LYR_PROMI
ID LYR_PROMI Reviewed; 407 AA.
AC M4GGR9;
DT 08-MAY-2019, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2013, sequence version 1.
DT 03-AUG-2022, entry version 56.
DE RecName: Full=Lysine racemase {ECO:0000303|PubMed:23118975, ECO:0000303|Ref.1};
DE EC=5.1.1.5 {ECO:0000269|PubMed:23118975, ECO:0000269|Ref.1};
DE Flags: Precursor;
GN Name=lyr {ECO:0000303|Ref.1};
OS Proteus mirabilis.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Morganellaceae; Proteus.
OX NCBI_TaxID=584;
RN [1]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, ACTIVITY REGULATION,
RP BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, MUTAGENESIS OF LYS-74 AND SER-394,
RP AND PYRIDOXAL PHOSPHATE AT LYS-74.
RC STRAIN=BCRC 10725;
RX DOI=10.1016/j.procbio.2011.06.019;
RA Kuana Y.C., Kaob C.H., Chenc C.H., Chend C.C., Hue H.Y., Hsua W.H.;
RT "Biochemical characterization of a novel lysine racemase from Proteus
RT mirabilis BCRC10725.";
RL Process Biochem. 46:1914-1920(2011).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.74 ANGSTROMS) IN COMPLEX WITH PLP, FUNCTION,
RP CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, COFACTOR, SUBUNIT, ACTIVE SITES,
RP REACTION MECHANISM, AND MUTAGENESIS OF ARG-173; ASN-174 AND THR-391.
RC STRAIN=BCRC 10725;
RX PubMed=23118975; DOI=10.1371/journal.pone.0048301;
RA Wu H.M., Kuan Y.C., Chu C.H., Hsu W.H., Wang W.C.;
RT "Crystal structures of lysine-preferred racemases, the non-antibiotic
RT selectable markers for transgenic plants.";
RL PLoS ONE 7:E48301-E48301(2012).
CC -!- FUNCTION: Amino-acid racemase that catalyzes the interconversion of L-
CC lysine and D-lysine. To a lesser extent, is also able to interconvert
CC arginine enantiomers (Ref.1, PubMed:23118975). Cannot use methionine,
CC asparagine, alanine, leucine, glutamine, phenylalanine and histidine as
CC substrates (Ref.1). {ECO:0000269|PubMed:23118975, ECO:0000269|Ref.1}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-lysine = D-lysine; Xref=Rhea:RHEA:22864, ChEBI:CHEBI:32551,
CC ChEBI:CHEBI:32557; EC=5.1.1.5; Evidence={ECO:0000269|PubMed:23118975,
CC ECO:0000269|Ref.1};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-arginine = D-arginine; Xref=Rhea:RHEA:18069,
CC ChEBI:CHEBI:32682, ChEBI:CHEBI:32689;
CC Evidence={ECO:0000269|PubMed:23118975, ECO:0000269|Ref.1};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_02212,
CC ECO:0000269|PubMed:23118975, ECO:0000269|Ref.1};
CC -!- ACTIVITY REGULATION: The racemization activity of Lyr is completely
CC inhibited by hydroxylamine. {ECO:0000269|Ref.1}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=21.8 mM for L-lysine {ECO:0000269|Ref.1};
CC KM=15.0 mM for D-lysine {ECO:0000269|Ref.1};
CC KM=14.9 mM for L-arginine {ECO:0000269|Ref.1};
CC Note=kcat is 3326 min(-1) with L-lysine as substrate. kcat is 650
CC min(-1) with L-arginine as substrate. {ECO:0000269|Ref.1};
CC pH dependence:
CC Optimum pH is 8.0-9.0. {ECO:0000269|Ref.1};
CC Temperature dependence:
CC Optimum temperature is 50 degrees Celsius. More than 78% of maximal
CC activity is observed at 40 degrees Celsius and 60 degrees Celsius.
CC {ECO:0000269|Ref.1};
CC -!- SUBUNIT: Forms a head-to-tail homodimer in the structure.
CC {ECO:0000269|PubMed:23118975}.
CC -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000255|PROSITE-
CC ProRule:PRU00303}; Lipid-anchor {ECO:0000255|PROSITE-ProRule:PRU00303};
CC Periplasmic side {ECO:0000305}. Periplasm
CC {ECO:0000250|UniProtKB:I0J1I6}.
CC -!- MISCELLANEOUS: The active-site cleft is located at the dimeric
CC interface and contains the two conserved catalytic residues, a lysine
CC from one subunit and a tyrosine from the other subunit.
CC {ECO:0000305|PubMed:23118975}.
CC -!- SIMILARITY: Belongs to the alanine racemase family. Bsr subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_02212, ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR RefSeq; WP_004243720.1; NZ_CP043870.1.
DR PDB; 4DZA; X-ray; 1.74 A; A=1-407.
DR PDBsum; 4DZA; -.
DR AlphaFoldDB; M4GGR9; -.
DR SMR; M4GGR9; -.
DR STRING; 584.AOUC001_06285; -.
DR BRENDA; 5.1.1.5; 5044.
DR GO; GO:0042597; C:periplasmic space; IEA:UniProtKB-SubCell.
DR GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0008784; F:alanine racemase activity; IEA:InterPro.
DR GO; GO:0047679; F:arginine racemase activity; IEA:RHEA.
DR GO; GO:0018113; F:lysine racemase activity; IEA:UniProtKB-EC.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IEA:UniProtKB-UniRule.
DR CDD; cd06826; PLPDE_III_AR2; 1.
DR Gene3D; 2.40.37.10; -; 1.
DR Gene3D; 3.20.20.10; -; 1.
DR HAMAP; MF_02212; Bsr_racemase; 1.
DR InterPro; IPR000821; Ala_racemase.
DR InterPro; IPR009006; Ala_racemase/Decarboxylase_C.
DR InterPro; IPR011079; Ala_racemase_C.
DR InterPro; IPR001608; Ala_racemase_N.
DR InterPro; IPR020622; Ala_racemase_pyridoxalP-BS.
DR InterPro; IPR029066; PLP-binding_barrel.
DR InterPro; IPR043698; Racemase_Bsr/Lyr.
DR Pfam; PF00842; Ala_racemase_C; 1.
DR Pfam; PF01168; Ala_racemase_N; 1.
DR PRINTS; PR00992; ALARACEMASE.
DR SMART; SM01005; Ala_racemase_C; 1.
DR SUPFAM; SSF50621; SSF50621; 1.
DR SUPFAM; SSF51419; SSF51419; 1.
DR TIGRFAMs; TIGR00492; alr; 1.
DR PROSITE; PS00395; ALANINE_RACEMASE; 1.
DR PROSITE; PS51257; PROKAR_LIPOPROTEIN; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cell membrane; Disulfide bond; Isomerase; Lipoprotein;
KW Membrane; Palmitate; Periplasm; Pyridoxal phosphate; Signal.
FT SIGNAL 1..18
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00303"
FT CHAIN 19..407
FT /note="Lysine racemase"
FT /id="PRO_5004053282"
FT ACT_SITE 74
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02212,
FT ECO:0000305|PubMed:23118975"
FT ACT_SITE 299
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02212,
FT ECO:0000305|PubMed:23118975"
FT BINDING 173
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02212"
FT BINDING 347
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02212"
FT MOD_RES 74
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02212,
FT ECO:0000269|PubMed:23118975, ECO:0000269|Ref.1"
FT LIPID 19
FT /note="N-palmitoyl cysteine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00303"
FT LIPID 19
FT /note="S-diacylglycerol cysteine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00303"
FT DISULFID 70..96
FT /evidence="ECO:0000250|UniProtKB:I0J1I6, ECO:0000255|HAMAP-
FT Rule:MF_02212"
FT MUTAGEN 74
FT /note="K->L: Completely loss of racemase activity towards
FT lysine."
FT /evidence="ECO:0000269|Ref.1"
FT MUTAGEN 173
FT /note="R->A,K: Loss of racemase activity towards both L-
FT lysine and L-arginine."
FT /evidence="ECO:0000269|PubMed:23118975"
FT MUTAGEN 174
FT /note="N->L: Loss of racemase activity towards both L-
FT lysine and L-arginine."
FT /evidence="ECO:0000269|PubMed:23118975"
FT MUTAGEN 391
FT /note="T->Y: Reduces the racemization activity towards L-
FT lysine by 2-fold. Does not affect racemase activity towards
FT L-arginine."
FT /evidence="ECO:0000269|PubMed:23118975"
FT MUTAGEN 394
FT /note="S->C,N,T,Y: Arginine racemization activity is
FT increased by 1.5-1.8 fold compared to the wild-type enzyme,
FT while activity towards L-lysine is decreased. Almost no
FT change in affinity for L-lysine and L-arginine."
FT /evidence="ECO:0000269|Ref.1"
FT STRAND 42..48
FT /evidence="ECO:0007829|PDB:4DZA"
FT HELIX 49..63
FT /evidence="ECO:0007829|PDB:4DZA"
FT STRAND 69..72
FT /evidence="ECO:0007829|PDB:4DZA"
FT TURN 76..80
FT /evidence="ECO:0007829|PDB:4DZA"
FT HELIX 82..91
FT /evidence="ECO:0007829|PDB:4DZA"
FT STRAND 96..99
FT /evidence="ECO:0007829|PDB:4DZA"
FT HELIX 102..110
FT /evidence="ECO:0007829|PDB:4DZA"
FT STRAND 115..119
FT /evidence="ECO:0007829|PDB:4DZA"
FT HELIX 125..131
FT /evidence="ECO:0007829|PDB:4DZA"
FT HELIX 132..134
FT /evidence="ECO:0007829|PDB:4DZA"
FT STRAND 136..140
FT /evidence="ECO:0007829|PDB:4DZA"
FT HELIX 143..156
FT /evidence="ECO:0007829|PDB:4DZA"
FT STRAND 160..166
FT /evidence="ECO:0007829|PDB:4DZA"
FT HELIX 181..191
FT /evidence="ECO:0007829|PDB:4DZA"
FT STRAND 196..202
FT /evidence="ECO:0007829|PDB:4DZA"
FT HELIX 210..231
FT /evidence="ECO:0007829|PDB:4DZA"
FT HELIX 235..237
FT /evidence="ECO:0007829|PDB:4DZA"
FT STRAND 238..241
FT /evidence="ECO:0007829|PDB:4DZA"
FT HELIX 245..250
FT /evidence="ECO:0007829|PDB:4DZA"
FT HELIX 252..255
FT /evidence="ECO:0007829|PDB:4DZA"
FT STRAND 258..262
FT /evidence="ECO:0007829|PDB:4DZA"
FT HELIX 263..266
FT /evidence="ECO:0007829|PDB:4DZA"
FT STRAND 279..284
FT /evidence="ECO:0007829|PDB:4DZA"
FT STRAND 287..291
FT /evidence="ECO:0007829|PDB:4DZA"
FT STRAND 296..298
FT /evidence="ECO:0007829|PDB:4DZA"
FT HELIX 299..301
FT /evidence="ECO:0007829|PDB:4DZA"
FT STRAND 306..315
FT /evidence="ECO:0007829|PDB:4DZA"
FT HELIX 318..320
FT /evidence="ECO:0007829|PDB:4DZA"
FT HELIX 324..326
FT /evidence="ECO:0007829|PDB:4DZA"
FT TURN 327..329
FT /evidence="ECO:0007829|PDB:4DZA"
FT STRAND 331..334
FT /evidence="ECO:0007829|PDB:4DZA"
FT STRAND 337..341
FT /evidence="ECO:0007829|PDB:4DZA"
FT STRAND 350..353
FT /evidence="ECO:0007829|PDB:4DZA"
FT STRAND 365..372
FT /evidence="ECO:0007829|PDB:4DZA"
FT STRAND 375..377
FT /evidence="ECO:0007829|PDB:4DZA"
FT HELIX 379..386
FT /evidence="ECO:0007829|PDB:4DZA"
FT HELIX 390..400
FT /evidence="ECO:0007829|PDB:4DZA"
FT STRAND 401..406
FT /evidence="ECO:0007829|PDB:4DZA"
SQ SEQUENCE 407 AA; 44917 MW; 4B81199404EA4501 CRC64;
MSLGIRYLAL LPLFVITACQ QPVNYNPPAT QVAQVQPAIV NNSWIEISRS ALDFNVKKVQ
SLLGKQSSLC AVLKGDAYGH DLSLVAPIMI ENNVKCIGVT NNQELKEVRD LGFKGRLMRV
RNATEQEMAQ ATNYNVEELI GDLDMAKRLD AIAKQQNKVI PIHLALNSGG MSRNGLEVDN
KSGLEKAKQI SQLANLKVVG IMSHYPEEDA NKVREDLARF KQQSQQVLEV MGLERNNVTL
HMANTFATIT VPESWLDMVR VGGIFYGDTI ASTDYKRVMT FKSNIASINY YPKGNTVGYD
RTYTLKRDSV LANIPVGYAD GYRRVFSNAG HALIAGQRVP VLGKTSMNTV IVDITSLNNI
KPGDEVVFFG KQGNSEITAE EIEDISGALF TEMSILWGAT NQRVLVD
