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PDBsum entry 1b8f
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Lyase PDB id
1b8f

 

 

 

 

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Contents
Protein chain
507 a.a. *
Ligands
SO4
GOL
Waters ×210
* Residue conservation analysis
PDB id:
1b8f
Name: Lyase
Title: Histidine ammonia-lyase (hal) from pseudomonas putida
Structure: Histidine ammonia-lyase. Chain: a. Synonym: hal, histidase. Engineered: yes. Mutation: yes
Source: Pseudomonas putida. Organism_taxid: 303. Atcc: 12633. Cellular_location: cytoplasm. Gene: huth. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Biol. unit: Tetramer (from PDB file)
Resolution:
2.10Å     R-factor:   0.197     R-free:   0.263
Authors: T.F.Schwede,G.E.Schulz
Key ref:
T.F.Schwede et al. (1999). Crystal structure of histidine ammonia-lyase revealing a novel polypeptide modification as the catalytic electrophile. Biochemistry, 38, 5355-5361. PubMed id: 10220322 DOI: 10.1021/bi982929q
Date:
31-Jan-99     Release date:   06-May-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P21310  (HUTH_PSEPU) -  Histidine ammonia-lyase from Pseudomonas putida
Seq:
Struc: 		510 a.a.
507 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.4.3.1.3  - histidine ammonia-lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway: 		Histidine Catabolism
      Reaction: L-histidine = trans-urocanate + NH4+
L-histidine
 = trans-urocanate
 + NH4(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Key reference    
 
 
DOI no: 10.1021/bi982929q Biochemistry 38:5355-5361 (1999)
PubMed id: 10220322  
 
 
Crystal structure of histidine ammonia-lyase revealing a novel polypeptide modification as the catalytic electrophile.
T.F.Schwede, J.Rétey, G.E.Schulz.
 
  ABSTRACT  
 
Histidine ammonia-lyase (EC 4.3.1.3) catalyzes the nonoxidative elimination of the alpha-amino group of histidine and is closely related to the important plant enzyme phenylalanine ammonia-lyase. The crystal structure of histidase from Pseudomonas putida was determined at 2.1 A resolution revealing a homotetramer with D2 symmetry, the molecular center of which is formed by 20 nearly parallel alpha-helices. The chain fold, but not the sequence, resembles those of fumarase C and related proteins. The structure shows that the reactive electrophile is a 4-methylidene-imidazole-5-one, which is formed autocatalytically by cyclization and dehydration of residues 142-144 with the sequence Ala-Ser-Gly. With respect to the first dehydration step, this modification resembles the chromophore of the green fluorescent protein. The active center is clearly established by the modification and by mutations. The observed geometry allowed us to model the bound substrate at a high confidence level. A reaction mechanism is proposed.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21131229 N.J.Turner (2011).
Ammonia lyases and aminomutases as biocatalysts for the synthesis of α-amino and β-amino acids.
  Curr Opin Chem Biol, 15, 234-240.  
21052759 X.Wang (2011).
Structure, function, and engineering of enzymes in isoflavonoid biosynthesis.
  Funct Integr Genomics, 11, 13-22.  
20577998 H.A.Cooke, and S.D.Bruner (2010).
Probing the active site of MIO-dependent aminomutases, key catalysts in the biosynthesis of beta-amino acids incorporated in secondary metabolites.
  Biopolymers, 93, 802-810.
PDB codes: 3kdy 3kdz
20353954 H.Hayashi, S.Tanase, and T.Yagi (2010).
Esmond E. Snell--the pathfinder of B vitamins and cofactors.
  J Biochem, 147, 451-457.  
21036782 S.Bartsch, and U.T.Bornscheuer (2010).
Mutational analysis of phenylalanine ammonia lyase to improve reactions rates for various substrates.
  Protein Eng Des Sel, 23, 929-933.  
19364318 A.A.Pakhomov, and V.I.Martynov (2009).
Posttranslational chemistry of proteins of the GFP family.
  Biochemistry (Mosc), 74, 250-259.  
19123196 B.Wu, W.Szymanski, P.Wietzes, S.de Wildeman, G.J.Poelarends, B.L.Feringa, and D.B.Janssen (2009).
Enzymatic Synthesis of Enantiopure alpha- and beta-Amino Acids by Phenylalanine Aminomutase-Catalysed Amination of Cinnamic Acid Derivatives.
  Chembiochem, 10, 338-344.  
19620019 H.A.Cooke, C.V.Christianson, and S.D.Bruner (2009).
Structure and chemistry of 4-methylideneimidazole-5-one containing enzymes.
  Curr Opin Chem Biol, 13, 460-468.  
18366185 A.S.Mishin, F.V.Subach, I.V.Yampolsky, W.King, K.A.Lukyanov, and V.V.Verkhusha (2008).
The first mutant of the Aequorea victoria green fluorescent protein that forms a red chromophore.
  Biochemistry, 47, 4666-4673.  
19030603 L.B.Davin, M.Jourdes, A.M.Patten, K.W.Kim, D.G.Vassão, and N.G.Lewis (2008).
Dissection of lignin macromolecular configuration and assembly: Comparison to related biochemical processes in allyl/propenyl phenol and lignan biosynthesis.
  Nat Prod Rep, 25, 1015-1090.  
  19079566 N.P.Lemay, A.L.Morgan, E.J.Archer, L.A.Dickson, C.M.Megley, and M.Zimmer (2008).
The Role of the Tight-Turn, Broken Hydrogen Bonding, Glu222 and Arg96 in the Post-translational Green Fluorescent Protein Chromophore Formation.
  Chem Phys, 348, 152-160.  
17456010 F.S.Sariaslani (2007).
Development of a combined biological and chemical process for production of industrial aromatics from renewable resources.
  Annu Rev Microbiol, 61, 51-69.  
17372780 G.Mocz (2007).
Fluorescent proteins and their use in marine biosciences, biotechnology, and proteomics.
  Mar Biotechnol (NY), 9, 305-328.  
17240984 M.C.Moffitt, G.V.Louie, M.E.Bowman, J.Pence, J.P.Noel, and B.S.Moore (2007).
Discovery of two cyanobacterial phenylalanine ammonia lyases: kinetic and structural characterization.
  Biochemistry, 46, 1004-1012.
PDB codes: 2nyf 2nyn
17612622 M.J.MacDonald, and G.B.D'Cunha (2007).
A modern view of phenylalanine ammonia lyase.
  Biochem Cell Biol, 85, 273-282.  
17717196 X.X.Zhang, and P.B.Rainey (2007).
Genetic analysis of the histidine utilization (hut) genes in Pseudomonas fluorescens SBW25.
  Genetics, 176, 2165-2176.  
17602252 Z.Xue, M.McCluskey, K.Cantera, F.S.Sariaslani, and L.Huang (2007).
Identification, characterization and functional expression of a tyrosine ammonia-lyase and its mutants from the photosynthetic bacterium Rhodobacter sphaeroides.
  J Ind Microbiol Biotechnol, 34, 599-604.  
17193285 A.Katona, M.I.Toşa, C.Paizs, and J.Rétey (2006).
Inhibition of histidine ammonia lyase by heteroaryl-alanines and acrylates.
  Chem Biodivers, 3, 502-508.  
17185228 G.V.Louie, M.E.Bowman, M.C.Moffitt, T.J.Baiga, B.S.Moore, and J.P.Noel (2006).
Structural determinants and modulation of substrate specificity in phenylalanine-tyrosine ammonia-lyases.
  Chem Biol, 13, 1327-1338.
PDB codes: 2o6y 2o78 2o7b 2o7d 2o7e 2o7f
17185227 K.T.Watts, B.N.Mijts, P.C.Lee, A.J.Manning, and C.Schmidt-Dannert (2006).
Discovery of a substrate selectivity switch in tyrosine ammonia-lyase, a member of the aromatic amino acid lyase family.
  Chem Biol, 13, 1317-1326.  
16547054 M.Berner, D.Krug, C.Bihlmaier, A.Vente, R.Müller, and A.Bechthold (2006).
Genes and enzymes involved in caffeic acid biosynthesis in the actinomycete Saccharothrix espanaensis.
  J Bacteriol, 188, 2666-2673.  
17064887 S.J.Remington (2006).
Fluorescent proteins: maturation, photochemistry and photophysics.
  Curr Opin Struct Biol, 16, 714-721.  
16478474 S.Pilbák, A.Tomin, J.Rétey, and L.Poppe (2006).
The essential tyrosine-containing loop conformation and the role of the C-terminal multi-helix region in eukaryotic phenylalanine ammonia-lyases.
  FEBS J, 273, 1004-1019.  
16990261 Y.Yu, Y.H.Liang, E.Brostromer, J.M.Quan, S.Panjikar, Y.H.Dong, and X.D.Su (2006).
A catalytic mechanism revealed by the crystal structures of the imidazolonepropionase from Bacillus subtilis.
  J Biol Chem, 281, 36929-36936.
PDB codes: 2bb0 2g3f
16267872 C.T.Walsh, S.Garneau-Tsodikova, and G.J.Gatto (2005).
Protein posttranslational modifications: the chemistry of proteome diversifications.
  Angew Chem Int Ed Engl, 44, 7342-7372.  
15906398 L.Poppe, and J.Rétey (2005).
Friedel-Crafts-type mechanism for the enzymatic elimination of ammonia from histidine and phenylalanine.
  Angew Chem Int Ed Engl, 44, 3668-3688.  
16218867 W.Buckel, B.M.Martins, A.Messerschmidt, and B.T.Golding (2005).
Radical-mediated dehydration reactions in anaerobic bacteria.
  Biol Chem, 386, 951-959.  
15857789 Y.Asano, I.Kira, and K.Yokozeki (2005).
Alteration of substrate specificity of aspartase by directed evolution.
  Biomol Eng, 22, 95.  
15494399 K.D.Walker, K.Klettke, T.Akiyama, and R.Croteau (2004).
Cloning, heterologous expression, and characterization of a phenylalanine aminomutase involved in Taxol biosynthesis.
  J Biol Chem, 279, 53947-53954.  
14523232 D.P.Barondeau, C.D.Putnam, C.J.Kassmann, J.A.Tainer, and E.D.Getzoff (2003).
Mechanism and energetics of green fluorescent protein chromophore synthesis revealed by trapped intermediate structures.
  Proc Natl Acad Sci U S A, 100, 12111-12116.
PDB codes: 1qxt 1qy3 1qyf 1qyo 1qyq
14580219 S.D.Christenson, W.Wu, M.A.Spies, B.Shen, and M.D.Toney (2003).
Kinetic analysis of the 4-methylideneimidazole-5-one-containing tyrosine aminomutase in enediyne antitumor antibiotic C-1027 biosynthesis.
  Biochemistry, 42, 12708-12718.  
11796115 C.W.Levy, P.A.Buckley, S.Sedelnikova, Y.Kato, Y.Asano, D.W.Rice, and P.J.Baker (2002).
Insights into enzyme evolution revealed by the structure of methylaspartate ammonia lyase.
  Structure, 10, 105-113.
PDB codes: 1kko 1kkr
12071972 D.Röther, L.Poppe, G.Morlock, S.Viergutz, and J.Rétey (2002).
An active site homology model of phenylalanine ammonia-lyase from Petroselinum crispum.
  Eur J Biochem, 269, 3065-3075.  
12082112 L.Xiang, and B.S.Moore (2002).
Inactivation, complementation, and heterologous expression of encP, a novel bacterial phenylalanine ammonia-lyase gene.
  J Biol Chem, 277, 32505-32509.  
11748244 M.Asuncion, W.Blankenfeldt, J.N.Barlow, D.Gani, and J.H.Naismith (2002).
The structure of 3-methylaspartase from Clostridium tetanomorphum functions via the common enolase chemical step.
  J Biol Chem, 277, 8306-8311.
PDB codes: 1kcz 1kd0
11895450 M.Baedeker, and G.E.Schulz (2002).
Structures of two histidine ammonia-lyase modifications and implications for the catalytic mechanism.
  Eur J Biochem, 269, 1790-1797.
PDB codes: 1gkj 1gkm
12325128 M.V.Matz, K.A.Lukyanov, and S.A.Lukyanov (2002).
Family of the green fluorescent protein: journey to the end of the rainbow.
  Bioessays, 24, 953-959.  
11717518 C.W.Levy, P.A.Buckley, P.J.Baker, S.Sedelnikova, F.Rodgers, Y.F.Li, Y.Kato, Y.Asano, and D.W.Rice (2001).
Crystallization and preliminary X-ray analysis of Citrobacter amalonaticus methylaspartate ammonia lyase.
  Acta Crystallogr D Biol Crystallogr, 57, 1922-1924.  
11732994 D.Röther, L.Poppe, S.Viergutz, B.Langer, and J.Rétey (2001).
Characterization of the active site of histidine ammonia-lyase from Pseudomonas putida.
  Eur J Biochem, 268, 6011-6019.  
11578924 L.Poppe (2001).
Methylidene-imidazolone: a novel electrophile for substrate activation.
  Curr Opin Chem Biol, 5, 512-524.  
11698675 L.Xie, and W.A.van der Donk (2001).
Homemade cofactors: self-processing in galactose oxidase.
  Proc Natl Acad Sci U S A, 98, 12863-12865.  
11320320 M.Asuncion, J.N.Barlow, J.Pollard, A.G.Staines, S.A.McMahon, W.Blankenfeldt, D.Gani, and J.H.Naismith (2001).
Overexpression, purification, crystallization and data collection of 3-methylaspartase from Clostridium tetanomorphum.
  Acta Crystallogr D Biol Crystallogr, 57, 731-733.  
11137817 J.Piel, C.Hertweck, P.R.Shipley, D.M.Hunt, M.S.Newman, and B.S.Moore (2000).
Cloning, sequencing and analysis of the enterocin biosynthesis gene cluster from the marine isolate 'Streptomyces maritimus': evidence for the derailment of an aromatic polyketide synthase.
  Chem Biol, 7, 943-955.  
10903941 N.M.Okeley, and W.A.van der Donk (2000).
Novel cofactors via post-translational modifications of enzyme active sites.
  Chem Biol, 7, R159-R171.  
10849007 S.Dickert, A.J.Pierik, D.Linder, and W.Buckel (2000).
The involvement of coenzyme A esters in the dehydration of (R)-phenyllactate to (E)-cinnamate by Clostridium sporogenes.
  Eur J Biochem, 267, 3874-3884.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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