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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Alkaliphilus metalliredigens (strain QYMF)
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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei13 – 131SubstrateUniRule annotation
Binding sitei47 – 471SubstrateUniRule annotation
Binding sitei65 – 651SubstrateUniRule annotation
Active sitei74 – 741Proton donor/acceptorUniRule annotation
Sitei165 – 1651Important for catalytic activityUniRule annotation
Binding sitei196 – 1961SubstrateUniRule annotation
Sitei214 – 2141Important for catalytic activityUniRule annotation
Active sitei223 – 2231Proton donor/acceptorUniRule annotation

GO - Molecular functioni

  1. diaminopimelate epimerase activity Source: UniProtKB-HAMAP

GO - Biological processi

  1. lysine biosynthetic process via diaminopimelate Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Biological processi

Amino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

BioCyciAMET293826:GI5P-2838-MONOMER.
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:Amet_2793
OrganismiAlkaliphilus metalliredigens (strain QYMF)
Taxonomic identifieri293826 [NCBI]
Taxonomic lineageiBacteriaFirmicutesClostridiaClostridialesClostridiaceaeAlkaliphilus
ProteomesiUP000001572 Componenti: Chromosome

Subcellular locationi

  1. Cytoplasm UniRule annotation

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 283283Diaminopimelate epimerasePRO_1000058535Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi74 ↔ 223

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi293826.Amet_2793.

Structurei

3D structure databases

ProteinModelPortaliA6TRX5.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni74 – 763Substrate bindingUniRule annotation
Regioni214 – 2152Substrate bindingUniRule annotation
Regioni224 – 2252Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiMKFTKMH.
OrthoDBiEOG6ND0M5.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase.
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.

A6TRX5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEIKFKKMHG TGNDFIMIYY EDYPFEQHFN QLAKEVCHRH FGIGADGLMI
60 70 80 90 100
VKESSVADVQ MKYFNSDGSE AGMCGNGIRC FAKFVYDEGL VKKEIFTVET
110 120 130 140 150
LSGVKELQVA TVEEKVSSVR VNMGKMVLDP KQIPVNSEGL QFINEQLMID
160 170 180 190 200
GEKYTISTVL LGVPHTIIFM ETLDLDRVKR VGKIIENHQL FPENTNVNFA
210 220 230 240 250
QIINQNTIRV RTWERGAGYT LACGTGVSSV CGIANHLSLV GPNVVVEIEG
260 270 280
GKLDIEIAPE GDIYMEGPAK DICKGVYLNS LIK
Length:283
Mass (Da):31,494
Last modified:August 21, 2007 - v1
Checksum:i21CC67170F368330
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000724 Genomic DNA. Translation: ABR48943.1.
RefSeqiYP_001320602.1. NC_009633.1.

Genome annotation databases

EnsemblBacteriaiABR48943; ABR48943; Amet_2793.
KEGGiamt:Amet_2793.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000724 Genomic DNA. Translation: ABR48943.1.
RefSeqiYP_001320602.1. NC_009633.1.

3D structure databases

ProteinModelPortaliA6TRX5.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi293826.Amet_2793.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABR48943; ABR48943; Amet_2793.
KEGGiamt:Amet_2793.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiMKFTKMH.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciAMET293826:GI5P-2838-MONOMER.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase.
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...

Publicationsi

  1. "Complete sequence of Alkaliphilus metalliredigens QYMF."
    Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S., Chertkov O., Brettin T., Bruce D., Han C., Schmutz J., Larimer F., Land M.
    , Hauser L., Kyrpides N., Mikhailova N., Ye Q., Zhou J., Fields M., Richardson P.
    Submitted (JUN-2007) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: QYMF.

Entry informationi

Entry nameiDAPF_ALKMQ
AccessioniPrimary (citable) accession number: A6TRX5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 5, 2008
Last sequence update: August 21, 2007
Last modified: April 29, 2015
This is version 54 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

External Data

Dasty 3

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 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.