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Metabolic Modeling Tutorial
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MetaCyc Enzyme: alanine racemase 1, PLP-binding, biosynthetic

Gene: alr Accession Numbers: EG10001 (MetaCyc), b4053, ECK4045

Synonyms: alr5

Species: Escherichia coli K-12 substr. MG1655

Summary:
Alanine racemase 1 (Alr) catalyzes the interconversion of D- and L-alanine.

E. coli has two alanine racemases, the constitutive Alr and the metabolically regulated DadX. Alr is the minor racemase, being much less abundant than derepressed DadX [Wild85, Lilley93].

Locations: cytosol

Map Position: [4,263,805 -> 4,264,884]

Molecular Weight of Polypeptide: 39.153 kD (from nucleotide sequence), 40.0 kD (experimental) [Lilley93 ]

Unification Links: ASAP:ABE-0013272 , CGSC:1034 , EchoBASE:EB0001 , EcoGene:EG10001 , EcoliWiki:b4053 , ModBase:P0A6B4 , OU-Microarray:b4053 , PortEco:alr , PR:PRO_000022086 , Pride:P0A6B4 , Protein Model Portal:P0A6B4 , RefSeq:NP_418477 , RegulonDB:EG10001 , SMR:P0A6B4 , String:511145.b4053 , UniProt:P0A6B4

Relationship Links: InterPro:IN-FAMILY:IPR000821 , InterPro:IN-FAMILY:IPR001608 , InterPro:IN-FAMILY:IPR009006 , InterPro:IN-FAMILY:IPR011079 , InterPro:IN-FAMILY:IPR020622 , PDB:Structure:2RJG , PDB:Structure:2RJH , PDB:Structure:3B8T , PDB:Structure:3B8U , PDB:Structure:3B8V , PDB:Structure:3B8W , Pfam:IN-FAMILY:PF00842 , Pfam:IN-FAMILY:PF01168 , Prints:IN-FAMILY:PR00992 , Prosite:IN-FAMILY:PS00395 , Smart:IN-FAMILY:SM01005

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006522 - alanine metabolic process Inferred by computational analysis [GOA06, GOA01a]
GO:0008360 - regulation of cell shape Inferred by computational analysis [UniProtGOA11a]
GO:0009252 - peptidoglycan biosynthetic process Inferred by computational analysis [UniProtGOA12, UniProtGOA11a]
GO:0030632 - D-alanine biosynthetic process Inferred by computational analysis [UniProtGOA12]
GO:0071555 - cell wall organization Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0008784 - alanine racemase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Noda05]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0016853 - isomerase activity Inferred by computational analysis [UniProtGOA11a]
GO:0030170 - pyridoxal phosphate binding Inferred by computational analysis [GOA06]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism biosynthesis of building blocks amino acids alanine

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International


Enzymatic reaction of: alanine racemase

EC Number: 5.1.1.1

L-alanine <=> D-alanine

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

This reaction is reversible. [Noda05]

In Pathways: superpathway of alanine biosynthesis , alanine biosynthesis I

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International

Summary:
The Kcat for the D- to L-alanine conversion is 1,700, and the Kcat for the L- to D-alanine conversion is 1,660 [Noda05].

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
L-alanine
17400.0
[Ju11, BRENDA14]
L-alanine
290.0
27.6
[Noda05, BRENDA14]
L-alanine
1049.0, 1401.0, 1516.0, 1562.0, 1993.0, 2057.0, 3030.0, 3603.0
2.8, 16.72, 22.47, 41.82, 51.77, 53.98, 67.07, 68.23, 70.92
[Wu08, BRENDA14]
D-alanine
6900.0
[Ju11, BRENDA14]
D-alanine
250.0
2.0
[Noda05, BRENDA14]
D-alanine
304.0, 311.0, 402.0, 439.0, 513.0, 528.0, 592.0, 604.0, 615.0, 1008.0
0.33, 1.32, 4.0, 4.47, 5.27, 5.78, 6.35, 6.82, 7.62
[Wu08, BRENDA14]


Sequence Features

Feature Class Location Citations Comment
Active-Site 34
[UniProt13]
UniProt: Proton acceptor; specific for D-alanine.
N6-pyridoxal-phosphate-Lys-Modification 34
[UniProt11a]
UniProt: N6-(pyridoxal phosphate)lysine; Non-Experimental Qualifier: by similarity.
N6-carboxylysine-Modification 122
[UniProt13]
UniProt: N6-carboxylysine.
Amino-Acid-Sites-That-Bind 129
[UniProt13]
UniProt: Substrate.
Mutagenesis-Variant 164
[Wu08, UniProt13]
Alternate sequence: K; UniProt: Reduces catalytic activity. Slightly reduces affinity for D-Ala and L-Ala.
Alternate sequence: A; UniProt: Slightly reduces affinity for D-Ala and L-Ala.
Mutagenesis-Variant 165
[Wu08, UniProt13]
Alternate sequence: K; UniProt: Reduces catalytic activity. Slightly reduces affinity for D-Ala and L-Ala.
Alternate sequence: A; UniProt: Slightly reduces affinity for D-Ala and L-Ala.
Mutagenesis-Variant 219
[Wu08, UniProt13]
Alternate sequence: A; UniProt: No effect on catalytic activity. No effect on affinity for D-Ala and L-Ala.
Mutagenesis-Variant 221
[Wu08, UniProt13]
Alternate sequence: P; UniProt: Slightly increases catalytic activity. Slightly increases affinity for D-Ala and L-Ala.
Alternate sequence: K; UniProt: Slightly increases catalytic activity. Slightly increases affinity for D-Ala and L-Ala.
Alternate sequence: A; UniProt: Slightly increases catalytic activity. Slightly increases affinity for D-Ala and L-Ala.
Active-Site 255
[UniProt10]
UniProt: Proton acceptor; specific for L-alanine; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 303
[UniProt13]
UniProt: Substrate; via amide nitrogen.

History:
10/20/97 Gene b4053 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10001; confirmed by SwissProt match.


References

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Ju11: Ju J, Xu S, Furukawa Y, Zhang Y, Misono H, Minamino T, Namba K, Zhao B, Ohnishi K (2011). "Correlation between catalytic activity and monomer-dimer equilibrium of bacterial alanine racemases." J Biochem 149(1);83-9. PMID: 20971724

Lilley93: Lilley PE, Stamford NP, Vasudevan SG, Dixon NE (1993). "The 92-min region of the Escherichia coli chromosome: location and cloning of the ubiA and alr genes." Gene 129(1);9-16. PMID: 8335265

Noda05: Noda M, Matoba Y, Kumagai T, Sugiyama M (2005). "A novel assay method for an amino acid racemase reaction based on circular dichroism." Biochem J 389(Pt 2);491-6. PMID: 15796715

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-11 released on 2011-11-22 00:00:00." Database.

UniProt13: UniProt Consortium (2013). "UniProt version 2013-08 released on 2013-08-01 00:00:00." Database.

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."

Wild85: Wild J, Hennig J, Lobocka M, Walczak W, Klopotowski T (1985). "Identification of the dadX gene coding for the predominant isozyme of alanine racemase in Escherichia coli K12." Mol Gen Genet 1985;198(2);315-22. PMID: 3920477

Wu08: Wu D, Hu T, Zhang L, Chen J, Du J, Ding J, Jiang H, Shen X (2008). "Residues Asp164 and Glu165 at the substrate entryway function potently in substrate orientation of alanine racemase from E. coli: Enzymatic characterization with crystal structure analysis." Protein Sci 17(6);1066-76. PMID: 18434499


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Fri Nov 21, 2014, BIOCYC14A.