Q500B6 (DAPF_PSEU2) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Diaminopimelate epimerase
Short name=DAP epimerase
EC=5.1.1.7

Gene names

Name:	dapF
Ordered Locus Names:	Psyr_0183

Organism

Pseudomonas syringae pv. syringae (strain B728a) [Complete proteome] [HAMAP]

Taxonomic identifier

205918 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Pseudomonadales › Pseudomonadaceae › Pseudomonas › Pseudomonas syringae group › Pseudomonas syringae group genomosp. 1 › Pseudomonas syringae › Pseudomonas syringae pv. syringae

Protein attributes

Sequence length	276 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the stereoinversion of LL-2,6-diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso-DAP), a precursor of L-lysine and an essential component of the bacterial peptidoglycan By similarity. HAMAP-Rule MF_00197
Catalytic activity	LL-2,6-diaminoheptanedioate = meso-diaminoheptanedioate. HAMAP-Rule MF_00197
Pathway	Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; DL-2,6-diaminopimelate from LL-2,6-diaminopimelate: step 1/1. HAMAP-Rule MF_00197
Subcellular location	Cytoplasm By similarity.
Sequence similarities	Belongs to the diaminopimelate epimerase family.

Ontologies

Keywords
Biological process	Amino-acid biosynthesis Lysine biosynthesis
Cellular component	Cytoplasm
Molecular function	Isomerase
PTM	Disulfide bond
Technical term	Complete proteome
Gene Ontology (GO)
Biological_process	lysine biosynthetic process via diaminopimelate Inferred from electronic annotation. Source: HAMAP
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	diaminopimelate epimerase activity Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 276	276	Diaminopimelate epimerase HAMAP-Rule MF_00197		PRO_1000011936
Regions
	Region	10 – 11	2	Substrate binding By similarity
	Region	75 – 77	3	Substrate binding By similarity
	Region	210 – 211	2	Substrate binding By similarity
	Region	220 – 221	2	Substrate binding By similarity
Sites
	Active site	75	1	Proton donor/acceptor By similarity
	Active site	219	1	Proton donor/acceptor By similarity
	Binding site	13	1	Substrate By similarity
	Binding site	46	1	Substrate By similarity
	Binding site	66	1	Substrate By similarity
	Binding site	159	1	Substrate By similarity
	Binding site	192	1	Substrate By similarity
	Site	161	1	Important for catalytic activity By similarity
	Site	210	1	Important for catalytic activity By similarity
Amino acid modifications
	Disulfide bond	75 ↔ 219		HAMAP-Rule MF_00197

Sequences

	Sequence		Length	Mass (Da)
	Q500B6 [UniParc]. Last modified June 7, 2005. Version 1. Checksum: DE1C20A3AE921DAA	FASTA	276	30,399
	10 20 30 40 50 60 MLLRFTKMHG LGNDFMVLDL VSQHAHILPK HAKQWGDRHT GIGFDQLLLV EAPNNPDVDF 70 80 90 100 110 120 RYRIFNSDGS EVEQCGNGAR CFARFVLDKR LTAKKQIRVE TKSGIIELDI RSDGQISVDM 130 140 150 160 170 180 GPPRFVPEEI PFEAAEQATC YTVDVDGQHV DMAAVSMGNP HAVLRVDDIN NAPVHELGPK 190 200 210 220 230 240 IEHHPRFPAR VNVGFLHVVD RQRAQLRVWE RGAGETQACG TGACAAAVAA ISQGWMDSPL 250 260 270 LIDLPGGRLS IEWAGPGHSV MMTGPAVRVY EGQVRL

References

[1]

"Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000." Feil H., Feil W.S., Chain P., Larimer F., Dibartolo G., Copeland A., Lykidis A., Trong S., Nolan M., Goltsman E., Thiel J., Malfatti S., Loper J.E., Lapidus A., Detter J.C., Land M., Richardson P.M., Kyrpides N.C., Ivanova N., Lindow S.E. Proc. Natl. Acad. Sci. U.S.A. 102:11064-11069(2005) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: B728a.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP000075 Genomic DNA. Translation: AAY35256.1.
RefSeq	YP_233294.1. NC_007005.1.
3D structure databases
HSSP	HSSP built from PDB template 2GKE based on UniProtKB P44859.
ProteinModelPortal	Q500B6.
SMR	Q500B6. Positions 3-276.
ModBase	Search...
Protein-protein interaction databases
STRING	205918.Psyr_0183.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAY35256; AAY35256; Psyr_0183.
GeneID	3365659.
KEGG	psb:Psyr_0183.
PATRIC	19980747. VBIPseSyr42314_0179.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG0253.
HOGENOM	HOG000220466.
KO	K01778.
OMA	RFTKMQG.
ProtClustDB	PRK00450.
Enzyme and pathway databases
BioCyc	PSYR205918:GJ94-184-MONOMER.
UniPathway	UPA00034; UER00025.
Family and domain databases
HAMAP	MF_00197. DAP_epimerase.
InterPro	IPR018510. DAP_epimerase_AS. IPR001653. DAP_epimerase_DapF. [Graphical view]
Pfam	PF01678. DAP_epimerase. 2 hits. [Graphical view]
TIGRFAMs	TIGR00652. DapF. 1 hit.
PROSITE	PS01326. DAP_EPIMERASE. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

DAPF_PSEU2

Accession

Primary (citable) accession number: Q500B6

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 15, 2008
Last sequence update:	June 7, 2005
Last modified:	May 1, 2013
This is version 57 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program