Reviewed, UniProtKB/Swiss-Prot Q88N74 (DDLB_PSEPK)

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
Ordered Locus Names:	PP_1339

Organism

Pseudomonas putida (strain KT2440) [Complete proteome] [HAMAP]

Taxonomic identifier

160488 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Pseudomonadales › Pseudomonadaceae › Pseudomonas

Protein attributes

Sequence length	318 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Inferred from homology.

General annotation (Comments)

Function	Cell wall formation By similarity.
Catalytic activity	ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine.
Cofactor	Binds 2 magnesium or manganese ions per subunit By similarity.
Pathway	Cell wall biogenesis; peptidoglycan biosynthesis.
Subcellular location	CytoplasmBy similarity.
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	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	cell wall Inferred from electronic annotation. Source: InterPro cytoplasm Inferred from electronic annotation. Source: HAMAP
Molecular function	ATP binding Inferred from electronic annotation. Source: InterPro 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...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 318	318	D-alanine--D-alanine ligase B		PRO_0000177858
Regions
	Domain	116 – 311	196	ATP-grasp
	Nucleotide binding	142 – 197	56	ATP By similarity
Sites
	Metal binding	265	1	Magnesium or manganese 1 By similarity
	Metal binding	278	1	Magnesium or manganese 1 By similarity
	Metal binding	278	1	Magnesium or manganese 2 By similarity
	Metal binding	280	1	Magnesium or manganese 2 By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q88N74-1 [UniParc]. Last modified June 1, 2003. Version 1. Checksum: D43D416D65ACFBDF	FASTA	318	34,131
	10 20 30 40 50 60 MTSAYDKLHS TLDVKAFGRV AVLYGGKSAE REVSLKSGAA VIDALSTAGV DVVAIDVGDD 70 80 90 100 110 120 LLARLQSEKI DRAFIILHGR GGEDGSMQGL LECLGIPYTG SGILASALAM DKLRTKQVWQ 130 140 150 160 170 180 SLGIPTPRHA VLASESDCLQ ASTELGFPLI VKPAHEGSSI GMAKVNSTQE LVAAWQDAAK 190 200 210 220 230 240 YDSQVLVEQW IHGPEFTIAV LRGQVLPPIA LGTPHVFYDY DAKYIVNDTQ YRIPCGLDSV 250 260 270 280 290 300 KEQELIDLTA RACDAIGIEG WGRLDVMQDE QGRFWLLEVN TAPGMTDHSL VPMAARAAGL 310 DFQQLVLAIL AESVATRG

References

[1]

"Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440." Nelson K.E., Weinel C., Paulsen I.T., Dodson R.J., Hilbert H., Martins dos Santos V.A.P., Fouts D.E., Gill S.R., Pop M., Holmes M., Brinkac L.M., Beanan M.J., DeBoy R.T., Daugherty S.C., Kolonay J.F., Madupu R., Nelson W.C., White O. , Peterson J.D., Khouri H.M., Hance I., Chris Lee P., Holtzapple E.K., Scanlan D., Tran K., Moazzez A., Utterback T.R., Rizzo M., Lee K., Kosack D., Moestl D., Wedler H., Lauber J., Stjepandic D., Hoheisel J., Straetz M., Heim S., Kiewitz C., Eisen J.A., Timmis K.N., Duesterhoeft A., Tuemmler B., Fraser C.M. Environ. Microbiol. 4:799-808(2002) [PubMed: 12534463] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Cross-references

Sequence databases
EMBLGenBankDDBJ	AE015451 Genomic DNA. Translation: AAN66962.1.
RefSeq	NP_743498.1.
3D structure databases
HSSP	HSSP built from PDB template 1IOW based on UniProtKB P07862.
ModBase	Search...
Genome annotation databases
GeneID	1044021.
GenomeReviews	Gene locus PP_1339 in contig AE015451_GR.
KEGG	ppu:PP_1339.
NMPDR	fig|160488.1.peg.1328.
TIGR	PP_1339.
Phylogenomic databases
HOGENOM	Q88N74.
Enzyme and pathway databases
BioCyc	PPUT160488:PP_1339-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...

Entry information

Entry name

DDLB_PSEPK

Accession

Primary (citable) accession number: Q88N74

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 15, 2003
Last sequence update:	June 1, 2003
Last modified:	November 25, 2008
This is version 43 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)