ID F1ZCI9_9SPHN Unreviewed; 269 AA.
AC F1ZCI9;
DT 31-MAY-2011, integrated into UniProtKB/TrEMBL.
DT 31-MAY-2011, sequence version 1.
DT 24-JAN-2024, entry version 53.
DE RecName: Full=Diaminopimelate epimerase {ECO:0000256|ARBA:ARBA00013080, ECO:0000256|HAMAP-Rule:MF_00197};
DE Short=DAP epimerase {ECO:0000256|HAMAP-Rule:MF_00197};
DE EC=5.1.1.7 {ECO:0000256|ARBA:ARBA00013080, ECO:0000256|HAMAP-Rule:MF_00197};
DE AltName: Full=PLP-independent amino acid racemase {ECO:0000256|HAMAP-Rule:MF_00197};
GN Name=dapF {ECO:0000256|HAMAP-Rule:MF_00197};
GN ORFNames=Y88_3055 {ECO:0000313|EMBL:EGD57729.1};
OS Novosphingobium nitrogenifigens DSM 19370.
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales;
OC Sphingomonadaceae; Novosphingobium.
OX NCBI_TaxID=983920 {ECO:0000313|EMBL:EGD57729.1, ECO:0000313|Proteomes:UP000004728};
RN [1] {ECO:0000313|EMBL:EGD57729.1, ECO:0000313|Proteomes:UP000004728}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 19370 {ECO:0000313|EMBL:EGD57729.1,
RC ECO:0000313|Proteomes:UP000004728};
RX PubMed=22156397; DOI=10.1128/JB.06381-11;
RA Strabala T.J., Macdonald L., Liu V., Smit A.M.;
RT "Draft Genome Sequence of Novosphingobium nitrogenifigens Y88T.";
RL J. Bacteriol. 194:201-201(2012).
CC -!- FUNCTION: Catalyzes the stereoinversion of LL-2,6-diaminoheptanedioate
CC (L,L-DAP) to meso-diaminoheptanedioate (meso-DAP), a precursor of L-
CC lysine and an essential component of the bacterial peptidoglycan.
CC {ECO:0000256|HAMAP-Rule:MF_00197}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(2S,6S)-2,6-diaminoheptanedioate = meso-2,6-
CC diaminoheptanedioate; Xref=Rhea:RHEA:15393, ChEBI:CHEBI:57609,
CC ChEBI:CHEBI:57791; EC=5.1.1.7;
CC Evidence={ECO:0000256|ARBA:ARBA00000599, ECO:0000256|HAMAP-
CC Rule:MF_00197};
CC -!- PATHWAY: Amino-acid biosynthesis; L-lysine biosynthesis via DAP
CC pathway; DL-2,6-diaminopimelate from LL-2,6-diaminopimelate: step 1/1.
CC {ECO:0000256|ARBA:ARBA00005196, ECO:0000256|HAMAP-Rule:MF_00197}.
CC -!- SUBUNIT: Homodimer. {ECO:0000256|HAMAP-Rule:MF_00197}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00197}.
CC -!- SIMILARITY: Belongs to the diaminopimelate epimerase family.
CC {ECO:0000256|ARBA:ARBA00010219, ECO:0000256|HAMAP-Rule:MF_00197}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:EGD57729.1}.
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DR EMBL; AEWJ01000054; EGD57729.1; -; Genomic_DNA.
DR RefSeq; WP_008070973.1; NZ_GL876934.1.
DR AlphaFoldDB; F1ZCI9; -.
DR STRING; 983920.Y88_3055; -.
DR eggNOG; COG0253; Bacteria.
DR HOGENOM; CLU_053306_1_0_5; -.
DR InParanoid; F1ZCI9; -.
DR OrthoDB; 9805408at2; -.
DR UniPathway; UPA00034; UER00025.
DR Proteomes; UP000004728; Unassembled WGS sequence.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0008837; F:diaminopimelate epimerase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0009089; P:lysine biosynthetic process via diaminopimelate; IEA:UniProtKB-UniRule.
DR HAMAP; MF_00197; DAP_epimerase; 1.
DR InterPro; IPR018510; DAP_epimerase_AS.
DR InterPro; IPR001653; DAP_epimerase_DapF.
DR NCBIfam; TIGR00652; DapF; 1.
DR PANTHER; PTHR31689:SF0; DIAMINOPIMELATE EPIMERASE; 1.
DR PANTHER; PTHR31689; DIAMINOPIMELATE EPIMERASE, CHLOROPLASTIC; 1.
DR Pfam; PF01678; DAP_epimerase; 2.
DR SUPFAM; SSF54506; Diaminopimelate epimerase-like; 2.
DR PROSITE; PS01326; DAP_EPIMERASE; 1.
PE 3: Inferred from homology;
KW Amino-acid biosynthesis {ECO:0000256|ARBA:ARBA00022605, ECO:0000256|HAMAP-
KW Rule:MF_00197}; Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00197};
KW Isomerase {ECO:0000256|ARBA:ARBA00023235, ECO:0000256|HAMAP-Rule:MF_00197};
KW Lysine biosynthesis {ECO:0000256|ARBA:ARBA00023154, ECO:0000256|HAMAP-
KW Rule:MF_00197}; Reference proteome {ECO:0000313|Proteomes:UP000004728}.
FT ACT_SITE 73
FT /evidence="ECO:0000256|PROSITE-ProRule:PRU10125"
FT ACT_SITE 73
FT /note="Proton donor"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT ACT_SITE 208
FT /note="Proton acceptor"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT BINDING 13
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT BINDING 46
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT BINDING 64
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT BINDING 74..75
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT BINDING 148
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT BINDING 181
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT BINDING 199..200
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT BINDING 209..210
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT SITE 150
FT /note="Could be important to modulate the pK values of the
FT two catalytic cysteine residues"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT SITE 199
FT /note="Could be important to modulate the pK values of the
FT two catalytic cysteine residues"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
SQ SEQUENCE 269 AA; 28813 MW; E94A1FC4B54A786E CRC64;
MRIPFRKMHG LGNDFVVIDA RERAVEMSAR RAAALADRHT GIGCDQLILL EPSETADVRM
RIFNPDGGEV EACGNASRAV GLYLGGDKRI ETLGGIIAAS TSDTGISVAM GRPRFGWDEI
PLAYPMDTLT MPVGWEDLVE PVAVNVGNPH VIFFVPDTHS VDLARLGPLI ENDPLFPRRI
NVNVATLTGP DALDLRVWER AAGLTRACGT GACASAIAAM RRKLTGRRVT VTLPGGPLVI
EWTDADEIIM TGPATTSFEG SFGTSDYPA
//
