Letunic et al. (2017) Nucleic Acids Res doi: 10.1093/nar/gkx922
Letunic et al. (2020) Nucleic Acids Res doi: 10.1093/nar/gkaa937

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Ala_racemase_C Alanine racemase, C-terminal domain

SMART accession number:	SM01005
Description:	Alanine racemase plays a role in providing the D-alanine required for cell wall biosynthesis by isomerising L-alanine to D-alanine. Proteins contains this domain are found in both prokaryotic and eukaryotic proteins (PUBMED:1676385),(PUBMED:7871888).
Interpro abstract (IPR011079):	Alanine racemase ( EC 5.1.1.1 ) plays a role in providing the D-alanine required for cell wall biosynthesis by isomerising L-alanine to D-alanine. The molecular structure of alanine racemase from Bacillus stearothermophilus (Geobacillus stearothermophilus) was determined by X-ray crystallography to a resolution of 1.9 A [ (PUBMED:9063881) ]. The alanine racemase monomer is composed of two domains, an eight-stranded alpha/beta barrel at the N terminus, and a C-terminal domain essentially composed of beta-strand. This entry represents the C-terminal domain.
Family alignment:	View or CHROMA formatHMM/Web logoCLUSTALW formatMSF formatFASTA formatPIR format

There are 25213 Ala_racemase_C domains in 25212 proteins in SMART's nrdb database.

Click on the following links for more information.

• Evolution (species in which this domain is found)

• Taxonomic distribution of proteins containing Ala_racemase_C domain.

  This tree includes only several representative species. The complete taxonomic breakdown of all proteins with Ala_racemase_C domain is also avaliable.

  Click on the protein counts, or double click on taxonomic names to display all proteins containing Ala_racemase_C domain in the selected taxonomic class.

• Cellular role (predicted cellular role)

• Cellular role: metabolism
  

• Literature (relevant references for this domain)

• Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.

  • Shaw JP, Petsko GA, Ringe D
  • Determination of the structure of alanine racemase from Bacillusstearothermophilus at 1.9-A resolution.
  • Biochemistry. 1997; 36: 1329-42
  • Display abstract

  • The molecular structure of alanine racemase from Bacillusstearothermophilus was determined by X-ray crystallography to a resolutionof 1.9 A. The alanine racemase monomer is composed of two domains, aneight-stranded alpha/beta barrel at the N-terminus, which includesresidues 1-240, and a C-terminal domain essentially composed ofbeta-strand (residues 241-388). In the structure of the dimer the mouth ofthe alpha/beta barrel of one monomer faces the second domain of the othermonomer. The pyridoxal 5'-phosphate (PLP) cofactor lies in and above themouth of the alpha/beta barrel and is covalently linked via an aldiminelinkage to Lys39, which is at the C-terminus of the first beta-strand ofthe alpha/beta barrel. This is the first example of a PLP cofactor bindingin the active site of a alpha/beta barrel. A number of other residues areinvolved in maintaining the position of the PLP in the protein. Of these,Arg219 is the most interesting, as it forms a hydrogen bond with thepyridine nitrogen of the cofactor. This is the first known occurrence ofsuch an interaction with PLP and is expected to influence the electrondelocalization in the PLP-alanine intermediates. A second arginineresidue, Arg136, donates a hydrogen bond to the phenolic oxygen of PLP andmay be involved in the binding of substrate as well as stabilization ofintermediates. Finally, Tyr265', from the second monomer, is postulated tobe 2 proton donor to the carbanion intermediate.

  • De Wergifosse P, Jacques B, Jonniaux JL, Purnelle B, Skala J, Goffeau A
  • The sequence of a 22.4 kb DNA fragment from the left arm of yeastchromosome II reveals homologues to bacterial proline synthetase andmurine alpha-adaptin, as well as a new permease and a DNA-binding protein.
  • Yeast. 1994; 10: 1489-96
  • Display abstract

  • We report the sequencing of a 22,470 bp DNA fragment from the left arm ofSaccharomyces cerevisiae chromosome II. Thirteen open reading frameslonger than 300 bp provisionally called YBL0520, YBL0401 to YBL0408 andYBL0410 to YBL0413 have been detected. Five genes were previouslysequenced: COR1, encoding a core protein of the mitochondrial coenzyme QH2cytochrome c reductase complex (Tzagaloff and Crivellone, 1986), PRS3, aproteasome subunit gene (Lee et al., 1992), ERD2, coding for a proteininvolved in the secretory pathway (Semeza et al., 1990), URA7, whichencodes a CTP synthetase (Ozier-Kalogeropoulos et al., 1991) and the genefor the ribosomal protein L16 (Pan et al., 1993). Among the others,YBL0406 shows striking homologies to FUR4 (Jund et al., 1988) and DAL4(Yoo et al., 1992), the uracyl and allantoin permeases; YBL0520 is aDNA-related protein, possibly involved in gene regulation; YBL0412 shareshomologies with the mouse alpha-adaptins A and C; and YBL0413 ishomologous to a protein of Pseudomonas aeruginosa that is likely to beinvolved in proline biosynthesis. YBL0401, internal to YBL0520, isprobably not expressed.

  • Whitchurch CB, Hobbs M, Livingston SP, Krishnapillai V, Mattick JS
  • Characterisation of a Pseudomonas aeruginosa twitching motility gene andevidence for a specialised protein export system widespread in eubacteria.
  • Gene. 1991; 101: 33-44
  • Display abstract

  • Type-4 fimbriae (pili) are associated with a phenomenon known as twitchingmotility, which appears to be involved with bacterial translocation acrosssolid surfaces. Pseudomonas aeruginosa mutants which produce fimbriae, butwhich have lost the twitching motility function, display altered colonymorphology and resistance to fimbrial-specific bacteriophage. We have usedphenotypic complementation of such mutants to isolate a region of DNAinvolved in twitching motility. This region was physically mapped to aSpeI fragment around 20 min on the P. aeruginosa PAO chromosome, remotefrom the major fimbrial locus (around 75 min) where the structuralsubunit-encoding gene (fimA/pilA) and ancillary genes required forfimbrial assembly (pilB, C and D) are found. A gene, pilT, within thetwitching motility region is predicted to encode a 344-amino acid proteinwhich has strong homology to a variety of other bacterial proteins. Theseinclude the P. aeruginosa PilB protein, the ComG ORF-1 protein from theBacillus subtilis comG operon (necessary for competence), the PulE proteinfrom the Klebsiella oxytoca (formerly K. pneumoniae) pulC-O operon(involved in pullulanase export), and the VirB-11 protein from the virBoperon (involved in virulence) which is located on the Agrobacteriumtumefaciens Ti plasmid. We have also identified other sets of homologiesbetween P. aeruginosa fimbrial assembly (Pil) proteins and B. subtilis Comand K. oxytoca Pul proteins, which suggest that these are all relatedmembers of a specialised protein export pathway which is widespread in theeubacteria.

• Structure (3D structures containing this domain)

• 3D Structures of Ala_racemase_C domains in PDB

  PDB code	Main view	Title
  1bd0		ALANINE RACEMASE COMPLEXED WITH ALANINE PHOSPHONATE
  1epv		ALANINE RACEMASE WITH BOUND INHIBITOR DERIVED FROM D-CYCLOSERINE
  1ftx		Crystal stucture of alanine racemase in complex with D-alanine phosphonate
  1l6f		Alanine racemase bound with N-(5'-phosphopyridoxyl)-L-alanine
  1l6g		Alanine racemase bound with N-(5'-phosphopyridoxyl)-D-alanine
  1niu		ALANINE RACEMASE WITH BOUND INHIBITOR DERIVED FROM L-CYCLOSERINE
  1rcq		The 1.45 A crystal structure of alanine racemase from a pathogenic bacterium, Pseudomonas aeruginosa, contains both internal and external aldimine forms
  1sft		ALANINE RACEMASE
  1vfh		Crystal structure of alanine racemase from D-cycloserine producing Streptomyces lavendulae
  1vfs		Crystal structure of D-cycloserine-bound form of alanine racemase from D-cycloserine-producing Streptomyces lavendulae
  1vft		Crystal structure of L-cycloserine-bound form of alanine racemase from D-cycloserine-producing Streptomyces lavendulae
  1xfc		The 1.9 A crystal structure of alanine racemase from Mycobacterium tuberculosis contains a conserved entryway into the active site
  1xqk		Effect of a Y265F Mutant on the Transamination Based Cycloserine Inactivation of Alanine Racemase
  1xql		Effect of a Y265F Mutant on the Transamination Based Cycloserine Inactivation of Alanine Racemase
  2dy3		Crystal Structure of alanine racemase from Corynebacterium glutamicum
  2odo		Crystal structure of Pseudomonas Fluorescens alanine racemase
  2rjg		Crystal structure of biosynthetic alaine racemase from Escherichia coli
  2rjh		Crystal structure of biosynthetic alaine racemase in D-cycloserine-bound form from Escherichia coli
  2sfp		ALANINE RACEMASE WITH BOUND PROPIONATE INHIBITOR
  2vd8		The crystal structure of alanine racemase from Bacillus anthracis ( BA0252)
  2vd9		The crystal structure of alanine racemase from Bacillus anthracis ( BA0252) with bound L-Ala-P
  3b8t		Crystal structure of Escherichia coli alaine racemase mutant P219A
  3b8u		Crystal structure of Escherichia coli alaine racemase mutant E221A
  3b8v		Crystal structure of Escherichia coli alaine racemase mutant E221K
  3b8w		Crystal structure of Escherichia coli alaine racemase mutant E221P
  3co8		Crystal structure of alanine racemase from Oenococcus oeni
  3e5p		Crystal structure of alanine racemase from E.faecalis
  3e6e		Crystal structure of Alanine racemase from E.faecalis complex with cycloserine
  3ha1		Alanine racemase from Bacillus Anthracis (Ames)
  3hur		Crystal structure of alanine racemase from Oenococcus oeni
  3kw3		Crystal structure of alanine racemase from Bartonella henselae with covalently bound pyridoxal phosphate
  3oo2		2.37 Angstrom resolution crystal structure of an alanine racemase (alr) from Staphylococcus aureus subsp. aureus COL
  3s46		The crystal structure of alanine racemase from streptococcus pneumoniae
  3uw6		Crystal Structure of Engineered Protein, Northeast Structural Genomics Consortium Target OR120
  4a3q		The 2.15 Angstrom resolution crystal structure of Staphylococcus aureus alanine racemase
  4beq		Structure of Vibrio cholerae broad spectrum racemase double mutant R173A, N174A
  4beu		Structure of Vibrio cholerae broad spectrum racemase
  4bf5		Structure of broad spectrum racemase from Aeromonas hydrophila
  4bhy		Structure of alanine racemase from Aeromonas hydrophila
  4dyj		Crystal structure of a broad specificity amino acid racemase (Bar) within internal aldimine linkage
  4dza		Crystal structure of a lysine racemase within internal aldimine linkage
  4ecl		Crystal structure of the cytoplasmic domain of vancomycin resistance serine racemase VanTg
  4fs9		Complex structure of a broad specificity amino acid racemase (Bar) within the reactive intermediate
  4ils		Crystal structure of engineered protein. northeast structural genomics Consortium target or117
  4lus		4LUS
  4lut		4LUT
  4luy		4LUY
  4qhr		4QHR
  4wr3		4WR3
  4xbj		4XBJ
  4y2w		4Y2W

• Links (links to other resources describing this domain)

• INTERPRO	IPR011079
  PFAM	Ala_racemase_C

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