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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Acinetobacter baumannii (strain AB307-0294)
Status
Reviewed-Annotation score: 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: L-lysine biosynthesis via DAP pathway

This protein is involved in step 1 of the subpathway that synthesizes DL-2,6-diaminopimelate from LL-2,6-diaminopimelate.UniRule annotation
Proteins known to be involved in this subpathway in this organism are:
  1. Diaminopimelate epimerase (dapF)
This subpathway is part of the pathway L-lysine biosynthesis via DAP pathway, which is itself part of Amino-acid biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes DL-2,6-diaminopimelate from LL-2,6-diaminopimelate, the pathway L-lysine biosynthesis via DAP pathway and in Amino-acid biosynthesis.

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 sitei160 – 1601SubstrateUniRule annotation
Sitei162 – 1621Important for catalytic activityUniRule annotation
Binding sitei193 – 1931SubstrateUniRule annotation
Sitei211 – 2111Important for catalytic activityUniRule annotation
Active sitei220 – 2201Proton donor/acceptorUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Biological processi

Amino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

BioCyciABAU557600:GKC3-854-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:ABBFA_000848
OrganismiAcinetobacter baumannii (strain AB307-0294)
Taxonomic identifieri557600 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesMoraxellaceaeAcinetobacterAcinetobacter calcoaceticus/baumannii complex

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 281281Diaminopimelate epimerasePRO_1000118659Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi75 ↔ 220

Keywords - PTMi

Disulfide bond

Structurei

Secondary structure

1
281
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 108Combined sources
Beta strandi13 – 197Combined sources
Helixi29 – 368Combined sources
Turni38 – 403Combined sources
Beta strandi45 – 517Combined sources
Beta strandi59 – 668Combined sources
Helixi78 – 8811Combined sources
Beta strandi99 – 1013Combined sources
Beta strandi104 – 1063Combined sources
Helixi112 – 1143Combined sources
Beta strandi116 – 1194Combined sources
Helixi127 – 1293Combined sources
Beta strandi141 – 1444Combined sources
Helixi146 – 1483Combined sources
Beta strandi150 – 16617Combined sources
Turni170 – 1723Combined sources
Helixi175 – 1839Combined sources
Beta strandi193 – 2019Combined sources
Beta strandi204 – 2118Combined sources
Turni212 – 2143Combined sources
Beta strandi215 – 2184Combined sources
Helixi221 – 23313Combined sources
Beta strandi239 – 2457Combined sources
Beta strandi248 – 2536Combined sources
Beta strandi261 – 2644Combined sources
Beta strandi267 – 2748Combined sources
Helixi276 – 2794Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
5HA4X-ray1.85A/B1-280[»]
ProteinModelPortaliB7GY71.
SMRiB7GY71. Positions 3-276.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni10 – 112Substrate bindingUniRule annotation
Regioni75 – 773Substrate bindingUniRule annotation
Regioni211 – 2122Substrate bindingUniRule annotation
Regioni221 – 2222Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

HOGENOMiHOG000220466.
KOiK01778.
OMAiRFTKMQG.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase. 1 hit.
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.

B7GY71-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLLEFTKMHG LGNDFMVVDL ISQRAYLDTA TIQRLADRHF GVGFDQLLIV
60 70 80 90 100
EPPDVPEADF KYRIFNADGS EVEQCGNGVR CFARFVHERH LTNKTNITVQ
110 120 130 140 150
TKAGIVKPEL GQNGWVRVNM GYPKFLPNEI PFVAEEPEAL YTLELANDQN
160 170 180 190 200
ISIDVVNMGN PHAVTIVPDV LTADVAGIGP QVESHKRFPE RVNAGFMQVI
210 220 230 240 250
DDKHVRLRVF ERGVGETLAC GTGACAAAVS GMRRGLLANS VEVELAGGKL
260 270 280
QIEWQEGDVV WMTGPTTHVY DGRLDLRYFQ G
Length:281
Mass (Da):31,139
Last modified:February 10, 2009 - v1
Checksum:i700E4DB6C3C49032
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001172 Genomic DNA. Translation: ACJ59349.1.
RefSeqiWP_000923484.1. NC_011595.1.

Genome annotation databases

EnsemblBacteriaiACJ59349; ACJ59349; ABBFA_000848.
KEGGiabb:ABBFA_000848.
PATRICi20703220. VBIAciBau42682_0806.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001172 Genomic DNA. Translation: ACJ59349.1.
RefSeqiWP_000923484.1. NC_011595.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
5HA4X-ray1.85A/B1-280[»]
ProteinModelPortaliB7GY71.
SMRiB7GY71. Positions 3-276.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACJ59349; ACJ59349; ABBFA_000848.
KEGGiabb:ABBFA_000848.
PATRICi20703220. VBIAciBau42682_0806.

Phylogenomic databases

HOGENOMiHOG000220466.
KOiK01778.
OMAiRFTKMQG.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciABAU557600:GKC3-854-MONOMER.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase. 1 hit.
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]
ProtoNetiSearch...

Entry informationi

Entry nameiDAPF_ACIB3
AccessioniPrimary (citable) accession number: B7GY71
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 14, 2009
Last sequence update: February 10, 2009
Last modified: September 7, 2016
This is version 51 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

3D-structure

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

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 one 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.