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P07862

- DDLB_ECOLI

UniProt

P07862 - DDLB_ECOLI

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Protein

D-alanine--D-alanine ligase B

Gene

ddlB

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

Cell wall formation.

Catalytic activityi

ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine.

Cofactori

Binds 2 magnesium or manganese ions per subunit.By similarity

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei15 – 151
Active sitei150 – 1501
Metal bindingi257 – 2571Magnesium or manganese 1By similarity
Metal bindingi270 – 2701Magnesium or manganese 1By similarity
Metal bindingi270 – 2701Magnesium or manganese 2By similarity
Metal bindingi272 – 2721Magnesium or manganese 2By similarity
Active sitei281 – 2811

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi134 – 18956ATPBy similarityAdd
BLAST

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-HAMAP
  2. D-alanine-D-alanine ligase activity Source: EcoCyc
  3. magnesium ion binding Source: UniProtKB-HAMAP
  4. manganese ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. cell wall organization Source: UniProtKB-KW
  2. peptidoglycan biosynthetic process Source: EcoCyc
  3. regulation of cell shape Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

Cell shape, Cell wall biogenesis/degradation, Peptidoglycan synthesis

Keywords - Ligandi

ATP-binding, Magnesium, Manganese, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciEcoCyc:DALADALALIGB-MONOMER.
ECOL316407:JW0090-MONOMER.
MetaCyc:DALADALALIGB-MONOMER.
UniPathwayiUPA00219.

Names & Taxonomyi

Protein namesi
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 namesi
Name:ddlB
Synonyms:ddl
Ordered Locus Names:b0092, JW0090
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG10214. ddlB.

Subcellular locationi

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed
Chaini2 – 306305D-alanine--D-alanine ligase BPRO_0000177818Add
BLAST

Proteomic databases

PaxDbiP07862.
PRIDEiP07862.

Expressioni

Gene expression databases

GenevestigatoriP07862.

Interactioni

Subunit structurei

Monomer.

Protein-protein interaction databases

IntActiP07862. 4 interactions.
STRINGi511145.b0092.

Structurei

Secondary structure

1
306
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 85
Helixi16 – 3217
Beta strandi36 – 405
Turni42 – 443
Helixi47 – 493
Turni50 – 545
Beta strandi55 – 606
Turni65 – 673
Beta strandi68 – 703
Helixi71 – 799
Beta strandi83 – 853
Helixi88 – 958
Helixi97 – 10610
Beta strandi114 – 1185
Helixi119 – 1246
Helixi129 – 1357
Beta strandi139 – 1457
Turni150 – 1534
Beta strandi155 – 1595
Helixi160 – 1623
Helixi163 – 1708
Turni171 – 1733
Beta strandi175 – 1817
Beta strandi187 – 1937
Beta strandi201 – 2044
Beta strandi206 – 2105
Helixi212 – 2165
Beta strandi222 – 2265
Helixi231 – 24818
Beta strandi252 – 2609
Beta strandi266 – 2749
Helixi282 – 2898
Helixi294 – 30310

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1IOVX-ray2.20A1-306[»]
1IOWX-ray1.90A1-306[»]
2DLNX-ray2.30A1-306[»]
ProteinModelPortaliP07862.
SMRiP07862. Positions 1-306.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP07862.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini101 – 303203ATP-graspAdd
BLAST

Sequence similaritiesi

Belongs to the D-alanine--D-alanine ligase family.Curated
Contains 1 ATP-grasp domain.Curated

Phylogenomic databases

eggNOGiCOG1181.
HOGENOMiHOG000011592.
InParanoidiP07862.
KOiK01921.
OMAiEDPARES.
OrthoDBiEOG6ND0KB.
PhylomeDBiP07862.

Family and domain databases

Gene3Di3.30.1490.20. 1 hit.
3.30.470.20. 2 hits.
3.40.50.20. 1 hit.
HAMAPiMF_00047. Dala_Dala_lig.
InterProiIPR011761. 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]
PANTHERiPTHR23132. PTHR23132. 1 hit.
PfamiPF07478. Dala_Dala_lig_C. 1 hit.
PF01820. Dala_Dala_lig_N. 2 hits.
[Graphical view]
SUPFAMiSSF52440. SSF52440. 1 hit.
TIGRFAMsiTIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITEiPS50975. ATP_GRASP. 1 hit.
PS00843. DALA_DALA_LIGASE_1. 1 hit.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P07862-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MTDKIAVLLG GTSAEREVSL NSGAAVLAGL REGGIDAYPV DPKEVDVTQL
60 70 80 90 100
KSMGFQKVFI ALHGRGGEDG TLQGMLELMG LPYTGSGVMA SALSMDKLRS
110 120 130 140 150
KLLWQGAGLP VAPWVALTRA EFEKGLSDKQ LAEISALGLP VIVKPSREGS
160 170 180 190 200
SVGMSKVVAE NALQDALRLA FQHDEEVLIE KWLSGPEFTV AILGEEILPS
210 220 230 240 250
IRIQPSGTFY DYEAKYLSDE TQYFCPAGLE ASQEANLQAL VLKAWTTLGC
260 270 280 290 300
KGWGRIDVML DSDGQFYLLE ANTSPGMTSH SLVPMAARQA GMSFSQLVVR

ILELAD
Length:306
Mass (Da):32,840
Last modified:January 23, 2007 - v3
Checksum:iF2D401C323A04471
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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.
PIRiA30289. CEECDL.
RefSeqiNP_414634.1. NC_000913.3.
YP_488397.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC73203; AAC73203; b0092.
BAB96660; BAB96660; BAB96660.
GeneIDi12932120.
946324.
KEGGiecj:Y75_p0091.
eco:b0092.
PATRICi32115289. VBIEscCol129921_0096.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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 .
PIRi A30289. CEECDL.
RefSeqi NP_414634.1. NC_000913.3.
YP_488397.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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 [» ]
ProteinModelPortali P07862.
SMRi P07862. Positions 1-306.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

IntActi P07862. 4 interactions.
STRINGi 511145.b0092.

Chemistry

ChEMBLi CHEMBL1956.

Proteomic databases

PaxDbi P07862.
PRIDEi P07862.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC73203 ; AAC73203 ; b0092 .
BAB96660 ; BAB96660 ; BAB96660 .
GeneIDi 12932120.
946324.
KEGGi ecj:Y75_p0091.
eco:b0092.
PATRICi 32115289. VBIEscCol129921_0096.

Organism-specific databases

EchoBASEi EB0210.
EcoGenei EG10214. ddlB.

Phylogenomic databases

eggNOGi COG1181.
HOGENOMi HOG000011592.
InParanoidi P07862.
KOi K01921.
OMAi EDPARES.
OrthoDBi EOG6ND0KB.
PhylomeDBi P07862.

Enzyme and pathway databases

UniPathwayi UPA00219 .
BioCyci EcoCyc:DALADALALIGB-MONOMER.
ECOL316407:JW0090-MONOMER.
MetaCyc:DALADALALIGB-MONOMER.

Miscellaneous databases

EvolutionaryTracei P07862.
PROi P07862.

Gene expression databases

Genevestigatori P07862.

Family and domain databases

Gene3Di 3.30.1490.20. 1 hit.
3.30.470.20. 2 hits.
3.40.50.20. 1 hit.
HAMAPi MF_00047. Dala_Dala_lig.
InterProi 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 ]
PANTHERi PTHR23132. PTHR23132. 1 hit.
Pfami PF07478. Dala_Dala_lig_C. 1 hit.
PF01820. Dala_Dala_lig_N. 2 hits.
[Graphical view ]
SUPFAMi SSF52440. SSF52440. 1 hit.
TIGRFAMsi TIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITEi PS50975. ATP_GRASP. 1 hit.
PS00843. DALA_DALA_LIGASE_1. 1 hit.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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. 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).

Entry informationi

Entry nameiDDLB_ECOLI
AccessioniPrimary (citable) accession number: P07862
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1988
Last sequence update: January 23, 2007
Last modified: October 29, 2014
This is version 147 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3