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Q3JEA2

- DAPF_NITOC

UniProt

Q3JEA2 - DAPF_NITOC

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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Nitrosococcus oceani (strain ATCC 19707 / NCIMB 11848)
Status
Reviewed - 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 sitei46 – 461SubstrateUniRule annotation
Binding sitei66 – 661SubstrateUniRule annotation
Active sitei75 – 751Proton donor/acceptorUniRule annotation
Binding sitei159 – 1591SubstrateUniRule annotation
Sitei161 – 1611Important for catalytic activityUniRule annotation
Binding sitei192 – 1921SubstrateUniRule annotation
Sitei210 – 2101Important for catalytic activityUniRule annotation
Active sitei219 – 2191Proton 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

BioCyciNOCE323261:GCI3-320-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:Noc_0316
OrganismiNitrosococcus oceani (strain ATCC 19707 / NCIMB 11848)
Taxonomic identifieri323261 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaChromatialesChromatiaceaeNitrosococcus
ProteomesiUP000006838: Chromosome

Subcellular locationi

Cytoplasm UniRule annotation

GO - Cellular componenti

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

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 276276Diaminopimelate epimerasePRO_1000011919Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi75 ↔ 219

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi323261.Noc_0316.

Structurei

3D structure databases

ProteinModelPortaliQ3JEA2.
SMRiQ3JEA2. Positions 3-276.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni10 – 112Substrate bindingUniRule annotation
Regioni75 – 773Substrate bindingUniRule annotation
Regioni210 – 2112Substrate bindingUniRule annotation
Regioni220 – 2212Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiLIVEPPY.
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.

Q3JEA2-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MRIAFTKMQG LGNDFVVIDA LSQPLSLTAS QVRWIANRRL GIGCDQVLLV
60 70 80 90 100
TPASLPAIDF GYRIFNADGG EVEQCGNGAR CFARFVREQG LTDKNVLRVQ
110 120 130 140 150
TASGIIELQL ETDGQITVDM GVPRFAPHQI PFKVDQEADY YSLELDGQQV
160 170 180 190 200
EIGAVSMGNP HCVLRVPAVD TAPVAHWGPL LESHPRFPQR VNVGFAQIVS
210 220 230 240 250
PGHLRLRVYE RGAGETPACG TGACAAAVIG KRRGWLSGQV NVDLPGGRLG
260 270
IHWEGDGKSV WMSGPAEIVF KGSIEL
Length:276
Mass (Da):29,812
Last modified:November 8, 2005 - v1
Checksum:i702EBE5207799457
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000127 Genomic DNA. Translation: ABA56844.1.
RefSeqiYP_342374.1. NC_007484.1.

Genome annotation databases

EnsemblBacteriaiABA56844; ABA56844; Noc_0316.
GeneIDi3706487.
KEGGinoc:Noc_0316.
PATRICi22704336. VBINitOce57959_0412.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000127 Genomic DNA. Translation: ABA56844.1 .
RefSeqi YP_342374.1. NC_007484.1.

3D structure databases

ProteinModelPortali Q3JEA2.
SMRi Q3JEA2. Positions 3-276.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 323261.Noc_0316.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ABA56844 ; ABA56844 ; Noc_0316 .
GeneIDi 3706487.
KEGGi noc:Noc_0316.
PATRICi 22704336. VBINitOce57959_0412.

Phylogenomic databases

eggNOGi COG0253.
HOGENOMi HOG000220466.
KOi K01778.
OMAi LIVEPPY.
OrthoDBi EOG6ND0M5.

Enzyme and pathway databases

UniPathwayi UPA00034 ; UER00025 .
BioCyci NOCE323261:GCI3-320-MONOMER.

Family and domain databases

HAMAPi MF_00197. DAP_epimerase.
InterProi IPR018510. DAP_epimerase_AS.
IPR001653. DAP_epimerase_DapF.
[Graphical view ]
PANTHERi PTHR31689. PTHR31689. 1 hit.
Pfami PF01678. DAP_epimerase. 2 hits.
[Graphical view ]
TIGRFAMsi TIGR00652. DapF. 1 hit.
PROSITEi PS01326. DAP_EPIMERASE. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "Complete genome sequence of the marine, chemolithoautotrophic, ammonia-oxidizing bacterium Nitrosococcus oceani ATCC 19707."
    Klotz M.G., Arp D.J., Chain P.S.G., El-Sheikh A.F., Hauser L.J., Hommes N.G., Larimer F.W., Malfatti S.A., Norton J.M., Poret-Peterson A.T., Vergez L.M., Ward B.B.
    Appl. Environ. Microbiol. 72:6299-6315(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 19707 / NCIMB 11848.

Entry informationi

Entry nameiDAPF_NITOC
AccessioniPrimary (citable) accession number: Q3JEA2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: November 8, 2005
Last modified: October 29, 2014
This is version 61 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