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Entry version 54 (23 Feb 2022)
Sequence version 1 (01 May 2013)
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Protein

Lysine racemase

Gene

lyr

Organism
Proteus mirabilis
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>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 Publications

Miscellaneous

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

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the 'Function' section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

pyridoxal 5'-phosphateUniRule annotation2 Publications

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes regulatory mechanisms for enzymes, transporters or microbial transcription factors, and reports the components which regulate (by activation or inhibition) the reaction.<p><a href='/help/activity_regulation' target='_top'>More...</a></p>Activity regulationi

The racemization activity of Lyr is completely inhibited by hydroxylamine.1 Publication

<p>This subsection of the 'Function' section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>Kineticsi

kcat is 3326 min(-1) with L-lysine as substrate. kcat is 650 min(-1) with L-arginine as substrate.1 Publication
  1. KM=21.8 mM for L-lysine1 Publication
  2. KM=15.0 mM for D-lysine1 Publication
  3. 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 keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei74Proton acceptorUniRule annotation1 Publication1
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei173SubstrateUniRule annotation1
Active sitei299Proton acceptorUniRule annotation1 Publication1
Binding sitei347Substrate; via amide nitrogenUniRule annotation1

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionIsomerase
LigandPyridoxal phosphate

Enzyme and pathway databases

BRENDA Comprehensive Enzyme Information System

More...
BRENDAi
5.1.1.5, 5044

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Lysine racemase2 Publications (EC:5.1.1.52 Publications)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:lyr1 Publication
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiProteus mirabilis
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri584 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesMorganellaceaeProteus

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Keywords - Cellular componenti

Cell membrane, Membrane, Periplasm

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology%5Fand%5Fbiotech%5Fsection">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi74K → L: Completely loss of racemase activity towards lysine. 1 Publication1
Mutagenesisi173R → A or K: Loss of racemase activity towards both L-lysine and L-arginine. 1 Publication1
Mutagenesisi174N → L: Loss of racemase activity towards both L-lysine and L-arginine. 1 Publication1
Mutagenesisi391T → Y: Reduces the racemization activity towards L-lysine by 2-fold. Does not affect racemase activity towards L-arginine. 1 Publication1
Mutagenesisi394S → 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 Publication1

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section denotes the presence of an N-terminal signal peptide.<p><a href='/help/signal' target='_top'>More...</a></p>Signal peptidei1 – 18PROSITE-ProRule annotationAdd BLAST18
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_500405328219 – 407Lysine racemaseAdd BLAST389

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/ptm%5Fprocessing%5Fsection">PTM / Processing</a> section specifies the position(s) and the type of covalently attached lipid group(s).<p><a href='/help/lipid' target='_top'>More...</a></p>Lipidationi19N-palmitoyl cysteinePROSITE-ProRule annotation1
Lipidationi19S-diacylglycerol cysteinePROSITE-ProRule annotation1
<p>This subsection of the PTM / Processing":/help/ptm_processing_section section describes the positions of cysteine residues participating in disulfide bonds.<p><a href='/help/disulfid' target='_top'>More...</a></p>Disulfide bondi70 ↔ 96UniRule annotationBy similarity
<p>This subsection of the 'PTM / Processing' section specifies the position and type of each modified residue excluding <a href="http://www.uniprot.org/manual/lipid">lipids</a>, <a href="http://www.uniprot.org/manual/carbohyd">glycans</a> and <a href="http://www.uniprot.org/manual/crosslnk">protein cross-links</a>.<p><a href='/help/mod_res' target='_top'>More...</a></p>Modified residuei74N6-(pyridoxal phosphate)lysineUniRule annotation2 Publications1

Keywords - PTMi

Disulfide bond, Lipoprotein, Palmitate

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction%5Fsection">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Forms a head-to-tail homodimer in the structure.

1 Publication

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
584.AOUC001_06285

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1407
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...
SMRi
M4GGR9

Database of comparative protein structure models

More...
ModBasei
Search...

Protein Data Bank in Europe - Knowledge Base

More...
PDBe-KBi
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the alanine racemase family. Bsr subfamily.UniRule annotationCurated

Keywords - Domaini

Signal

Family and domain databases

Conserved Domains Database

More...
CDDi
cd06826, PLPDE_III_AR2, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
2.40.37.10, 1 hit
3.20.20.10, 1 hit

HAMAP database of protein families

More...
HAMAPi
MF_02212, Bsr_racemase, 1 hit

Integrated resource of protein families, domains and functional sites

More...
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

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF00842, Ala_racemase_C, 1 hit
PF01168, Ala_racemase_N, 1 hit

Protein Motif fingerprint database; a protein domain database

More...
PRINTSi
PR00992, ALARACEMASE

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM01005, Ala_racemase_C, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF50621, SSF50621, 1 hit
SSF51419, SSF51419, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR00492, alr, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS00395, ALANINE_RACEMASE, 1 hit
PS51257, PROKAR_LIPOPROTEIN, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is in its mature form or if it represents the precursor.<p><a href='/help/sequence_processing' target='_top'>More...</a></p>Sequence processingi: The displayed sequence is further processed into a mature form.

M4GGR9-1 [UniParc]FASTAAdd to basket
« Hide
        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
Length:407
Mass (Da):44,917
Last modified:May 1, 2013 - v1
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i4B81199404EA4501
GO

Sequence databases

NCBI Reference Sequences

More...
RefSeqi
WP_004243720.1, NZ_CP043870.1

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

RefSeqiWP_004243720.1, NZ_CP043870.1

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

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RCSB PDBi

Protein Data Bank Japan

More...
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4DZAX-ray1.74A1-407[»]
SMRiM4GGR9
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

STRINGi584.AOUC001_06285

Enzyme and pathway databases

BRENDAi5.1.1.5, 5044

Family and domain databases

CDDicd06826, PLPDE_III_AR2, 1 hit
Gene3Di2.40.37.10, 1 hit
3.20.20.10, 1 hit
HAMAPiMF_02212, Bsr_racemase, 1 hit
InterProiView 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
PfamiView protein in Pfam
PF00842, Ala_racemase_C, 1 hit
PF01168, Ala_racemase_N, 1 hit
PRINTSiPR00992, ALARACEMASE
SMARTiView protein in SMART
SM01005, Ala_racemase_C, 1 hit
SUPFAMiSSF50621, SSF50621, 1 hit
SSF51419, SSF51419, 1 hit
TIGRFAMsiTIGR00492, alr, 1 hit
PROSITEiView protein in PROSITE
PS00395, ALANINE_RACEMASE, 1 hit
PS51257, PROKAR_LIPOPROTEIN, 1 hit

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiLYR_PROMI
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: M4GGR9
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated 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.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
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