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Protein

Diaminopimelate epimerase 1

Gene

dapF1

Organism
Nostoc sp. (strain PCC 7120 / 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.By similarity

Catalytic activityi

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

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei11 – 111SubstrateBy similarity
Binding sitei44 – 441SubstrateBy similarity
Binding sitei63 – 631SubstrateBy similarity
Active sitei72 – 721Proton donor/acceptorBy similarity
Binding sitei158 – 1581SubstrateBy similarity
Sitei160 – 1601Important for catalytic activityBy similarity
Binding sitei191 – 1911SubstrateBy similarity
Sitei209 – 2091Important for catalytic activityBy similarity
Active sitei218 – 2181Proton donor/acceptorBy similarity

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 epimerase 1 (EC:5.1.1.7)
Short name:
DAP epimerase 1
Gene namesi
Name:dapF1
Synonyms:dapF
Ordered Locus Names:alr4841
OrganismiNostoc sp. (strain PCC 7120 / UTEX 2576)
Taxonomic identifieri103690 [NCBI]
Taxonomic lineageiBacteriaCyanobacteriaNostocalesNostocaceaeNostoc
ProteomesiUP000002483 Componenti: Chromosome

Subcellular locationi

  1. Cytoplasm By similarity

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 – 285285Diaminopimelate epimerase 1PRO_0000149816Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi103690.alr4841.

Structurei

3D structure databases

ProteinModelPortaliP54897.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni8 – 92Substrate bindingBy similarity
Regioni209 – 2102Substrate bindingBy similarity

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.Curated

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiNDYLVCH.
OrthoDBiEOG6ND0M5.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase.
InterProiIPR001653. DAP_epimerase_DapF.
[Graphical view]
PANTHERiPTHR31689. PTHR31689. 1 hit.
PfamiPF01678. DAP_epimerase. 2 hits.
[Graphical view]
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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti223 – 2231Missing in CAA87006 (PubMed:9139910).Curated

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.
RefSeqiNP_488881.1. NC_003272.1.
WP_010998969.1. NC_003272.1.

Genome annotation databases

EnsemblBacteriaiBAB76540; BAB76540; BAB76540.
KEGGiana:alr4841.
PATRICi22780337. VBINosSp37423_5611.

Cross-referencesi

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.
RefSeqiNP_488881.1. NC_003272.1.
WP_010998969.1. NC_003272.1.

3D structure databases

ProteinModelPortaliP54897.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi103690.alr4841.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAB76540; BAB76540; BAB76540.
KEGGiana:alr4841.
PATRICi22780337. VBINosSp37423_5611.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiNDYLVCH.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase.
InterProiIPR001653. DAP_epimerase_DapF.
[Graphical view]
PANTHERiPTHR31689. PTHR31689. 1 hit.
PfamiPF01678. DAP_epimerase. 2 hits.
[Graphical view]
TIGRFAMsiTIGR00652. DapF. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Identification and characterization of the nifV-nifZ-nifT gene region from the filamentous cyanobacterium Anabaena sp. strain PCC 7120."
    Stricker O., Masepohl B., Klipp W., Boehme H.
    J. Bacteriol. 179:2930-2937(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: PCC 7120 / UTEX 2576.

Entry informationi

Entry nameiDAPF1_NOSS1
AccessioniPrimary (citable) accession number: P54897
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: January 23, 2002
Last modified: April 29, 2015
This is version 93 of the entry and version 2 of the sequence. [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

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.