P95803 (DDL_STRMU) 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:	SMU_599

Organism

Streptococcus mutans serotype c (strain ATCC 700610 / UA159) [Complete proteome] [HAMAP]

Taxonomic identifier

210007 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Firmicutes › Bacilli › Lactobacillales › Streptococcaceae › Streptococcus › Streptococcus mutans

Protein attributes

Sequence length	349 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Cell wall formation By similarity. HAMAP-Rule MF_00047
Catalytic activity	ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine. HAMAP-Rule MF_00047
Cofactor	Binds 2 magnesium or manganese ions per subunit By similarity.
Pathway	Cell wall biogenesis; peptidoglycan biosynthesis. HAMAP-Rule MF_00047
Subcellular location	Cytoplasm By similarity HAMAP-Rule 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	peptidoglycan biosynthetic process Inferred from electronic annotation. Source: HAMAP regulation of cell shape Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	ATP binding Inferred from electronic annotation. Source: HAMAP D-alanine-D-alanine ligase activity Inferred from electronic annotation. Source: HAMAP magnesium ion binding Inferred from electronic annotation. Source: HAMAP manganese ion binding Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 349

349

D-alanine--D-alanine ligase HAMAP-Rule MF_00047

PRO_0000177886

Regions

Domain

133 – 335

203

ATP-grasp

Nucleotide binding

163 – 218

56

ATP By similarity

Sites

Metal binding

289

1

Magnesium or manganese 1 By similarity

Metal binding

302

1

Magnesium or manganese 1 By similarity

Metal binding

302

1

Magnesium or manganese 2 By similarity

Metal binding

304

1

Magnesium or manganese 2 By similarity

Experimental info

Sequence conflict

132

1

N → K in AAB41854. Ref.2

Sequence conflict

238

1

D → V in AAB41854. Ref.2

Sequence conflict

273

1

A → R in AAB41854. Ref.2

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

349

Helix Strand Turn

Details...

Beta strand

4 – 11

8

Helix

17 – 30

14

Turn

33 – 35

3

Beta strand

36 – 43

8

Beta strand

49 – 57

9

Helix

73 – 75

3

Helix

79 – 82

4

Beta strand

88 – 92

5

Turn

96 – 98

3

Beta strand

99 – 101

3

Helix

102 – 109

8

Beta strand

114 – 116

3

Helix

119 – 126

8

Helix

128 – 138

11

Beta strand

146 – 150

5

Helix

155 – 165

11

Beta strand

168 – 174

7

Beta strand

184 – 188

5

Helix

189 – 202

14

Beta strand

204 – 210

7

Beta strand

214 – 226

13

Beta strand

233 – 235

3

Beta strand

255 – 258

4

Helix

263 – 279

17

Beta strand

284 – 292

9

Beta strand

298 – 306

9

Helix

314 – 321

8

Helix

326 – 345

20

Sequences

	Sequence		Length	Mass (Da)
	P95803 [UniParc]. Last modified November 28, 2002. Version 2. Checksum: FFDAAD9942CAE7EF	FASTA	349	38,838
	10 20 30 40 50 60 MSKETLVLLY GGRSAERDVS VLSAESVMRA INYDNFLVKT YFITQAGDFI KTQEFDSQPS 70 80 90 100 110 120 ETDKLMTNDT IIASQKIKPS DIYEEEAVVF PVLHGPMGED GSIQGFLEVL KMPYVGTNIL 130 140 150 160 170 180 SSSVAMDKIT TNQVLESATT IPQVAYVALI EGEPLESKLA EVEEKLIYPV FVKPANMGSS 190 200 210 220 230 240 VGISKAENRT DLKQAIALAL KYDSRVLIEQ GVDAREIEVG ILGNTDVKTT LPGEIVKDVA 250 260 270 280 290 300 FYDYEAKYID NKITMAIPAE IDPVIVEKMR DYAATAFRTL GCCGLSRCDF FLTEDGKVYL 310 320 330 340 NELNTMPGFT QWSMYPLLWE NMGLSYSVLI EELVSLAKEM FDKRESHLV

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Genome sequence of Streptococcus mutans UA159, a cariogenic dental pathogen." Ajdic D.J., McShan W.M., McLaughlin R.E., Savic G., Chang J., Carson M.B., Primeaux C., Tian R., Kenton S., Jia H.G., Lin S.P., Qian Y., Li S., Zhu H., Najar F.Z., Lai H., White J., Roe B.A., Ferretti J.J. Proc. Natl. Acad. Sci. U.S.A. 99:14434-14439(2002) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 700610 / UA159.
[2]	Garnier F., Gerbaud G., Courvalin P., Galimand M. Submitted (FEB-1997) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 106-303. Strain: ATCC 25175 / DSM 20523 / JCM 5705 / NBRC 13955 / NCIMB 702062 / NCTC 10449.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AE014133 Genomic DNA. Translation: AAN58338.1.
U69165 Genomic DNA. Translation: AAB41854.1.

RefSeq

NP_721032.1. NC_004350.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3K3P	X-ray	2.23	A/B	1-349	[»]

ProteinModelPortal

P95803.

ModBase

Search...

Protein-protein interaction databases

STRING

210007.SMU.599.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAN58338; AAN58338; SMU_599.

GeneID

1029384.

KEGG

smu:SMU_599.

PATRIC

19663399. VBIStrMut61772_0532.

Organism-specific databases

CMR

Search...

Phylogenomic databases

eggNOG

COG1181.

KO

K01921.

OMA

LLHGPFG.

ProtClustDB

PRK01966.

Enzyme and pathway databases

BioCyc

SMUT210007:GC7Z-588-MONOMER.

UniPathway

UPA00219.

Family and domain databases

Gene3D

3.30.1490.20. 1 hit.
3.30.470.20. 2 hits.
3.40.50.20. 1 hit.

HAMAP

MF_00047. Dala_Dala_lig.

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.
IPR016185. PreATP-grasp_dom.
[Graphical view]

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...

Other

EvolutionaryTrace

P95803.

Entry information

Entry name

DDL_STRMU

Accession

Primary (citable) accession number: P95803

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	November 28, 2002
Last modified:	May 29, 2013
This is version 101 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program