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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
Status
Reviewed-Annotation score: Annotation score: 5 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. Only accepts DAP isomers with the L configuration.1 Publication

Catalytic activityi

LL-2,6-diaminoheptanedioate = meso-diaminoheptanedioate.1 Publication

Enzyme regulationi

Inhibited by LL-aziridino (LL-AziDAP), DL-aziridino (DL-AziDAP), (2S,3R,6S)-2,6-diamino-3-fluoropimelate (L,L-3-fluoro-DAP) and (2R,3S,6S)-2,6-diamino-3-fluoropimelate (D,L-3-fluoro-DAP).2 Publications

Kineticsi

Kcat is 128 and 82 (sec-1) for L,L-DAP and D,L-DAP, respectively.

  1. KM=0.7 mM for L,L-DAP (at pH 7.8)1 Publication
  2. KM=1.1 mM for D,L-DAP (at pH 7.8)1 Publication

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei11 – 111Substrate
Binding sitei44 – 441Substrate
Binding sitei64 – 641Substrate
Active sitei73 – 731Proton donor/acceptor
Binding sitei157 – 1571Substrate
Sitei159 – 1591Important for catalytic activitySequence Analysis
Binding sitei190 – 1901Substrate
Sitei208 – 2081Important for catalytic activitySequence Analysis
Active sitei217 – 2171Proton donor/acceptor

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

BRENDAi5.1.1.7. 2529.
UniPathwayiUPA00034; UER00025.

Names & Taxonomyi

Protein namesi
Recommended name:
Diaminopimelate epimerase (EC:5.1.1.7)
Short name:
DAP epimerase
Alternative name(s):
PLP-Independent Amino Acid Racemases
Gene namesi
Name:dapF
Ordered Locus Names:HI_0750
OrganismiHaemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
Taxonomic identifieri71421 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPasteurellalesPasteurellaceaeHaemophilus
ProteomesiUP000000579 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi73 – 731C → A: Inactive as epimerases, but it is able to rapidly catalyze the HF eliminatio via abstraction of the C-2 hydrogen of the D,L-3-fluoro-DAP analog and is essentially unable to catalyze the same elimination with the L,L-3-fluoro-DAP analog. 2 Publications
Mutagenesisi73 – 731C → S: It is able to catalyze both epimerization of DAP and HF elimination of L,L-3-fluoro-DAP and D,L-3-fluoro-DAP. Able to slowly eliminate HF but does not catalyze epimerization; when associated with S-217. 2 Publications
Mutagenesisi217 – 2171C → A: Inactive as epimerases. It is able to rapidly catalyze the HF eliminatio via abstraction of the C-2 hydrogen of the L,L-3-fluoro-DAP analog and is essentially unable to catalyze the same elimination with the D,L-3-fluoro-DAP analog. 2 Publications
Mutagenesisi217 – 2171C → S: It is able to catalyze both epimerization of DAP and HF elimination of L,L-3-fluoro-DAP and D,L-3-fluoro-DAP. Able to slowly eliminate HF but does not catalyze epimerization; when associated with S-73. 2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 274274Diaminopimelate epimerasePRO_0000149842Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi73 ↔ 2171 Publication

Keywords - PTMi

Disulfide bond

Interactioni

Subunit structurei

Monomer.3 Publications

Protein-protein interaction databases

STRINGi71421.HI0750.

Structurei

Secondary structure

1
274
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 87Combined sources
Beta strandi11 – 177Combined sources
Beta strandi19 – 213Combined sources
Helixi27 – 348Combined sources
Turni36 – 383Combined sources
Beta strandi43 – 497Combined sources
Beta strandi56 – 649Combined sources
Beta strandi69 – 713Combined sources
Helixi74 – 8613Combined sources
Beta strandi93 – 986Combined sources
Beta strandi103 – 1086Combined sources
Beta strandi114 – 1174Combined sources
Helixi125 – 1273Combined sources
Beta strandi137 – 1426Combined sources
Beta strandi147 – 16317Combined sources
Turni167 – 1693Combined sources
Helixi172 – 1809Combined sources
Beta strandi190 – 1989Combined sources
Beta strandi201 – 2088Combined sources
Turni209 – 2113Combined sources
Helixi218 – 23013Combined sources
Beta strandi236 – 2427Combined sources
Beta strandi245 – 2517Combined sources
Beta strandi258 – 2625Combined sources
Beta strandi265 – 2717Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1BWZX-ray2.72A1-274[»]
1GQZX-ray1.75A1-274[»]
2GKEX-ray1.35A1-274[»]
2GKJX-ray1.70A1-274[»]
2Q9HX-ray2.30A1-274[»]
2Q9JX-ray2.20A1-274[»]
ProteinModelPortaliP44859.
SMRiP44859. Positions 1-274.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP44859.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni8 – 92Substrate
Regioni73 – 753Substrate binding
Regioni208 – 2092Substrate binding
Regioni218 – 2192Substrate binding

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.Curated

Phylogenomic databases

eggNOGiCOG0253.
KOiK01778.
OMAiMKFTKMH.
OrthoDBiEOG6ND0M5.
PhylomeDBiP44859.

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.

P44859-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQFSKMHGLG NDFVVVDGVT QNVFFTPETI RRLANRHCGI GFDQLLIVEA
60 70 80 90 100
PYDPELDFHY RIFNADGSEV SQCGNGARCF ARFVTLKGLT NKKDISVSTQ
110 120 130 140 150
KGNMVLTVKD DNQIRVNMGE PIWEPAKIPF TANKFEKNYI LRTDIQTVLC
160 170 180 190 200
GAVSMGNPHC VVQVDDIQTA NVEQLGPLLE SHERFPERVN AGFMQIINKE
210 220 230 240 250
HIKLRVYERG AGETQACGSG ACAAVAVGIM QGLLNNNVQV DLPGGSLMIE
260 270
WNGVGHPLYM TGEATHIYDG FITL
Length:274
Mass (Da):30,249
Last modified:November 1, 1995 - v1
Checksum:i321B3CDAFFE81EDA
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L42023 Genomic DNA. Translation: AAC22409.1.
PIRiF64090.
RefSeqiNP_438909.1. NC_000907.1.

Genome annotation databases

EnsemblBacteriaiAAC22409; AAC22409; HI_0750.
GeneIDi949560.
KEGGihin:HI0750.
PATRICi20190143. VBIHaeInf48452_0787.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L42023 Genomic DNA. Translation: AAC22409.1.
PIRiF64090.
RefSeqiNP_438909.1. NC_000907.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1BWZX-ray2.72A1-274[»]
1GQZX-ray1.75A1-274[»]
2GKEX-ray1.35A1-274[»]
2GKJX-ray1.70A1-274[»]
2Q9HX-ray2.30A1-274[»]
2Q9JX-ray2.20A1-274[»]
ProteinModelPortaliP44859.
SMRiP44859. Positions 1-274.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi71421.HI0750.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC22409; AAC22409; HI_0750.
GeneIDi949560.
KEGGihin:HI0750.
PATRICi20190143. VBIHaeInf48452_0787.

Phylogenomic databases

eggNOGiCOG0253.
KOiK01778.
OMAiMKFTKMH.
OrthoDBiEOG6ND0M5.
PhylomeDBiP44859.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BRENDAi5.1.1.7. 2529.

Miscellaneous databases

EvolutionaryTraceiP44859.

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]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 51907 / DSM 11121 / KW20 / Rd.
  2. "Chemical mechanism of Haemophilus influenzae diaminopimelate epimerase."
    Koo C.W., Blanchard J.S.
    Biochemistry 38:4416-4422(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, REACTION MECHANISM, BIOPHYSICOCHEMICAL PROPERTIES.
  3. "Identification of active site cysteine residues that function as general bases: diaminopimelate epimerase."
    Koo C.W., Sutherland A., Vederas J.C., Blanchard J.S.
    J. Am. Chem. Soc. 122:6122-6123(1999)
    Cited for: MUTAGENESIS OF CYS-73 AND CYS-217, ACTIVE SITE, ENZYME REGULATION.
  4. "Structural symmetry: the three-dimensional structure of Haemophilus influenzae diaminopimelate epimerase."
    Cirilli M., Zheng R., Scapin G., Blanchard J.S.
    Biochemistry 37:16452-16458(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.72 ANGSTROMS), ACTIVE SITE, DISULFIDE BOND, SUBUNIT.
  5. "Refinement of Haemophilus influenzae diaminopimelic acid epimerase (DapF) at 1.75 A resolution suggests a mechanism for stereocontrol during catalysis."
    Lloyd A.J., Huyton T., Turkenburg J., Roper D.I.
    Acta Crystallogr. D 60:397-400(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS), REACTION MECHANISM.
  6. "Structural insights into stereochemical inversion by diaminopimelate epimerase: an antibacterial drug target."
    Pillai B., Cherney M.M., Diaper C.M., Sutherland A., Blanchard J.S., Vederas J.C., James M.N.
    Proc. Natl. Acad. Sci. U.S.A. 103:8668-8673(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.35 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS, SUBSTRATE SPECIFICITY, ENZYME REGULATION.
  7. "Dynamics of catalysis revealed from the crystal structures of mutants of diaminopimelate epimerase."
    Pillai B., Cherney M., Diaper C.M., Sutherland A., Blanchard J.S., Vederas J.C., James M.N.
    Biochem. Biophys. Res. Commun. 363:547-553(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) OF MUTANT SER-73 AND SER-217 IN COMPLEX WITH SUBSTRATE ANALOGS, MUTAGENESIS OF CYS-73 AND CYS-217.

Entry informationi

Entry nameiDAPF_HAEIN
AccessioniPrimary (citable) accession number: P44859
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: November 1, 1995
Last modified: April 1, 2015
This is version 108 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, Complete proteome, Reference proteome

Documents

  1. Haemophilus influenzae
    Haemophilus influenzae (strain Rd): entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.