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B2KDH2

- DAPF_ELUMP

UniProt

B2KDH2 - DAPF_ELUMP

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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Elusimicrobium minutum (strain Pei191)
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 sitei11 – 111SubstrateUniRule annotation
Binding sitei44 – 441SubstrateUniRule annotation
Binding sitei62 – 621SubstrateUniRule annotation
Active sitei71 – 711Proton donor/acceptorUniRule annotation
Binding sitei157 – 1571SubstrateUniRule annotation
Sitei159 – 1591Important for catalytic activityUniRule annotation
Binding sitei190 – 1901SubstrateUniRule annotation
Sitei208 – 2081Important for catalytic activityUniRule annotation
Active sitei217 – 2171Proton 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

BioCyciEMIN445932:GHM0-1049-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:Emin_1015
OrganismiElusimicrobium minutum (strain Pei191)
Taxonomic identifieri445932 [NCBI]
Taxonomic lineageiBacteriaElusimicrobiaElusimicrobiaElusimicrobialesElusimicrobiaceaeElusimicrobium
ProteomesiUP000001029: 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 – 274274Diaminopimelate epimerasePRO_1000099235Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi71 ↔ 217

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi445932.Emin_1015.

Structurei

3D structure databases

ProteinModelPortaliB2KDH2.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni8 – 92Substrate bindingUniRule annotation
Regioni71 – 733Substrate bindingUniRule annotation
Regioni208 – 2092Substrate bindingUniRule annotation
Regioni218 – 2192Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiVFDRYFL.
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.

B2KDH2-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MEFVKYQGLG NDFILIDCVK IKIDGLNALG KKLCDRHFGI GADGLIAVFP
60 70 80 90 100
SASADYKIRI INSDGTEPEM CGNGIRCAMR FVFDYIKPQR KLTFETLAGP
110 120 130 140 150
IKTELLAENL VKVDMGAPKL TAAQIPLNIS DSDGRAVDIP VKLEGGKIKG
160 170 180 190 200
TGVSMGNPHF VIFVEDIKKT DVAKTGKEVE NNTAFPQKTN VEFVQVITPS
210 220 230 240 250
RLCMKVWERG VGITLACGTG ACASLVAGVL NNKTERLALV ELDGGQLTVE
260 270
WPDDGASVFM TGPATEVFSG VFKE
Length:274
Mass (Da):29,503
Last modified:June 10, 2008 - v1
Checksum:i1BF0D0C1A6D25039
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001055 Genomic DNA. Translation: ACC98568.1.
RefSeqiWP_012415183.1. NC_010644.1.
YP_001875905.1. NC_010644.1.

Genome annotation databases

EnsemblBacteriaiACC98568; ACC98568; Emin_1015.
GeneIDi6263152.
KEGGiemi:Emin_1015.
PATRICi21849252. VBIEluMin86178_1053.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001055 Genomic DNA. Translation: ACC98568.1 .
RefSeqi WP_012415183.1. NC_010644.1.
YP_001875905.1. NC_010644.1.

3D structure databases

ProteinModelPortali B2KDH2.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 445932.Emin_1015.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ACC98568 ; ACC98568 ; Emin_1015 .
GeneIDi 6263152.
KEGGi emi:Emin_1015.
PATRICi 21849252. VBIEluMin86178_1053.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayi UPA00034 ; UER00025 .
BioCyci EMIN445932:GHM0-1049-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. "Genomic analysis of 'Elusimicrobium minutum,' the first cultivated representative of the phylum 'Elusimicrobia' (formerly termite group 1)."
    Herlemann D.P.R., Geissinger O., Ikeda-Ohtsubo W., Kunin V., Sun H., Lapidus A., Hugenholtz P., Brune A.
    Appl. Environ. Microbiol. 75:2841-2849(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Pei191.

Entry informationi

Entry nameiDAPF_ELUMP
AccessioniPrimary (citable) accession number: B2KDH2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: June 10, 2008
Last modified: November 26, 2014
This is version 49 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