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UniProtKB - M4GGR9 (LYR_PROMI)
Protein
Lysine racemase
Gene
lyr
Organism
Proteus mirabilis
Status
Functioni
Amino-acid racemase that catalyzes the interconversion of L-lysine and D-lysine. To a lesser extent, is also able to interconvert arginine enantiomers (Ref. 1, PubMed:23118975). Cannot use methionine, asparagine, alanine, leucine, glutamine, phenylalanine and histidine as substrates (Ref. 1).
2 PublicationsMiscellaneous
The active-site cleft is located at the dimeric interface and contains the two conserved catalytic residues, a lysine from one subunit and a tyrosine from the other subunit.1 Publication
Catalytic activityi
- EC:5.1.1.52 Publications
Cofactori
pyridoxal 5'-phosphateUniRule annotation2 Publications
Activity regulationi
The racemization activity of Lyr is completely inhibited by hydroxylamine.1 Publication
Kineticsi
kcat is 3326 min(-1) with L-lysine as substrate. kcat is 650 min(-1) with L-arginine as substrate.1 Publication
- KM=21.8 mM for L-lysine1 Publication
- KM=15.0 mM for D-lysine1 Publication
- KM=14.9 mM for L-arginine1 Publication
pH dependencei
Optimum pH is 8.0-9.0.1 Publication
Temperature dependencei
Optimum temperature is 50 degrees Celsius. More than 78% of maximal activity is observed at 40 degrees Celsius and 60 degrees Celsius.1 Publication
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Active sitei | 74 | Proton acceptorUniRule annotation1 Publication | 1 | |
Binding sitei | 173 | SubstrateUniRule annotation | 1 | |
Active sitei | 299 | Proton acceptorUniRule annotation1 Publication | 1 | |
Binding sitei | 347 | Substrate; via amide nitrogenUniRule annotation | 1 |
GO - Molecular functioni
- alanine racemase activity Source: InterPro
- arginine racemase activity Source: RHEA
- lysine racemase activity Source: UniProtKB-EC
- pyridoxal phosphate binding Source: UniProtKB-UniRule
Keywordsi
Molecular function | Isomerase |
Ligand | Pyridoxal phosphate |
Enzyme and pathway databases
BRENDAi | 5.1.1.5, 5044 |
Names & Taxonomyi
Protein namesi | |
Gene namesi | Name:lyr1 Publication |
Organismi | Proteus mirabilis |
Taxonomic identifieri | 584 [NCBI] |
Taxonomic lineagei | Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Morganellaceae › Proteus |
Subcellular locationi
Plasma membrane
- Cell membrane PROSITE-ProRule annotation; Lipid-anchor PROSITE-ProRule annotation; Periplasmic side Curated
Other locations
- Periplasm By similarity
Plasma Membrane
- plasma membrane Source: UniProtKB-SubCell
Other locations
- periplasmic space Source: UniProtKB-SubCell
Keywords - Cellular componenti
Cell membrane, Membrane, PeriplasmPathology & Biotechi
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 74 | K → L: Completely loss of racemase activity towards lysine. 1 Publication | 1 | |
Mutagenesisi | 173 | R → A or K: Loss of racemase activity towards both L-lysine and L-arginine. 1 Publication | 1 | |
Mutagenesisi | 174 | N → L: Loss of racemase activity towards both L-lysine and L-arginine. 1 Publication | 1 | |
Mutagenesisi | 391 | T → Y: Reduces the racemization activity towards L-lysine by 2-fold. Does not affect racemase activity towards L-arginine. 1 Publication | 1 | |
Mutagenesisi | 394 | S → C, N, T or Y: Arginine racemization activity is increased by 1.5-1.8 fold compared to the wild-type enzyme, while activity towards L-lysine is decreased. Almost no change in affinity for L-lysine and L-arginine. 1 Publication | 1 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Signal peptidei | 1 – 18 | PROSITE-ProRule annotationAdd BLAST | 18 | |
ChainiPRO_5004053282 | 19 – 407 | Lysine racemaseAdd BLAST | 389 |
Amino acid modifications
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Lipidationi | 19 | N-palmitoyl cysteinePROSITE-ProRule annotation | 1 | |
Lipidationi | 19 | S-diacylglycerol cysteinePROSITE-ProRule annotation | 1 | |
Disulfide bondi | 70 ↔ 96 | UniRule annotationBy similarity | ||
Modified residuei | 74 | N6-(pyridoxal phosphate)lysineUniRule annotation2 Publications | 1 |
Keywords - PTMi
Disulfide bond, Lipoprotein, PalmitateInteractioni
Subunit structurei
Forms a head-to-tail homodimer in the structure.
1 PublicationProtein-protein interaction databases
STRINGi | 584.AOUC001_06285 |
Structurei
Secondary structure
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details3D structure databases
SMRi | M4GGR9 |
ModBasei | Search... |
PDBe-KBi | Search... |
Family & Domainsi
Sequence similaritiesi
Keywords - Domaini
SignalFamily and domain databases
CDDi | cd06826, PLPDE_III_AR2, 1 hit |
Gene3Di | 2.40.37.10, 1 hit 3.20.20.10, 1 hit |
HAMAPi | MF_02212, Bsr_racemase, 1 hit |
InterProi | View protein in InterPro IPR000821, Ala_racemase IPR009006, Ala_racemase/Decarboxylase_C IPR011079, Ala_racemase_C IPR001608, Ala_racemase_N IPR020622, Ala_racemase_pyridoxalP-BS IPR029066, PLP-binding_barrel IPR043698, Racemase_Bsr/Lyr |
Pfami | View protein in Pfam PF00842, Ala_racemase_C, 1 hit PF01168, Ala_racemase_N, 1 hit |
PRINTSi | PR00992, ALARACEMASE |
SMARTi | View protein in SMART SM01005, Ala_racemase_C, 1 hit |
SUPFAMi | SSF50621, SSF50621, 1 hit SSF51419, SSF51419, 1 hit |
TIGRFAMsi | TIGR00492, alr, 1 hit |
PROSITEi | View protein in PROSITE PS00395, ALANINE_RACEMASE, 1 hit PS51257, PROKAR_LIPOPROTEIN, 1 hit |
i Sequence
Sequence statusi: Complete.
: The displayed sequence is further processed into a mature form. Sequence processingi
M4GGR9-1 [UniParc]FASTAAdd to basket
10 20 30 40 50
MSLGIRYLAL LPLFVITACQ QPVNYNPPAT QVAQVQPAIV NNSWIEISRS
60 70 80 90 100
ALDFNVKKVQ SLLGKQSSLC AVLKGDAYGH DLSLVAPIMI ENNVKCIGVT
110 120 130 140 150
NNQELKEVRD LGFKGRLMRV RNATEQEMAQ ATNYNVEELI GDLDMAKRLD
160 170 180 190 200
AIAKQQNKVI PIHLALNSGG MSRNGLEVDN KSGLEKAKQI SQLANLKVVG
210 220 230 240 250
IMSHYPEEDA NKVREDLARF KQQSQQVLEV MGLERNNVTL HMANTFATIT
260 270 280 290 300
VPESWLDMVR VGGIFYGDTI ASTDYKRVMT FKSNIASINY YPKGNTVGYD
310 320 330 340 350
RTYTLKRDSV LANIPVGYAD GYRRVFSNAG HALIAGQRVP VLGKTSMNTV
360 370 380 390 400
IVDITSLNNI KPGDEVVFFG KQGNSEITAE EIEDISGALF TEMSILWGAT
NQRVLVD
Sequence databases
RefSeqi | WP_004243720.1, NZ_CP043870.1 |
Similar proteinsi
Cross-referencesi
Sequence databases
RefSeqi | WP_004243720.1, NZ_CP043870.1 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
4DZA | X-ray | 1.74 | A | 1-407 | [»] | |
SMRi | M4GGR9 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
STRINGi | 584.AOUC001_06285 |
Enzyme and pathway databases
BRENDAi | 5.1.1.5, 5044 |
Family and domain databases
CDDi | cd06826, PLPDE_III_AR2, 1 hit |
Gene3Di | 2.40.37.10, 1 hit 3.20.20.10, 1 hit |
HAMAPi | MF_02212, Bsr_racemase, 1 hit |
InterProi | View protein in InterPro IPR000821, Ala_racemase IPR009006, Ala_racemase/Decarboxylase_C IPR011079, Ala_racemase_C IPR001608, Ala_racemase_N IPR020622, Ala_racemase_pyridoxalP-BS IPR029066, PLP-binding_barrel IPR043698, Racemase_Bsr/Lyr |
Pfami | View protein in Pfam PF00842, Ala_racemase_C, 1 hit PF01168, Ala_racemase_N, 1 hit |
PRINTSi | PR00992, ALARACEMASE |
SMARTi | View protein in SMART SM01005, Ala_racemase_C, 1 hit |
SUPFAMi | SSF50621, SSF50621, 1 hit SSF51419, SSF51419, 1 hit |
TIGRFAMsi | TIGR00492, alr, 1 hit |
PROSITEi | View protein in PROSITE PS00395, ALANINE_RACEMASE, 1 hit PS51257, PROKAR_LIPOPROTEIN, 1 hit |
MobiDBi | Search... |
Entry informationi
Entry namei | LYR_PROMI | |
Accessioni | M4GGR9Primary (citable) accession number: M4GGR9 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | May 8, 2019 |
Last sequence update: | May 1, 2013 | |
Last modified: | February 23, 2022 | |
This is version 54 of the entry and version 1 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Prokaryotic Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
3D-structureDocuments
- PDB cross-references
Index of Protein Data Bank (PDB) cross-references - SIMILARITY comments
Index of protein domains and families