Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
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)DescriptionActionsGraphical viewLength
Binding sitei13SubstrateUniRule annotation1
Binding sitei46SubstrateUniRule annotation1
Binding sitei66SubstrateUniRule annotation1
Active sitei75Proton donor/acceptorUniRule annotation1
Binding sitei160SubstrateUniRule annotation1
Sitei162Important for catalytic activityUniRule annotation1
Binding sitei193SubstrateUniRule annotation1
Sitei211Important for catalytic activityUniRule annotation1
Active sitei220Proton donor/acceptorUniRule annotation1

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

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)DescriptionActionsGraphical viewLength
ChainiPRO_10001186591 – 281Diaminopimelate epimeraseAdd BLAST281

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi75 ↔ 220

Keywords - PTMi

Disulfide bond

Structurei

Secondary structure

1281
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 10Combined sources8
Beta strandi13 – 19Combined sources7
Helixi29 – 36Combined sources8
Turni38 – 40Combined sources3
Beta strandi45 – 51Combined sources7
Beta strandi59 – 66Combined sources8
Helixi78 – 88Combined sources11
Beta strandi99 – 101Combined sources3
Beta strandi104 – 106Combined sources3
Helixi112 – 114Combined sources3
Beta strandi116 – 119Combined sources4
Helixi127 – 129Combined sources3
Beta strandi141 – 144Combined sources4
Helixi146 – 148Combined sources3
Beta strandi150 – 166Combined sources17
Turni170 – 172Combined sources3
Helixi175 – 183Combined sources9
Beta strandi193 – 201Combined sources9
Beta strandi204 – 211Combined sources8
Turni212 – 214Combined sources3
Beta strandi215 – 218Combined sources4
Helixi221 – 233Combined sources13
Beta strandi239 – 245Combined sources7
Beta strandi248 – 253Combined sources6
Beta strandi261 – 264Combined sources4
Beta strandi267 – 274Combined sources8
Helixi276 – 279Combined sources4

3D structure databases

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

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni10 – 11Substrate bindingUniRule annotation2
Regioni75 – 77Substrate bindingUniRule annotation3
Regioni211 – 212Substrate bindingUniRule annotation2
Regioni221 – 222Substrate bindingUniRule annotation2

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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5HA4X-ray1.85A/B1-280[»]
ProteinModelPortaliB7GY71.
SMRiB7GY71.
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.

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: November 2, 2016
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

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.