelPortal

Q5HEB7.

SMR

Q5HEB7. Positions 3-356.

ModBase

Search...

Protein-protein interaction databases

STRING

Q5HEB7.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBSTAT00000010363; EBSTAP00000010098; EBSTAG00000010362.

GeneID

3238133.

GenomeReviews

Gene locus SACOL2074 in contig CP000046_GR.

KEGG

sac:SACOL2074.

PATRIC

19530419. VBIStaAur112458_2021.

TIGR

SACOL2074.

Phylogenomic databases

eggNOG

COG1181.

GeneTree

EBGT00050000025415.

HOGENOM

HBG427092.

OMA

LLHGPFG.

PhylomeDB

Q5HEB7.

ProtClustDB

PRK01966.

Enzyme and pathway databases

BioCyc

MetaCyc:MONOMER-15463.
SAUR93062:SACOL2074-MONOMER.

Family and domain databases

HAMAP

MF_00047. Dala_Dala_lig.
[Tree]

InterPro

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

Gene3D

G3DSA:3.30.1490.20. ATP_grasp_subdomain_1. 1 hit.
G3DSA:3.30.470.20. ATP_grasp_subdomain_2. 1 hit.
G3DSA:3.40.50.20. Pre-ATP_grasp. 1 hit.

KO

K01921.

PANTHER

PTHR23132. PTHR23132. 1 hit.

Pfam

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

SUPFAM

SSF52440. PreATP-grasp-like. 1 hit.

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...

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:	January 25, 2012
This is version 58 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program