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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Flavobacterium psychrophilum (strain JIP02/86 / ATCC 49511)
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 sitei11 – 111SubstrateUniRule annotation
Binding sitei45 – 451SubstrateUniRule annotation
Binding sitei63 – 631SubstrateUniRule annotation
Active sitei72 – 721Proton donor/acceptorUniRule annotation
Sitei137 – 1371Important for catalytic activityUniRule annotation
Binding sitei169 – 1691SubstrateUniRule annotation
Sitei187 – 1871Important for catalytic activityUniRule annotation
Active sitei197 – 1971Proton 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

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:FP1215
OrganismiFlavobacterium psychrophilum (strain JIP02/86 / ATCC 49511)
Taxonomic identifieri402612 [NCBI]
Taxonomic lineageiBacteriaBacteroidetesFlavobacteriiaFlavobacterialesFlavobacteriaceaeFlavobacterium
ProteomesiUP000006394: Chromosome

Subcellular locationi

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 – 256256Diaminopimelate epimerasePRO_1000099237Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi72 ↔ 197

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi402612.FP1215.

Structurei

3D structure databases

ProteinModelPortaliA6GYX5.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni72 – 743Substrate bindingUniRule annotation
Regioni187 – 1882Substrate bindingUniRule annotation
Regioni198 – 1992Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiHEGFGAD.
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.

A6GYX5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKLYKYQGTG NDFIMIDNRL QIFPKQNTAL IQKLCDRRFG IGADGLILLE
60 70 80 90 100
NDQSTDFKMV YYNSDGNQST MCGNGGRCLV AFAKKLNIIK NKTTFIAIDG
110 120 130 140 150
LHHATINEND IISLQMKNVE EVNIHDNYVF LNTGSPHHVQ FADNLSNFDV
160 170 180 190 200
KNEGAKIRYS DLYGQAGSNI NFVHQTSPTQ FSIRTYERGV EDETLSCGTG
210 220 230 240 250
ATATAIAMKA TGKTNSNNIT INVQGGKLEV SFNQENSIFT NIFLKGPAEF

VFETTI
Length:256
Mass (Da):28,463
Last modified:July 24, 2007 - v1
Checksum:i42633776D96E3A8B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AM398681 Genomic DNA. Translation: CAL43298.1.
RefSeqiYP_001296109.1. NC_009613.3.

Genome annotation databases

EnsemblBacteriaiCAL43298; CAL43298; FP1215.
GeneIDi5298992.
KEGGifps:FP1215.
PATRICi21907336. VBIFlaPsy4505_1229.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AM398681 Genomic DNA. Translation: CAL43298.1.
RefSeqiYP_001296109.1. NC_009613.3.

3D structure databases

ProteinModelPortaliA6GYX5.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi402612.FP1215.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAL43298; CAL43298; FP1215.
GeneIDi5298992.
KEGGifps:FP1215.
PATRICi21907336. VBIFlaPsy4505_1229.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiHEGFGAD.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.

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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: JIP02/86 / ATCC 49511.

Entry informationi

Entry nameiDAPF_FLAPJ
AccessioniPrimary (citable) accession number: A6GYX5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: July 24, 2007
Last modified: January 7, 2015
This is version 55 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.