ddlB:Gene Product(s)

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Nomenclature Function Interactions Localization Sequence Domains Structure Resources Accessions Links References Suggestions

Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name

DdlB

Synonyms

D-alanine:D-alanine ligase[1], B0092[2][1], Ddl[2][1], DdlB[2][1] , ddl, ECK0093, JW0090, b0092

Product description

ddlB[2][3];

Component of D-alanine-D-alanine ligase B[2][3]

D-alanine:D-alanine ligase B, ADP-forming[4]

EC number (for enzymes)
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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status
GO:0008716

D-alanine-D-alanine ligase activity

PMID:8756703[5]

IMP: Inferred from Mutant Phenotype

F

complete

GO:0000166

nucleotide binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0547

F

Seeded from EcoCyc (v14.0)

complete

GO:0000287

magnesium ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0460

F

Seeded from EcoCyc (v14.0)

complete

GO:0008716

D-alanine-D-alanine ligase activity

PMID:1993184[6]

IDA: Inferred from Direct Assay

F

Tables II and III

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011761

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013816

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013817

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR016185

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0067

F

Seeded from EcoCyc (v14.0)

complete

GO:0005618

cell wall

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011127

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00047

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005905

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0963

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-0086

C

Seeded from EcoCyc (v14.0)

complete

GO:0007047

cellular cell wall organization

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0961

P

Seeded from EcoCyc (v14.0)

complete

GO:0008360

regulation of cell shape

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0133

P

Seeded from EcoCyc (v14.0)

complete

GO:0008716

D-alanine-D-alanine ligase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00047

F

Seeded from EcoCyc (v14.0)

complete

GO:0008716

D-alanine-D-alanine ligase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000291

F

Seeded from EcoCyc (v14.0)

complete

GO:0008716

D-alanine-D-alanine ligase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005905

F

Seeded from EcoCyc (v14.0)

complete

GO:0008716

D-alanine-D-alanine ligase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011095

F

Seeded from EcoCyc (v14.0)

complete

GO:0008716

D-alanine-D-alanine ligase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011127

F

Seeded from EcoCyc (v14.0)

complete

GO:0008716

D-alanine-D-alanine ligase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:6.3.2.4

F

Seeded from EcoCyc (v14.0)

complete

GO:0009252

peptidoglycan biosynthetic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00047

P

Seeded from EcoCyc (v14.0)

complete

GO:0009252

peptidoglycan biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000291

P

Seeded from EcoCyc (v14.0)

complete

GO:0009252

peptidoglycan biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005905

P

Seeded from EcoCyc (v14.0)

complete

GO:0009252

peptidoglycan biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011095

P

Seeded from EcoCyc (v14.0)

complete

GO:0009252

peptidoglycan biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011127

P

Seeded from EcoCyc (v14.0)

complete

GO:0009252

peptidoglycan biosynthetic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0573

P

Seeded from EcoCyc (v14.0)

complete

GO:0030145

manganese ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0464

F

Seeded from EcoCyc (v14.0)

complete

GO:0046872

metal ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0479

F

Seeded from EcoCyc (v14.0)

complete

GO:0008716

D-alanine-D-alanine ligase activity

PMID:1554356[7]

IDA: Inferred from Direct Assay

F

Table 1, Fig. 3

complete

GO:0008716

D-alanine-D-alanine ligase activity

PMID:1993184[6]

IDA: Inferred from Direct Assay

F

Tables II and III

complete

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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type Partner Notes References Evidence

Protein

Subunits of D-alanine-D-alanine ligase B

could be indirect


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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes

cytoplasm

From EcoCyc[3]


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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence

at EcoCyc 

MTDKIAVLLG GTSAEREVSL NSGAAVLAGL REGGIDAYPV DPKEVDVTQL KSMGFQKVFI
ALHGRGGEDG TLQGMLELMG LPYTGSGVMA SALSMDKLRS KLLWQGAGLP VAPWVALTRA
EFEKGLSDKQ LAEISALGLP VIVKPSREGS SVGMSKVVAE NALQDALRLA FQHDEEVLIE
KWLSGPEFTV AILGEEILPS IRIQPSGTFY DYEAKYLSDE TQYFCPAGLE ASQEANLQAL
VLKAWTTLGC KGWGRIDVML DSDGQFYLLE ANTSPGMTSH SLVPMAARQA GMSFSQLVVR
ILELAD
Length

306

Mol. Wt

32.84 kDa

pI

4.6 (calculated)

Extinction coefficient

37,930 - 38,180 (calc based on 7 Y, 5 W, and 2 C residues)

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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type Residues Description Notes References

Initiator Methionine

1

Removed

UniProt:P07862

Domain

3..54

PF01820 D-ala D-ala ligase N-terminus

PMID:19920124[8]

Domain

43..86

PF01820 D-ala D-ala ligase N-terminus

PMID:19920124[8]

Domain

103..303

PF07478 D-ala D-ala ligase C-terminus

PMID:19920124[8]

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<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=ddlB taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16128085

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946324

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000326

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P07862

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10214

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10214

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946324

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000208

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0210

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.0 1.1 1.2 1.3 1.4 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 2.4 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 3.2 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ Park, IS et al. (1996) Gain of D-alanyl-D-lactate or D-lactyl-D-alanine synthetase activities in three active-site mutants of the Escherichia coli D-alanyl-D-alanine ligase B. Biochemistry 35 10464-71 PubMed
  6. ↑ 6.0 6.1 Zawadzke, LE et al. (1991) Existence of two D-alanine:D-alanine ligases in Escherichia coli: cloning and sequencing of the ddlA gene and purification and characterization of the DdlA and DdlB enzymes. Biochemistry 30 1673-82 PubMed
  7. ↑ al-Bar, OA et al. (1992) D-alanine: D-alanine ligase of Escherichia coli. Expression, purification and inhibitory studies on the cloned enzyme. Biochem. J. 282 ( Pt 3) 747-52 PubMed
  8. ↑ 8.0 8.1 8.2 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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