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A5F4I6

- DAPF_VIBC3

UniProt

A5F4I6 - DAPF_VIBC3

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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)
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

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:VC0395_A2393, VC395_0054
OrganismiVibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)
Taxonomic identifieri345073 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
ProteomesiUP000000249: Chromosome 2, UP000001630: Chromosome I

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_1000071717Add
BLAST

Amino acid modifications

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

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi345073.VC0395_A2393.

Structurei

3D structure databases

ProteinModelPortaliA5F4I6.
SMRiA5F4I6. Positions 4-275.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

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

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiLIVEPPY.

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.

A5F4I6 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MHFHFSKMHG LGNDFMVVDC ITQNVFFSPE LIRRLADRHT GVGFDQLLVV
60 70 80 90 100
EAPYDPESDF HYRIFNADGS EVEQCGNGAR CFARFVRMKG LTNKYTIHVS
110 120 130 140 150
TKKGKMVLNV EEEDLITVNM GVPEFEPNKI PFRAKQSEKT YILRVGEHTL
160 170 180 190 200
FCGAVSMGNP HVVTVVDDIR TAAVETLGPL LESHERFPER VNAGFMQVVS
210 220 230 240 250
RDEINLRVYE RGAGETQACG SGACAAVAVG ILQGLLDEQV RVHLPGGELE
260 270
IHWQGPGKPL YMTGPATHIY DGQISC
Length:276
Mass (Da):30,651
Last modified:June 12, 2007 - v1
Checksum:i8FCFEC10E5DD714B
GO

Sequence cautioni

The sequence ACP08082.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000627 Genomic DNA. Translation: ABQ19755.1.
CP001235 Genomic DNA. Translation: ACP08082.1. Different initiation.
RefSeqiYP_001218293.1. NC_009457.1.
YP_002818318.1. NC_012582.1.

Genome annotation databases

EnsemblBacteriaiABQ19755; ABQ19755; VC0395_A2393.
ACP08082; ACP08082; VC395_0054.
GeneIDi5137009.
7776703.
KEGGivco:VC0395_A2393.
vcr:VC395_0054.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000627 Genomic DNA. Translation: ABQ19755.1 .
CP001235 Genomic DNA. Translation: ACP08082.1 . Different initiation.
RefSeqi YP_001218293.1. NC_009457.1.
YP_002818318.1. NC_012582.1.

3D structure databases

ProteinModelPortali A5F4I6.
SMRi A5F4I6. Positions 4-275.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 345073.VC0395_A2393.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ABQ19755 ; ABQ19755 ; VC0395_A2393 .
ACP08082 ; ACP08082 ; VC395_0054 .
GeneIDi 5137009.
7776703.
KEGGi vco:VC0395_A2393.
vcr:VC395_0054.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayi UPA00034 ; UER00025 .

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. Heidelberg J.
    Submitted (MAR-2007) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 39541 / Classical Ogawa 395 / O395.
  2. "A recalibrated molecular clock and independent origins for the cholera pandemic clones."
    Feng L., Reeves P.R., Lan R., Ren Y., Gao C., Zhou Z., Ren Y., Cheng J., Wang W., Wang J., Qian W., Li D., Wang L.
    PLoS ONE 3:E4053-E4053(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 39541 / Classical Ogawa 395 / O395.

Entry informationi

Entry nameiDAPF_VIBC3
AccessioniPrimary (citable) accession number: A5F4I6
Secondary accession number(s): C3M2B8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 26, 2008
Last sequence update: June 12, 2007
Last modified: October 29, 2014
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

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3