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B4RCE2 (DAPF_PHEZH) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 40. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Diaminopimelate epimerase

Short name=DAP epimerase
EC=5.1.1.7
Gene names
Name:dapF
Ordered Locus Names:PHZ_c0127
OrganismPhenylobacterium zucineum (strain HLK1) [Complete proteome] [HAMAP]
Taxonomic identifier450851 [NCBI]
Taxonomic lineageBacteriaProteobacteriaAlphaproteobacteriaCaulobacteralesCaulobacteraceaePhenylobacterium

Protein attributes

Sequence length277 AA.
Sequence statusComplete.
Protein existenceEvidence 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 HAMAP-Rule MF_00197.

Sequence similarities

Belongs to the diaminopimelate epimerase family.

Ontologies

Keywords
   Biological processAmino-acid biosynthesis
Lysine biosynthesis
   Cellular componentCytoplasm
   Molecular functionIsomerase
   PTMDisulfide bond
   Technical termComplete proteome
Gene Ontology (GO)
   Biological_processlysine biosynthetic process via diaminopimelate

Inferred from electronic annotation. Source: UniProtKB-HAMAP

   Cellular_componentcytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functiondiaminopimelate epimerase activity

Inferred from electronic annotation. Source: UniProtKB-HAMAP

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 277277Diaminopimelate epimerase HAMAP-Rule MF_00197
PRO_1000099255

Regions

Region14 – 152Substrate binding By similarity
Region77 – 793Substrate binding By similarity
Region213 – 2142Substrate binding By similarity
Region223 – 2242Substrate binding By similarity

Sites

Active site771Proton donor/acceptor By similarity
Active site2221Proton donor/acceptor By similarity
Binding site171Substrate By similarity
Binding site501Substrate By similarity
Binding site681Substrate By similarity
Binding site1621Substrate By similarity
Binding site1951Substrate By similarity
Site1641Important for catalytic activity By similarity
Site2131Important for catalytic activity By similarity

Amino acid modifications

Disulfide bond77 ↔ 222 HAMAP-Rule MF_00197

Sequences

Sequence LengthMass (Da)Tools
B4RCE2 [UniParc].

Last modified September 23, 2008. Version 1.
Checksum: 1EF73A28BBD0AE80

FASTA27729,372
        10         20         30         40         50         60 
MSAAMGRPFL KMNGLGNDFV VVETRSAPFE PTAAQVRAIA DRATGIGCDQ LIAVDPAEGA 

        70         80         90        100        110        120 
DAHVRFWNAD GEEVGACGNG TRCVGWLLMQ SSGKDEAVIE TRAGRLVATR AGERLVSVDM 

       130        140        150        160        170        180 
GPPRLEWNEI PLAEPHDTRA LDVVLYHHAD LMAPPGCVSM GNPHVVFFVP DAEQAPAAEA 

       190        200        210        220        230        240 
GPAIEGHPLF PEHVNVGFAQ VKAPDRIRLR VWERGAGLTK ACGTGACAAM VAASRRGLIG 

       250        260        270 
RHATMELDGG ELFVEWRADG HVIMTGPAAV DFQGELP 

« Hide

References

[1]"Complete genome of Phenylobacterium zucineum - a novel facultative intracellular bacterium isolated from human erythroleukemia cell line K562."
Luo Y., Xu X., Ding Z., Liu Z., Zhang B., Yan Z., Sun J., Hu S., Hu X.
BMC Genomics 9:386-386(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: HLK1.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
CP000747 Genomic DNA. Translation: ACG76541.1.
RefSeqYP_002128970.1. NC_011144.1.

3D structure databases

ProteinModelPortalB4RCE2.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING450851.PHZ_c0127.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaACG76541; ACG76541; PHZ_c0127.
GeneID6789615.
KEGGpzu:PHZ_c0127.
PATRIC22922770. VBIPheZuc44517_0482.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0253.
HOGENOMHOG000220466.
KOK01778.
OMAKMRIFNN.
OrthoDBEOG6ND0M5.

Enzyme and pathway databases

BioCycPZUC450851:GHUG-129-MONOMER.
UniPathwayUPA00034; UER00025.

Family and domain databases

HAMAPMF_00197. DAP_epimerase.
InterProIPR018510. DAP_epimerase_AS.
IPR001653. DAP_epimerase_DapF.
[Graphical view]
PANTHERPTHR31689. PTHR31689. 1 hit.
PfamPF01678. DAP_epimerase. 2 hits.
[Graphical view]
TIGRFAMsTIGR00652. DapF. 1 hit.
PROSITEPS01326. DAP_EPIMERASE. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameDAPF_PHEZH
AccessionPrimary (citable) accession number: B4RCE2
Entry history
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: September 23, 2008
Last modified: June 11, 2014
This is version 40 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PATHWAY comments

Index of metabolic and biosynthesis pathways