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

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Reviewed, UniProtKB/Swiss-Prot P07862 (DDLB_ECOLI)

Last modified June 16, 2009. Version 102. 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 B
    EC=6.3.2.4
Alternative name(s):
    D-alanylalanine synthetase B
    D-Ala-D-Ala ligase B

Gene names

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

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

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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.

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General annotation (Comments)

Function	Cell wall formation. 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
Subunit structure	Monomer. HAMAP MF_00047
Subcellular location	Cytoplasm. 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 Direct protein sequencing
Gene Ontology (GO)
Biological process	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

Initiator methionine

Removed HAMAP MF_00047

Chain

2 – 306

305

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

PRO_0000177818

Regions

Domain

101 – 303

203

ATP-grasp

Nucleotide binding

134 – 189

ATP By similarity

Sites

Active site

Active site

Active site

Metal binding

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...

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Sequences

Sequence

Length

Mass (Da)

Tools

P07862-1 [UniParc].

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

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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: 3528126] [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: 1630901] [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: 9278503] [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: 16738553] [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: 2197603] [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: 2228979] [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: 1554356] [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: 7939684] [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: 9054558] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).

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Cross-references

Sequence databases

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

AP_000755.1.
NP_414634.1.

3D structure databases

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	[»]

ModBase

Search...

Genome annotation databases

GeneID

946324.

GenomeReviews

Gene locus JW0090 in contig AP009048_GR.
Gene locus b0092 in contig U00096_GR.

KEGG

ecj:JW0090.
eco:b0092.

Organism-specific databases

EchoBASE

EB0210.

EcoGene

EG10214. ddlB.

CMR

Search...

Phylogenomic databases

HOGENOM

P07862.

OMA

P07862. RAFIILH.

Enzyme and pathway databases

BioCyc

EcoCyc:DALADALALIGB-MON.
MetaCyc:DALADALALIGB-MON.

Family and domain databases

HAMAP

MF_00047.
[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.
[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

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:	June 16, 2009
This is version 102 of the entry and version 3 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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