B5ZTH4 (DAPF_RHILW) 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:	Rleg2_3748

Organism

Rhizobium leguminosarum bv. trifolii (strain WSM2304) [Complete proteome] [HAMAP]

Taxonomic identifier

395492 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Alphaproteobacteria › Rhizobiales › Rhizobiaceae › Rhizobium/Agrobacterium group › Rhizobium › Rhizobium leguminosarum › Rhizobium leguminosarum bv. trifolii

Protein attributes

Sequence length	301 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 – 301	301	Diaminopimelate epimerase HAMAP-Rule MF_00197		PRO_1000099259
Regions
	Region	12 – 13	2	Substrate binding By similarity
	Region	76 – 78	3	Substrate binding By similarity
	Region	215 – 216	2	Substrate binding By similarity
Sites
	Active site	76	1	Proton donor/acceptor By similarity
	Active site	224	1	Proton donor/acceptor By similarity
	Binding site	15	1	Substrate By similarity
	Binding site	47	1	Substrate By similarity
	Binding site	67	1	Substrate By similarity
	Binding site	163	1	Substrate By similarity
	Binding site	197	1	Substrate By similarity
	Site	165	1	Important for catalytic activity By similarity
	Site	215	1	Important for catalytic activity By similarity
Amino acid modifications
	Disulfide bond	76 ↔ 224		HAMAP-Rule MF_00197

Sequences

	Sequence		Length	Mass (Da)
	B5ZTH4 [UniParc]. Last modified November 25, 2008. Version 1. Checksum: B915EA356E415DF5	FASTA	301	32,387
	10 20 30 40 50 60 MSATVEFARM NGLGNKILVV DMRGRPDKVT PAAAVALNAD PQTEFDQIMA IHDPKADGTD 70 80 90 100 110 120 AFIDILNSDG SKAQACGNGT RCVVQALAAE TGRKAFTFQT VAGILNAVEH EDGTISVDMG 130 140 150 160 170 180 RPVFDWNRIP LAEEFHDTSR IELQIGPIDN PVLHSPSAMS MGNPHAIFWV DRDVMSYDLA 190 200 210 220 230 240 RFGPLLENHP MFPERANITL AQVTSPTSMT TRTWERGAGL TLACGSAACS AAVSAARTGR 250 260 270 280 290 300 TGRKVTINVA SAKPPATLSI EWRERDDHVI MTGPAEWEWS GSLDPSTGLW SRDGTQEAGA R

References

[1]

"Complete sequence of chromosome of Rhizobium leguminosarum bv. trifolii WSM2304." US DOE Joint Genome Institute Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Pitluck S., Chain P., Malfatti S., Shin M., Vergez L., Lang D., Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N., Yates R. , Ardley J., Tiwari R.P., O'Hara G., Howieson J., Brau L., Reeve W. Submitted (OCT-2008) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: WSM2304.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP001191 Genomic DNA. Translation: ACI57010.1.
RefSeq	YP_002283236.1. NC_011369.1.
3D structure databases
ProteinModelPortal	B5ZTH4.
ModBase	Search...
Protein-protein interaction databases
STRING	395492.Rleg2_3748.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	ACI57010; ACI57010; Rleg2_3748.
GeneID	6982510.
KEGG	rlt:Rleg2_3748.
PATRIC	23131772. VBIRhiLeg95088_5687.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG0253.
HOGENOM	HOG000220466.
KO	K01778.
OMA	GMGNPHC.
ProtClustDB	PRK00450.
Enzyme and pathway databases
BioCyc	RLEG395492:GJB3-3802-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_RHILW

Accession

Primary (citable) accession number: B5ZTH4

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 24, 2009
Last sequence update:	November 25, 2008
Last modified:	May 1, 2013
This is version 31 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program