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A4XNX4

- DAPF_PSEMY

UniProt

A4XNX4 - DAPF_PSEMY

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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Pseudomonas mendocina (strain ymp)
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

BioCyciPMEN399739:GHR6-266-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:Pmen_0266
OrganismiPseudomonas mendocina (strain ymp)
Taxonomic identifieri399739 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas
ProteomesiUP000000229: 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_1000011934Add
BLAST

Amino acid modifications

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

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi399739.Pmen_0266.

Structurei

3D structure databases

ProteinModelPortaliA4XNX4.
SMRiA4XNX4. 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.

A4XNX4-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MLLRFTKMHG LGNDFMVLDL ISQHAHVQPK HAKQWGDRHT GVGFDQLLIV
60 70 80 90 100
EPPSHPDVDF RYRIFNSDGS EVEQCGNGAR CFARFVLDKR LTTKKTIRVE
110 120 130 140 150
TKSGVIELRV QNDGQVCVNM GAPRLEPAQV PFQAEQAALT YRVDVEGQSV
160 170 180 190 200
ELAALSMGNP HAVLRVDNVD SAPVHTLGPK LEHHPRFPQR VNVGFLQVLD
210 220 230 240 250
RKHARLRVWE RGAGETQACG TGACAAAVAA IRQGWMDSPV QLELPGGKLS
260 270
IEWAGEGQPV MMTGPAARVY EGQVRL
Length:276
Mass (Da):30,436
Last modified:May 29, 2007 - v1
Checksum:i3F10B1214260EAC7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000680 Genomic DNA. Translation: ABP83040.1.
RefSeqiWP_011920560.1. NC_009439.1.
YP_001185772.1. NC_009439.1.

Genome annotation databases

EnsemblBacteriaiABP83040; ABP83040; Pmen_0266.
GeneIDi5106233.
KEGGipmy:Pmen_0266.
PATRICi19906945. VBIPseMen131592_0272.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000680 Genomic DNA. Translation: ABP83040.1 .
RefSeqi WP_011920560.1. NC_009439.1.
YP_001185772.1. NC_009439.1.

3D structure databases

ProteinModelPortali A4XNX4.
SMRi A4XNX4. Positions 3-276.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 399739.Pmen_0266.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ABP83040 ; ABP83040 ; Pmen_0266 .
GeneIDi 5106233.
KEGGi pmy:Pmen_0266.
PATRICi 19906945. VBIPseMen131592_0272.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayi UPA00034 ; UER00025 .
BioCyci PMEN399739:GHR6-266-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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ymp.

Entry informationi

Entry nameiDAPF_PSEMY
AccessioniPrimary (citable) accession number: A4XNX4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: May 29, 2007
Last modified: November 26, 2014
This is version 53 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