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Protein

Diaminopimelate epimerase 2

Gene

dapF2

Organism
Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

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.UniRule annotation

Catalytic activityi

LL-2,6-diaminoheptanedioate = meso-diaminoheptanedioate.UniRule annotation

Pathwayi: L-lysine biosynthesis via DAP pathway

This protein is involved in step 1 of the subpathway that synthesizes DL-2,6-diaminopimelate from LL-2,6-diaminopimelate.UniRule annotation
Proteins known to be involved in this subpathway in this organism are:
  1. Diaminopimelate epimerase 2 (dapF2), Diaminopimelate epimerase 1 (dapF1)
This subpathway is part of the pathway L-lysine biosynthesis via DAP pathway, which is itself part of Amino-acid biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes DL-2,6-diaminopimelate from LL-2,6-diaminopimelate, the pathway L-lysine biosynthesis via DAP pathway and in Amino-acid biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei11SubstrateUniRule annotation1
Binding sitei63SubstrateUniRule annotation1
Binding sitei158SubstrateUniRule annotation1
Sitei160Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Binding sitei191SubstrateUniRule annotation1
Sitei209Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionIsomerase
Biological processAmino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.

Names & Taxonomyi

Protein namesi
Recommended name:
Diaminopimelate epimerase 2UniRule annotation (EC:5.1.1.7UniRule annotation)
Short name:
DAP epimerase 2UniRule annotation
Alternative name(s):
PLP-independent amino acid racemase 2UniRule annotation
Gene namesi
Name:dapF2UniRule annotation
Synonyms:dapF
Ordered Locus Names:alr4841
OrganismiNostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)
Taxonomic identifieri103690 [NCBI]
Taxonomic lineageiBacteriaCyanobacteriaNostocalesNostocaceaeNostoc
Proteomesi
  • UP000002483 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001498161 – 285Diaminopimelate epimerase 2Add BLAST285

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi103690.alr4841.

Structurei

3D structure databases

ProteinModelPortaliP54897.
SMRiP54897.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni73 – 74Substrate bindingUniRule annotation2
Regioni209 – 210Substrate bindingUniRule annotation2
Regioni219 – 220Substrate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105E4Z. Bacteria.
COG0253. LUCA.
HOGENOMiHOG000220466.
KOiK01778.
OMAiTIQIEIW.
OrthoDBiPOG091H01QC.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase. 1 hit.
InterProiView protein in InterPro
IPR001653. DAP_epimerase_DapF.
PANTHERiPTHR31689. PTHR31689. 1 hit.
PfamiView protein in Pfam
PF01678. DAP_epimerase. 2 hits.
TIGRFAMsiTIGR00652. DapF. 1 hit.

Sequencei

Sequence statusi: Complete.

P54897-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKFYKYHALG NDYLVINPQD LKFPLTPEKI KIICHRNFGI GSDGILLGPL
60 70 80 90 100
ASTKAQFALR IFNPDGSEAE KSGNGLRIFS RYLWDMGLVD EKPFSIETAG
110 120 130 140 150
GIVESAIKDA GKTVQVEMGK VSFWSRDIPV IGDDREVIQE KIFLDEGIFT
160 170 180 190 200
FCAATIGNPH CVILLDDINS EVARNFGPIF EGYPLFPNRT NVQFMKVLDR
210 220 230 240 250
STIQIEIWER GAGYTLASGS SSSAAAATAH KLGLCDSKII VKMPGGDILI
260 270 280
QIKDDFHISM TDSVTKLAQG ELSTEIFAIE TVINI
Length:285
Mass (Da):31,355
Last modified:January 23, 2002 - v2
Checksum:iAE1613FFEAD75063
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti223Missing in CAA87006 (PubMed:9139910).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z46907 Genomic DNA. Translation: CAA87006.1.
BA000019 Genomic DNA. Translation: BAB76540.1.
PIRiAI2410.
S52295.
RefSeqiWP_010998969.1. NC_003272.1.

Genome annotation databases

EnsemblBacteriaiBAB76540; BAB76540; BAB76540.
KEGGiana:alr4841.

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.

Entry informationi

Entry nameiDAPF2_NOSS1
AccessioniPrimary (citable) accession number: P54897
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: January 23, 2002
Last modified: June 7, 2017
This is version 100 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Caution

Could lack activity as the potential active site Cys residues in positions 72 and 218 are both replaced by a Ser.Curated

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families