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InterPro: IPR015421 Pyridoxal phosphate-dependent transferase, major region, subdomain 1

Protein matchesHelp
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UniProtKB
Matches:
59892 proteins
AccessionHelp
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IPR015421 PyrdxlP-dep_Trfase_major_sub1
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Domain
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InterPro RelationshipsHelp
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Found in IPR000192 Aminotransferase, class V/Cysteine desulfurase
IPR000277 Cys/Met metabolism, pyridoxal phosphate-dependent enzyme
IPR000310 Orn/Lys/Arg decarboxylase, major domain
IPR000653 DegT/DnrJ/EryC1/StrS aminotransferase
IPR000796 Aspartate/other aminotransferase
IPR001085 Serine hydroxymethyltransferase
IPR001176 1-aminocyclopropane-1-carboxylate synthase
IPR001597 Aromatic amino acid beta-eliminating lyase/threonine aldolase
IPR002129 Pyridoxal phosphate-dependent decarboxylase
IPR003248 Phosphoserine aminotransferase
IPR003437 Glycine cleavage system P-protein
IPR004631 4-aminobutyrate aminotransferase, eukaryotic
IPR004632 4-aminobutyrate aminotransferase, bacterial
IPR004636 Acetylornithine/succinylornithine aminotransferase
IPR004637 Diaminobutyrate-2-oxoglutarate transaminase
IPR004639 Tetrapyrrole biosynthesis, glutamate-1-semialdehyde aminotransferase
IPR004723 8-amino-7-oxononanoate synthase
IPR004839 Aminotransferase, class I/II
IPR005814 Aminotransferase class-III
IPR005815 Adenosylmethionine--8-amino-7-oxononanoate aminotransferase
IPR005860 L-threonine-O-3-phosphate decarboxylase
IPR005861 Histidinol-phosphate aminotransferase
IPR005957 Tyrosine aminotransferase
IPR005958 Tyrosine/nicotianamine aminotransferase
IPR006233 Cystathionine beta-lyase, bacterial
IPR006234 O-succinylhomoserine sulfhydrylase
IPR006235 O-acetylhomoserine/O-acetylserine sulfhydrylase
IPR006237 Methionine gamma-lyase
IPR006238 Cystathionine beta-lyase, eukaryotic
IPR006271 Phosphoserine aminotransferase, Methanosarcina type
IPR006272 Phosphoserine aminotransferase, Mycobacterial type
IPR006337 Pyridoxal phosphate-dependent enzyme, SelA-like
IPR006948 Allinase, C-terminal
IPR008829 Soluble liver antigen/liver pancreas antigen
IPR009651 Aluminium resistance
IPR010107 Glutamate decarboxylase
IPR010111 Kynureninase
IPR010164 Ornithine aminotransferase
IPR010240 Cysteine desulfurase
IPR010961 Tetrapyrrole biosynthesis, 5-aminolevulinic acid synthase
IPR010962 Pyridoxal phosphate-dependent acyltransferase, putative
IPR010969 Cysteine desulfurase-related, unknown function
IPR010970 Cysteine desulfurase, SufS
IPR010977 Aromatic-L-amino-acid decarboxylase
IPR011166 Tryptophanase
IPR011193 Ornithine/lysine/arginine decarboxylase
IPR011282 2-amino-3-ketobutyrate coenzyme A ligase
IPR011340 Cysteine desulfurase-related
IPR011821 O-succinylhomoserine (thiol)-lyase
IPR012703 2-aminoethylphosphonate--pyruvate transaminase
IPR012749 TDP-4-keto-6-deoxy-D-glucose transaminase
IPR012773 Diaminobutyrate--2-oxoglutarate aminotransferase
IPR013375 O-phosphoseryl-tRNA:Cys-tRNA synthase, archaea
IPR013440 Tryptophanase, proteobacteria
IPR013441 Tyrosine phenol-lyase
IPR015424 Pyridoxal phosphate-dependent transferase, major domain
IPR016454 Cysteine desulfurase, NifS
IPR017644 Cysteine desulfurase, DndA
IPR017652 Succinylornithine transaminase family
IPR017657 L-lysine 6-transaminase
IPR017688 2-aminoethylphosphonate aminotransferase
IPR017747 Putrescine aminotransferase
IPR017772 Cysteine desulfurase, NifS, bacterial/archaeal
IPR017773 Cysteine desulfurase, NifS, proteobacteria
IPR019878 Succinyldiaminopimelate transaminase, beta/gammaproteobacteria
IPR019880 Succinyldiaminopimelate transaminase, actinobacteria
IPR019881 LL-diaminopimelate aminotransferase
IPR019942 LL-diaminopimelate aminotransferase, plant-related
IPR020026 Pseudaminic acid biosynthesis, PseC
IPR020033 Pyridoxal phosphate-dependent transferase, archaea
IPR020580 Glycine cleavage system P-protein, N-terminal
IPR020581 Glycine cleavage system P-protein-like
Contains IPR001917 Aminotransferase, class-II, pyridoxal-phosphate binding site
IPR004838 Aminotransferases, class-I, pyridoxal-phosphate-binding site
IPR018176 Tryptophanase, conserved site
IPR019798 Serine hydroxymethyltransferase, pyridoxal phosphate binding site
IPR020578 Aminotransferase class-V pyridoxal-phosphate binding site
GO Term annotationHelp
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Function GO:0003824 catalytic activity
GO:0030170 pyridoxal phosphate binding
InterPro annotation
BioMart Logo Entry Details in BioMart
AbstractHelp
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Pyridoxal phosphate is the active form of vitamin B6 (pyridoxine or pyridoxal). PLP is a versatile catalyst, acting as a coenzyme in a multitude of reactions, including decarboxylation, deamination and transamination [1, 2, 3]. PLP-dependent enzymes are primarily involved in the biosynthesis of amino acids and amino acid-derived metabolites, but they are also found in the biosynthetic pathways of amino sugars and in the synthesis or catabolism of neurotransmitters; pyridoxal phosphate can also inhibit DNA polymerases and several steroid receptors [4]. Inadequate levels of pyridoxal phosphate in the brain can cause neurological dysfunction, particularly epilepsy [5].

PLP enzymes exist in their resting state as a Schiff base, the aldehyde group of PLP forming a linkage with the epsilon-amino group of an active site lysine residue on the enzyme. The alpha-amino group of the substrate displaces the lysine epsilon-amino group, in the process forming a new aldimine with the substrate. This aldimine is the common central intermediate for all PLP-catalysed reactions, enzymatic and non-enzymatic [6].

This entry represents subdomain 1 of the major region of PLP-dependent transferases. This domain has a 3-layer alpha/beta/alpha sandwich topology. The major region can be found in the following PLP-dependent transferase families:

  • Aspartate aminotransferase (AAT)-like enzymes, such as aromatic aminoacid aminotransferase AroAT, glutamine aminotransferase and kynureninase [7].
  • Beta-eliminating lyases, such as tyrosine phenol lyase and tryptophanase [8].
  • Pyridoxal-dependent decarboxylases, such as DOPA decarboxylase and glutamate decarboxylase beta (GadB) [9].
  • Cystathionine synthase-like enzymes, such as cystalysin, methionine gamma-lyase (MGL), and cysteine desulphurase (IscS) [10].
  • GABA-aminotransferase-like enzymes, such as ornithine aminotransferase and serine hydroxymethyltransferase [11].
  • Ornithine decarboxylase major domain [12].
Structural linksHelp
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PDB - click here
1aam , 1aat , 1aaw , 1ahe , 1ahf , 1ahg , 1ahx , 1ahy , 1aia , 1aib , 1aic , 1ajr , 1ajs , 1aka , 1akb , 1akc , 1ama , 1amq , 1amr , 1ams , 1arg , 1arh , 1ari , 1ars , 1art , 1asa , 1asb , 1asc , 1asd , 1ase , 1asf , 1asg , 1asl , 1asm , 1asn , 1ax4 , 1ay4 , 1ay5 , 1ay8 , 1b4x , 1b5o , 1b5p , 1b8g , 1b9h , 1b9i , 1bj4 , 1bjn , 1bjo , 1bjw , 1bkg , 1bqa , 1bqd , 1bs0 , 1bt4 , 1bw0 , 1c0n , 1c4k , 1c7g , 1c7n , 1c7o , 1c9c , 1cj0 , 1cl1 , 1cl2 , 1cq6 , 1cq7 , 1cq8 , 1cs1 , 1czc , 1cze , 1d2f , 1d7r , 1d7s , 1d7u , 1d7v , 1dfo , 1dgd , 1dge , 1dj9 , 1dje , 1dju , 1dka , 1dty , 1e5e , 1e5f , 1ecx , 1eg5 , 1eji , 1elq , 1elu , 1eqb , 1fc4 , 1fg3 , 1fg7 , 1g4v , 1g4x , 1g7w , 1g7x , 1gbn , 1gc0 , 1gc2 , 1gc3 , 1gc4 , 1gck , 1gd9 , 1gde , 1gew , 1gex , 1gey , 1h1c , 1i29 , 1i41 , 1i43 , 1i48 , 1iax , 1iay , 1ibj , 1iji , 1iug , 1ivr , 1ix6 , 1ix7 , 1ix8 , 1j32 , 1jf9 , 1jg8 , 1js3 , 1js6 , 1kkj , 1kkp , 1kl1 , 1kl2 , 1kmj , 1kmk , 1lc5 , 1lc7 , 1lc8 , 1lk9 , 1lkc , 1ls3 , 1lw4 , 1lw5 , 1m0n , 1m0o , 1m0p , 1m0q , 1m32 , 1m4n , 1m6s , 1m7y , 1map , 1maq , 1mdo , 1mdx , 1mdz , 1mgv , 1mly , 1mlz , 1n2t , 1n31 , 1n8p , 1o4s , 1o61 , 1o62 , 1o69 , 1oat , 1ohv , 1ohw , 1ohy , 1ord , 1oxo , 1oxp , 1p3w , 1pff , 1pg8 , 1pmm , 1pmo , 1qgn , 1qir , 1qis , 1qit , 1qj3 , 1qj5 , 1rv3 , 1rv4 , 1rvu , 1rvy , 1s06 , 1s07 , 1s08 , 1s09 , 1s0a , 1sf2 , 1sff , 1spa , 1svv , 1szk , 1szs , 1szu , 1t3i , 1tar , 1tas , 1tat , 1toe , 1tog , 1toi , 1toj , 1tok , 1tpl , 1u08 , 1ukj , 1uu0 , 1uu1 , 1uu2 , 1v2d , 1v2e , 1v2f , 1v72 , 1vef , 1vjo , 1vp4 , 1w23 , 1w3u , 1w7l , 1w7m , 1w7n , 1wkg , 1wkh , 1wst , 1wyt , 1wyu , 1wyv , 1x0m , 1x28 , 1x29 , 1x2a , 1xey , 1xi9 , 1y4i , 1yaa , 1yiy , 1yiz , 1yjs , 1yjy , 1yjz , 1ynu , 1yoo , 1z3z , 1z7d , 1zc9 , 1zob , 1zod , 2a7v , 2aat , 2ay1 , 2ay2 , 2ay3 , 2ay4 , 2ay5 , 2ay6 , 2ay7 , 2ay8 , 2ay9 , 2bhx , 2bi1 , 2bi2 , 2bi3 , 2bi5 , 2bi9 , 2bia , 2bie , 2big , 2bkw , 2bwn , 2bwo , 2bwp , 2byj , 2byl , 2c0r , 2c44 , 2can , 2cfb , 2ch1 , 2ch2 , 2cst , 2ctz , 2cy8 , 2d5y , 2d61 , 2d63 , 2d64 , 2d65 , 2d66 , 2d7y , 2d7z , 2dgl , 2dgm , 2dkb , 2dkj , 2e54 , 2e7i , 2e7j , 2eh6 , 2ez1 , 2ez2 , 2f8j , 2fm1 , 2fn6 , 2fni , 2fnu , 2fq6 , 2g6w , 2gb3 , 2gqn , 2gsa , 2hor , 2hox , 2hoy , 2huf , 2hui , 2huu , 2nmp , 2o7c , 2oat , 2oga , 2oge , 2oqx , 2ord , 2pb0 , 2pb2 , 2q7w , 2qa3 , 2qb2 , 2qb3 , 2qbt , 2r5c , 2r5e , 2tpl , 2v0y , 2v1p , 2vgs , 2vgt , 2vgu , 2vgv , 2vgw , 2vi8 , 2vi9 , 2via , 2vib , 2yri , 2yrr , 2z67 , 3aat , 3bv0 , 3gsb , 3tat , 4gsa , 5bj3 , 5bj4 , 5eaa , 7aat , 8aat , 9aat

Taxonomic coverageHelp
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Overlapping InterPro entriesHelp
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IPR015421 Numbers of overlapping proteins Average numbers of overlapping amino acids

Example proteinsHelp
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P04181 Ornithine aminotransferase, mitochondrial

P05031 Aromatic-L-amino-acid decarboxylase

P08680 5-aminolevulinate synthase, erythroid-specific, mitochondrial

P23542 Aspartate aminotransferase, cytoplasmic

P34751 Probable aromatic-L-amino-acid decarboxylase

More proteins


Example Proteins Key


InterPro entry accession number/name and structure databases Colour code
IPR010164 Ornithine aminotransferase
IPR002129 Pyridoxal phosphate-dependent decarboxylase
IPR004838 Aminotransferases, class-I, pyridoxal-phosphate-binding site
IPR005814 Aminotransferase class-III
IPR004839 Aminotransferase, class I/II
IPR015424 Pyridoxal phosphate-dependent transferase, major domain
IPR010977 Aromatic-L-amino-acid decarboxylase
IPR010961 Tetrapyrrole biosynthesis, 5-aminolevulinic acid synthase
IPR015422 Pyridoxal phosphate-dependent transferase, major region, subdomain 2
IPR015421 Pyridoxal phosphate-dependent transferase, major region, subdomain 1
IPR001917 Aminotransferase, class-II, pyridoxal-phosphate binding site
IPR000796 Aspartate/other aminotransferase
IPR015118 5-aminolevulinate synthase presequence
PDB Chain
ModBase
CATH Domain
SWISS-MODEL
SCOP Domain

PublicationsHelp
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1. Hayashi H.
Pyridoxal enzymes: mechanistic diversity and uniformity.
J. Biochem. 118 463-73 1995 [PubMed: 8690703]
http://jb.oxfordjournals.org/cgi/content/abstract/118/3/463
2. John RA.
Pyridoxal phosphate-dependent enzymes.
Biochim. Biophys. Acta 1248 81-96 1995 [PubMed: 7748903]
http://dx.doi.org/10.1016/0167-4838(95)00025-P
3. Eliot AC, Kirsch JF.
Pyridoxal phosphate enzymes: mechanistic, structural, and evolutionary considerations.
Annu. Rev. Biochem. 73 383-415 2004 [PubMed: 15189147]
http://dx.doi.org/10.1146/annurev.biochem.73.011303.074021
4. Mozzarelli A, Bettati S.
Exploring the pyridoxal 5'-phosphate-dependent enzymes.
6 275-87 2006 [PubMed: 17109392]
5. Clayton PT.
B6-responsive disorders: a model of vitamin dependency.
J. Inherit. Metab. Dis. 29 317-26 2006 [PubMed: 16763894]
http://dx.doi.org/10.1007/s10545-005-0243-2
6. Toney MD.
Reaction specificity in pyridoxal phosphate enzymes.
Arch. Biochem. Biophys. 433 279-87 2005 [PubMed: 15581583]
http://dx.doi.org/10.1016/j.abb.2004.09.037
7. Lima S, Khristoforov R, Momany C, Phillips RS.
Crystal structure of Homo sapiens kynureninase.
Biochemistry 46 2735-44 2007 [PubMed: 17300176]
http://dx.doi.org/10.1021/bi0616697
8. Ku SY, Yip P, Howell PL.
Structure of Escherichia coli tryptophanase.
Acta Crystallogr. D Biol. Crystallogr. 62 814-23 2006 [PubMed: 16790938]
http://dx.doi.org/10.1107/S0907444906019895
9. Capitani G, De Biase D, Gut H, Ahmed S, Grutter MG.
Structural model of human GAD65: prediction and interpretation of biochemical and immunogenic features.
Proteins 59 7-14 2005 [PubMed: 15690345]
http://dx.doi.org/10.1002/prot.20372
10. Cellini B, Montioli R, Bossi A, Bertoldi M, Laurents DV, Voltattorni CB.
Holo- and apo-cystalysin from Treponema denticola: two different conformations.
Arch. Biochem. Biophys. 455 31-9 2006 [PubMed: 17014820]
http://dx.doi.org/10.1016/j.abb.2006.08.020
11. Franca TC, Pascutti PG, Ramalho TC, Figueroa-Villar JD.
A three-dimensional structure of Plasmodium falciparum serine hydroxymethyltransferase in complex with glycine and 5-formyl-tetrahydrofolate. Homology modeling and molecular dynamics.
Biophys. Chem. 115 1-10 2005 [PubMed: 15848278]
http://dx.doi.org/10.1016/j.bpc.2004.12.002
12. Vitali J, Carroll D, Chaudhry RG, Hackert ML.
Three-dimensional structure of the Gly121Tyr dimeric form of ornithine decarboxylase from Lactobacillus 30a.
Acta Crystallogr. D Biol. Crystallogr. 55 1978-85 1999 [PubMed: 10666573]
http://dx.doi.org/10.1107/S0907444999010756

Additional ReadingHelp
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Rajaram V, Ratna Prasuna P, Savithri HS, Murthy MR.
Structure of biosynthetic N-acetylornithine aminotransferase from Salmonella typhimurium: studies on substrate specificity and inhibitor binding.
Proteins 70 2008 429-41 [PubMed: 17680699]
http://dx.doi.org/10.1002/prot.21567
Sun Q, Collins R, Huang S, Holmberg-Schiavone L, Anand GS, Tan CH, van-den-Berg S, Deng LW, Moore PK, Karlberg T, Sivaraman J.
Structural basis for the inhibition mechanism of human cystathionine gamma-lyase, an enzyme responsible for the production of H(2)S.
J. Biol. Chem. 284 2009 3076-85 [PubMed: 19019829]
http://dx.doi.org/10.1074/jbc.M805459200
Vedadi M, Lew J, Artz J, Amani M, Zhao Y, Dong A, Wasney GA, Gao M, Hills T, Brokx S, Qiu W, Sharma S, Diassiti A, Alam Z, Melone M, Mulichak A, Wernimont A, Bray J, Loppnau P, Plotnikova O, Newberry K, Sundararajan E, Houston S, Walker J, Tempel W, Bochkarev A, Kozieradzki I, Edwards A, Arrowsmith C, Roos D, Kain K, Hui R.
Genome-scale protein expression and structural biology of Plasmodium falciparum and related Apicomplexan organisms.
Mol. Biochem. Parasitol. 151 2007 100-10 [PubMed: 17125854]
http://dx.doi.org/10.1016/j.molbiopara.2006.10.011
Han Q, Gao YG, Robinson H, Li J.
Structural insight into the mechanism of substrate specificity of aedes kynurenine aminotransferase.
Biochemistry 47 2008 1622-30 [PubMed: 18186649]
http://dx.doi.org/10.1021/bi701800j
Araiso Y, Palioura S, Ishitani R, Sherrer RL, O'Donoghue P, Yuan J, Oshikane H, Domae N, Defranco J, Soll D, Nureki O.
Structural insights into RNA-dependent eukaryal and archaeal selenocysteine formation.
Nucleic Acids Res. 36 2008 1187-99 [PubMed: 18158303]
http://dx.doi.org/10.1093/nar/gkm1122
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