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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Alkaliphilus oremlandii (strain OhILAs) (Clostridium oremlandii (strain OhILAs))
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

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 (dapF)
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 sitei13SubstrateUniRule annotation1
Binding sitei47SubstrateUniRule annotation1
Binding sitei65SubstrateUniRule annotation1
Active sitei74Proton donor/acceptorUniRule annotation1
Sitei165Important for catalytic activityUniRule annotation1
Binding sitei196SubstrateUniRule annotation1
Sitei214Important for catalytic activityUniRule annotation1
Active sitei223Proton donor/acceptorUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Biological processi

Amino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.

Names & Taxonomyi

Protein namesi
Recommended name:
Diaminopimelate epimeraseUniRule annotation (EC:5.1.1.7UniRule annotation)
Short name:
DAP epimeraseUniRule annotation
Gene namesi
Name:dapFUniRule annotation
Ordered Locus Names:Clos_1420
OrganismiAlkaliphilus oremlandii (strain OhILAs) (Clostridium oremlandii (strain OhILAs))
Taxonomic identifieri350688 [NCBI]
Taxonomic lineageiBacteriaFirmicutesClostridiaClostridialesClostridiaceaeAlkaliphilus
Proteomesi
  • UP000000269 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000585361 – 280Diaminopimelate epimeraseAdd BLAST280

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi74 ↔ 223

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi350688.Clos_1420.

Structurei

3D structure databases

ProteinModelPortaliA8MH77.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni74 – 76Substrate bindingUniRule annotation3
Regioni214 – 215Substrate bindingUniRule annotation2
Regioni224 – 225Substrate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

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

Family and domain databases

HAMAPiMF_00197. DAP_epimerase. 1 hit.
InterProiIPR018510. DAP_epimerase_AS.
IPR001653. DAP_epimerase_DapF.
[Graphical view]
PANTHERiPTHR31689. PTHR31689. 1 hit.
PfamiPF01678. DAP_epimerase. 2 hits.
[Graphical view]
TIGRFAMsiTIGR00652. DapF. 1 hit.
PROSITEiPS01326. DAP_EPIMERASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

A8MH77-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDVQFKKMQG TGNDFIVVKY DDFPFEEKLS QLAEKICDRH FGIGADGLLI
60 70 80 90 100
VNPSSIADIR MDYYNSDGSI AAMCGNGIRC FSKFVFDEGF LRTKQFSVET
110 120 130 140 150
LDGIKEIAII EEKGTVKSVE VNMGQVTYDT EKIPVVSEDG YFINKKITVG
160 170 180 190 200
GQDFIITAVS MGVPHVIIFT EKLDLEQIKF FGPLIEKHAI FPKKTNVNFV
210 220 230 240 250
HRIDKDNIAV RTWERGAGYT LACGTGSTSA VAVANKLGLV NNNVNVEVEG
260 270 280
GNIKIKIKES GNLFMEGPAE NICSGRFFFN
Length:280
Mass (Da):30,983
Last modified:December 4, 2007 - v1
Checksum:iA250AE65EC4C2419
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000853 Genomic DNA. Translation: ABW18964.1.
RefSeqiWP_012159276.1. NC_009922.1.

Genome annotation databases

EnsemblBacteriaiABW18964; ABW18964; Clos_1420.
KEGGiaoe:Clos_1420.
PATRICi20868065. VBIAlkOre124042_1489.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000853 Genomic DNA. Translation: ABW18964.1.
RefSeqiWP_012159276.1. NC_009922.1.

3D structure databases

ProteinModelPortaliA8MH77.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi350688.Clos_1420.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABW18964; ABW18964; Clos_1420.
KEGGiaoe:Clos_1420.
PATRICi20868065. VBIAlkOre124042_1489.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase. 1 hit.
InterProiIPR018510. DAP_epimerase_AS.
IPR001653. DAP_epimerase_DapF.
[Graphical view]
PANTHERiPTHR31689. PTHR31689. 1 hit.
PfamiPF01678. DAP_epimerase. 2 hits.
[Graphical view]
TIGRFAMsiTIGR00652. DapF. 1 hit.
PROSITEiPS01326. DAP_EPIMERASE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDAPF_ALKOO
AccessioniPrimary (citable) accession number: A8MH77
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 5, 2008
Last sequence update: December 4, 2007
Last modified: November 2, 2016
This is version 52 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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

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.