D-alanine--D-alanine ligase B - Escherichia coli (strain K12)

Contribute

Send feedback

Read comments (?) or add your own

P07862 (DDLB_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 136. History...

Clusters with 100%, 90%, 50% identity |

Documents (4) |

Third-party data

text xml rdf/xml gff fasta

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

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

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

Gene names

Name:	ddlB
Synonyms:	ddl
Ordered Locus Names:	b0092, JW0090

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	306 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Cell wall formation. 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
Subunit structure	Monomer.
Subcellular location	Cytoplasm 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 Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	peptidoglycan biosynthetic process Inferred from mutant phenotype PubMed 4567144. Source: EcoCyc 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: HAMAP D-alanine-D-alanine ligase activity Inferred from direct assay Ref.7. Source: EcoCyc 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

Initiator methionine

Removed HAMAP-Rule MF_00047

Chain

2 – 306

305

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

PRO_0000177818

Regions

Domain

101 – 303

203

ATP-grasp

Nucleotide binding

134 – 189

ATP By similarity

Sites

Active site

150

Active site

281

Metal binding

257

Magnesium or manganese 1 By similarity

Metal binding

270

Magnesium or manganese 1 By similarity

Metal binding

270

Magnesium or manganese 2 By similarity

Metal binding

272

Magnesium or manganese 2 By similarity

Secondary structure

306

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P07862 [UniParc].

Last modified January 23, 2007. Version 3.
Checksum: F2D401C323A04471
Show »

FASTA

306

32,840

        10         20         30         40         50         60 
MTDKIAVLLG GTSAEREVSL NSGAAVLAGL REGGIDAYPV DPKEVDVTQL KSMGFQKVFI 

        70         80         90        100        110        120 
ALHGRGGEDG TLQGMLELMG LPYTGSGVMA SALSMDKLRS KLLWQGAGLP VAPWVALTRA 

       130        140        150        160        170        180 
EFEKGLSDKQ LAEISALGLP VIVKPSREGS SVGMSKVVAE NALQDALRLA FQHDEEVLIE 

       190        200        210        220        230        240 
KWLSGPEFTV AILGEEILPS IRIQPSGTFY DYEAKYLSDE TQYFCPAGLE ASQEANLQAL 

       250        260        270        280        290        300 
VLKAWTTLGC KGWGRIDVML DSDGQFYLLE ANTSPGMTSH SLVPMAARQA GMSFSQLVVR 


ILELAD

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Further evidence for overlapping transcriptional units in an Escherichia coli cell envelope-cell division gene cluster: DNA sequence and transcriptional organization of the ddl ftsQ region." Robinson A.C., Kenan D.J., Sweeney J., Donachie W.D. J. Bacteriol. 167:809-817(1986) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[2]	"Systematic sequencing of the Escherichia coli genome: analysis of the 0-2.4 min region." Yura T., Mori H., Nagai H., Nagata T., Ishihama A., Fujita N., Isono K., Mizobuchi K., Nakata A. Nucleic Acids Res. 20:3305-3308(1992) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12.
[3]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[4]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"Nucleotide sequence involving murG and murC in the mra gene cluster region of Escherichia coli." Ikeda M., Wachi M., Jung H.K., Ishino F., Matsuhashi M. Nucleic Acids Res. 18:4014-4014(1990) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-41. Strain: K12.
[6]	"Regulation of expression of the ftsA cell division gene by sequences in upstream genes." Dewar S.J., Donachie W.D. J. Bacteriol. 172:6611-6614(1990) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 300-306.
[7]	"D-alanine:D-alanine ligase of Escherichia coli. Expression, purification and inhibitory studies on the cloned enzyme." Al-Bar O.A., O'Connor C.D., Giles I.G., Akhtar M. Biochem. J. 282:747-752(1992) [PubMed] [Europe PMC] [Abstract] Cited for: CHARACTERIZATION, PARTIAL PROTEIN SEQUENCE.
[8]	"Vancomycin resistance: structure of D-alanine:D-alanine ligase at 2.3-A resolution." Fan C., Moews P.C., Walsh C.T., Knox J.R. Science 266:439-443(1994) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
[9]	"D-alanine:D-alanine ligase: phosphonate and phosphinate intermediates with wild type and the Y216F mutant." Fan C., Park I.-S., Walsh C.T., Knox J.R. Biochemistry 36:2531-2538(1997) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M14029 Genomic DNA. Translation: AAA23672.1.
K02668 Genomic DNA. Translation: AAA23815.1.
X52644 Genomic DNA. Translation: CAA36869.1.
X55034 Genomic DNA. Translation: CAA38869.1.
U00096 Genomic DNA. Translation: AAC73203.1.
AP009048 Genomic DNA. Translation: BAB96660.1.

PIR

CEECDL. A30289.

RefSeq

NP_414634.1. NC_000913.2.
YP_488397.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1IOV	X-ray	2.20	A	1-306	[»]
1IOW	X-ray	1.90	A	1-306	[»]
2DLN	X-ray	2.30	A	1-306	[»]

ProteinModelPortal

P07862.

SMR

P07862. Positions 1-306.

ModBase

Search...

Protein-protein interaction databases

IntAct

P07862. 1 interaction.

STRING

511145.b0092.

Proteomic databases

PaxDb

P07862.

PRIDE

P07862.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC73203; AAC73203; b0092.
BAB96660; BAB96660; BAB96660.

GeneID

12932120.
946324.

KEGG

ecj:Y75_p0091.
eco:b0092.

PATRIC

32115289. VBIEscCol129921_0096.

Organism-specific databases

EchoBASE

EB0210.

EcoGene

EG10214. ddlB.

Phylogenomic databases

eggNOG

COG1181.

HOGENOM

HOG000011592.

K01921.

OMA

WREAARY.

ProtClustDB

PRK01372.

Enzyme and pathway databases

BioCyc

EcoCyc:DALADALALIGB-MONOMER.
ECOL316407:JW0090-MONOMER.
MetaCyc:DALADALALIGB-MONOMER.

UniPathway

UPA00219.

Gene expression databases

Genevestigator

P07862.

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. 2 hits.
[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

ChEMBL

CHEMBL1956.

EvolutionaryTrace

P07862.

Entry information

Entry name

DDLB_ECOLI

Accession

Primary (citable) accession number: P07862

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 1, 1988
Last sequence update:	January 23, 2007
Last modified:	May 1, 2013
This is version 136 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents