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PDBsum entry 3bwn

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protein ligands Protein-protein interface(s) links
Transferase PDB id
3bwn
Jmol
Contents
Protein chains
(+ 0 more) 362 a.a. *
Ligands
PMP ×4
PO4
PHE
Waters ×592
* Residue conservation analysis
PDB id:
3bwn
Name: Transferase
Title: L-tryptophan aminotransferase
Structure: L-tryptophan aminotransferase. Chain: a, b, d, e, f. Synonym: at1g70560. Engineered: yes. L-tryptophan aminotransferase. Chain: c. Engineered: yes
Source: Arabidopsis thaliana. Thale cress. Organism_taxid: 3702. Gene: at1g70560/f5a18_26, f5a18.26. Expressed in: escherichia coli. Expression_system_taxid: 511693.
Resolution:
2.25Å     R-factor:   0.225     R-free:   0.253
Authors: J.-L.Ferrer,J.P.Noel,F.Pojer,M.Bowman,J.Chory,Y.Tao
Key ref:
Y.Tao et al. (2008). Rapid synthesis of auxin via a new tryptophan-dependent pathway is required for shade avoidance in plants. Cell, 133, 164-176. PubMed id: 18394996 DOI: 10.1016/j.cell.2008.01.049
Date:
10-Jan-08     Release date:   29-Apr-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9S7N2  (TAA1_ARATH) -  L-tryptophan--pyruvate aminotransferase 1
Seq:
Struc:
391 a.a.
362 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 1: E.C.2.6.1.27  - Tryptophan transaminase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-tryptophan + 2-oxoglutarate = (indol-3-yl)pyruvate + L-glutamate
L-tryptophan
+ 2-oxoglutarate
= (indol-3-yl)pyruvate
+ L-glutamate
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
   Enzyme class 2: E.C.2.6.1.99  - L-tryptophan--pyruvate aminotransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-tryptophan + pyruvate = indole-3-pyruvate + L-alanine
L-tryptophan
+ pyruvate
= indole-3-pyruvate
+ L-alanine
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     response to ethylene stimulus   18 terms 
  Biochemical function     catalytic activity     15 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.cell.2008.01.049 Cell 133:164-176 (2008)
PubMed id: 18394996  
 
 
Rapid synthesis of auxin via a new tryptophan-dependent pathway is required for shade avoidance in plants.
Y.Tao, J.L.Ferrer, K.Ljung, F.Pojer, F.Hong, J.A.Long, L.Li, J.E.Moreno, M.E.Bowman, L.J.Ivans, Y.Cheng, J.Lim, Y.Zhao, C.L.Ballaré, G.Sandberg, J.P.Noel, J.Chory.
 
  ABSTRACT  
 
Plants grown at high densities perceive a decrease in the red to far-red (R:FR) ratio of incoming light, resulting from absorption of red light by canopy leaves and reflection of far-red light from neighboring plants. These changes in light quality trigger a series of responses known collectively as the shade avoidance syndrome. During shade avoidance, stems elongate at the expense of leaf and storage organ expansion, branching is inhibited, and flowering is accelerated. We identified several loci in Arabidopsis, mutations in which lead to plants defective in multiple shade avoidance responses. Here we describe TAA1, an aminotransferase, and show that TAA1 catalyzes the formation of indole-3-pyruvic acid (IPA) from L-tryptophan (L-Trp), the first step in a previously proposed, but uncharacterized, auxin biosynthetic pathway. This pathway is rapidly deployed to synthesize auxin at the high levels required to initiate the multiple changes in body plan associated with shade avoidance.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. TAA1 Is a Trp Aminotransferase Involved in Auxin Biosynthesis
(A) Schematic diagram of the proposed IAA biosynthetic pathways.
(B) Identification by LC/MS of indole pyruvic acid (IPA) as the product of TAA1 when L-Trp is used as substrate. Shown are the UV-chromatogram profiles of IPA control (1), reaction mixture (2), and reaction mixture without TAA1 (3). The number shown is the calculated mass of IPA.
Figure 7.
Figure 7. Enzymatic Characterization of TAA1
(A) Determination of Km and Vmax of TAA1 to L-Trp.
(B) sav3-2 is hypersensitive to 5-MT. Seedlings were grown on 1/2 MS medium supplemented with 20 μM 5-MT for 9 days in Wc.
(C) Superimposed structure of TAA1 and alliinase active sites. TAA1 monomers are represented as green and cyan ribbons. Alliinase monomers are represented in grey and wheat ribbons (PDB code: 2hox). Labels are those of TAA1 residues. Pyridoxamine phosphate (PMP) as observed in TAA1 structure is represented by yellow sticks. aminoacrylate-PLP as observed in alliinase structure is represented by orange sticks. Trp-PLP from an in silico docking experiment is represented as magenta sticks.
 
  The above figures are reprinted from an Open Access publication published by Cell Press: Cell (2008, 133, 164-176) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21205034 A.Galstyan, N.Cifuentes-Esquivel, J.Bou-Torrent, and J.F.Martinez-Garcia (2011).
The shade avoidance syndrome in Arabidopsis: a fundamental role for atypical basic helix-loop-helix proteins as transcriptional cofactors.
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Automated analysis of hypocotyl growth dynamics during shade avoidance in Arabidopsis.
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  21255164 C.Zhao, A.Hanada, S.Yamaguchi, Y.Kamiya, and E.P.Beers (2011).
The Arabidopsis Myb genes MYR1 and MYR2 are redundant negative regulators of flowering time under decreased light intensity.
  Plant J, 66, 502-515.  
21113043 E.Sasaki, C.Takahashi, T.Asami, and Y.Shimada (2011).
AtCAST, a tool for exploring gene expression similarities among DNA microarray experiments using networks.
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21289280 K.Baba, A.Karlberg, J.Schmidt, J.Schrader, T.R.Hvidsten, L.Bako, and R.P.Bhalerao (2011).
Activity-dormancy transition in the cambial meristem involves stage-specific modulation of auxin response in hybrid aspen.
  Proc Natl Acad Sci U S A, 108, 3418-3423.  
21220341 K.Kim, J.Shin, S.H.Lee, H.S.Kweon, J.N.Maloof, and G.Choi (2011).
Phytochromes inhibit hypocotyl negative gravitropism by regulating the development of endodermal amyloplasts through phytochrome-interacting factors.
  Proc Natl Acad Sci U S A, 108, 1729-1734.  
21460806 M.Grebe (2011).
Out of the shade and into the light.
  Nat Cell Biol, 13, 347-349.  
21210143 M.Z.Shi, and D.Y.Xie (2011).
Engineering of red cells of Arabidopsis thaliana and comparative genome-wide gene expression analysis of red cells versus wild-type cells.
  Planta, 233, 787-805.  
21734647 T.Vernoux, G.Brunoud, E.Farcot, V.Morin, H.Van den Daele, J.Legrand, M.Oliva, P.Das, A.Larrieu, D.Wells, Y.Guédon, L.Armitage, F.Picard, S.Guyomarc'h, C.Cellier, G.Parry, R.Koumproglou, J.H.Doonan, M.Estelle, C.Godin, S.Kepinski, M.Bennett, L.De Veylder, and J.Traas (2011).
The auxin signalling network translates dynamic input into robust patterning at the shoot apex.
  Mol Syst Biol, 7, 508.  
  21255165 Z.Y.Zhou, C.G.Zhang, L.Wu, C.G.Zhang, J.Chai, M.Wang, A.Jha, P.F.Jia, S.J.Cui, M.Yang, R.Chen, and G.Q.Guo (2011).
Functional characterization of the CKRC1/TAA1 gene and dissection of hormonal actions in the Arabidopsis root.
  Plant J, 66, 516-527.  
21150090 A.Kunihiro, T.Yamashino, and T.Mizuno (2010).
PHYTOCHROME-INTERACTING FACTORS PIF4 and PIF5 are implicated in the regulation of hypocotyl elongation in response to blue light in Arabidopsis thaliana.
  Biosci Biotechnol Biochem, 74, 2538-2541.  
21070414 C.D.Crocco, M.Holm, M.J.Yanovsky, and J.F.Botto (2010).
AtBBX21 and COP1 genetically interact in the regulation of shade avoidance.
  Plant J, 64, 551-562.  
  20404496 D.H.Keuskamp, R.Sasidharan, and R.Pierik (2010).
Physiological regulation and functional significance of shade avoidance responses to neighbors.
  Plant Signal Behav, 5, 655-662.  
21149713 D.H.Keuskamp, S.Pollmann, L.A.Voesenek, A.J.Peeters, and R.Pierik (2010).
Auxin transport through PIN-FORMED 3 (PIN3) controls shade avoidance and fitness during competition.
  Proc Natl Acad Sci U S A, 107, 22740-22744.  
19884227 F.Qiao, J.Petrásek, and P.Nick (2010).
Light can rescue auxin-dependent synchrony of cell division in a tobacco cell line.
  J Exp Bot, 61, 503-510.  
20712616 F.Santos, W.Teale, C.Fleck, M.Volpers, B.Ruperti, and K.Palme (2010).
Modelling polar auxin transport in developmental patterning.
  Plant Biol (Stuttg), 12, 3.  
  20182619 J.L.Stewart, and J.L.Nemhauser (2010).
Do trees grow on money? Auxin as the currency of the cellular economy.
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  20182605 J.Normanly (2010).
Approaching cellular and molecular resolution of auxin biosynthesis and metabolism.
  Cold Spring Harb Perspect Biol, 2, a001594.  
20080776 J.Zhang, T.Nodzynski, A.Pencík, J.Rolcík, and J.Friml (2010).
PIN phosphorylation is sufficient to mediate PIN polarity and direct auxin transport.
  Proc Natl Acad Sci U S A, 107, 918-922.  
20498067 K.Ruzicka, L.C.Strader, A.Bailly, H.Yang, J.Blakeslee, L.Langowski, E.Nejedlá, H.Fujita, H.Itoh, K.Syono, J.Hejátko, W.M.Gray, E.Martinoia, M.Geisler, B.Bartel, A.S.Murphy, and J.Friml (2010).
Arabidopsis PIS1 encodes the ABCG37 transporter of auxinic compounds including the auxin precursor indole-3-butyric acid.
  Proc Natl Acad Sci U S A, 107, 10749-10753.  
20234049 K.Soeno, H.Goda, T.Ishii, T.Ogura, T.Tachikawa, E.Sasaki, S.Yoshida, S.Fujioka, T.Asami, and Y.Shimada (2010).
Auxin biosynthesis inhibitors, identified by a genomics-based approach, provide insights into auxin biosynthesis.
  Plant Cell Physiol, 51, 524-536.  
21105933 L.C.Strader, G.L.Chen, and B.Bartel (2010).
Ethylene directs auxin to control root cell expansion.
  Plant J, 64, 874-884.  
20071603 M.de Carbonnel, P.Davis, M.R.Roelfsema, S.Inoue, I.Schepens, P.Lariguet, M.Geisler, K.Shimazaki, R.Hangarter, and C.Fankhauser (2010).
The Arabidopsis PHYTOCHROME KINASE SUBSTRATE2 protein is a phototropin signaling element that regulates leaf flattening and leaf positioning.
  Plant Physiol, 152, 1391-1405.  
20974893 N.D.Tivendale, N.W.Davies, P.P.Molesworth, S.E.Davidson, J.A.Smith, E.K.Lowe, J.B.Reid, and J.J.Ross (2010).
Reassessing the role of N-hydroxytryptamine in auxin biosynthesis.
  Plant Physiol, 154, 1957-1965.  
20668057 P.G.Dubois, G.T.Olsefski, S.Flint-Garcia, T.L.Setter, O.A.Hoekenga, and T.P.Brutnell (2010).
Physiological and genetic characterization of end-of-day far-red light response in maize seedlings.
  Plant Physiol, 154, 173-186.  
  20300208 P.McSteen (2010).
Auxin and monocot development.
  Cold Spring Harb Perspect Biol, 2, a001479.  
  20516130 P.Overvoorde, H.Fukaki, and T.Beeckman (2010).
Auxin control of root development.
  Cold Spring Harb Perspect Biol, 2, a001537.  
20924026 P.S.Chourey, Q.B.Li, and D.Kumar (2010).
Sugar-hormone cross-talk in seed development: two redundant pathways of IAA biosynthesis are regulated differentially in the invertase-deficient miniature1 (mn1) seed mutant in maize.
  Mol Plant, 3, 1026-1036.  
20501746 P.Stamm, and P.P.Kumar (2010).
The phytohormone signal network regulating elongation growth during shade avoidance.
  J Exp Bot, 61, 2889-2903.  
20182762 R.Appels, R.Barrerro, G.Keeble, and M.Bellgard (2010).
Advances in genome studies: The PAG 2010 conference.
  Funct Integr Genomics, 10, 1-9.  
20233857 R.P.Rao, A.Hunter, O.Kashpur, and J.Normanly (2010).
Aberrant synthesis of indole-3-acetic acid in Saccharomyces cerevisiae triggers morphogenic transition, a virulence trait of pathogenic fungi.
  Genetics, 185, 211-220.  
20154098 S.A.Finlayson, S.R.Krishnareddy, T.H.Kebrom, and J.J.Casal (2010).
Phytochrome regulation of branching in Arabidopsis.
  Plant Physiol, 152, 1914-1927.  
20298484 S.J.Himanen, J.D.Blande, T.Klemola, J.Pulkkinen, J.Heijari, and J.K.Holopainen (2010).
Birch (Betula spp.) leaves adsorb and re-release volatiles specific to neighbouring plants--a mechanism for associational herbivore resistance?
  New Phytol, 186, 722-732.  
20237017 S.LeCLere, E.A.Schmelz, and P.S.Chourey (2010).
Sugar levels regulate tryptophan-dependent auxin biosynthesis in developing maize kernels.
  Plant Physiol, 153, 306-318.  
20590451 S.Lumba, S.Cutler, and P.McCourt (2010).
Plant nuclear hormone receptors: a role for small molecules in protein-protein interactions.
  Annu Rev Cell Dev Biol, 26, 445-469.  
21071851 T.Ishii, K.Soeno, T.Asami, S.Fujioka, and Y.Shimada (2010).
Arabidopsis seedlings over-accumulated indole-3-acetic acid in response to aminooxyacetic acid.
  Biosci Biotechnol Biochem, 74, 2345-2347.  
20421476 T.Sakata, T.Oshino, S.Miura, M.Tomabechi, Y.Tsunaga, N.Higashitani, Y.Miyazawa, H.Takahashi, M.Watanabe, and A.Higashitani (2010).
Auxins reverse plant male sterility caused by high temperatures.
  Proc Natl Acad Sci U S A, 107, 8569-8574.  
  20452945 T.Vernoux, F.Besnard, and J.Traas (2010).
Auxin at the shoot apical meristem.
  Cold Spring Harb Perspect Biol, 2, a001487.  
20817774 V.Tzin, and G.Galili (2010).
New insights into the shikimate and aromatic amino acids biosynthesis pathways in plants.
  Mol Plant, 3, 956-972.  
20717140 W.Grunewald, and J.Friml (2010).
The march of the PINs: developmental plasticity by dynamic polar targeting in plant cells.
  EMBO J, 29, 2700-2714.  
20520656 Y.Jaillais, and J.Chory (2010).
Unraveling the paradoxes of plant hormone signaling integration.
  Nat Struct Mol Biol, 17, 642-645.  
19887500 Y.Mano, K.Nemoto, M.Suzuki, H.Seki, I.Fujii, and T.Muranaka (2010).
The AMI1 gene family: indole-3-acetamide hydrolase functions in auxin biosynthesis in plants.
  J Exp Bot, 61, 25-32.  
20192736 Y.Zhao (2010).
Auxin biosynthesis and its role in plant development.
  Annu Rev Plant Biol, 61, 49-64.  
20543136 Z.Ding, and J.Friml (2010).
Auxin regulates distal stem cell differentiation in Arabidopsis roots.
  Proc Natl Acad Sci U S A, 107, 12046-12051.  
19553990 A.Santner, and M.Estelle (2009).
Recent advances and emerging trends in plant hormone signalling.
  Nature, 459, 1071-1078.  
19752216 A.Tsuchisaka, G.Yu, H.Jin, J.M.Alonso, J.R.Ecker, X.Zhang, S.Gao, and A.Theologis (2009).
A combinatorial interplay among the 1-aminocyclopropane-1-carboxylate isoforms regulates ethylene biosynthesis in Arabidopsis thaliana.
  Genetics, 183, 979.  
  20066117 B.Möller, and D.Weijers (2009).
Auxin control of embryo patterning.
  Cold Spring Harbor Perspect Biol, 1, a001545.  
18797999 B.Veit (2009).
Hormone mediated regulation of the shoot apical meristem.
  Plant Mol Biol, 69, 397-408.  
19220784 C.L.Ballaré (2009).
Illuminated behaviour: phytochrome as a key regulator of light foraging and plant anti-herbivore defence.
  Plant Cell Environ, 32, 713-725.  
19392702 C.Sorin, M.Salla-Martret, J.Bou-Torrent, I.Roig-Villanova, and J.F.Martínez-García (2009).
ATHB4, a regulator of shade avoidance, modulates hormone response in Arabidopsis seedlings.
  Plant J, 59, 266-277.  
18797998 D.Alabadí, and M.A.Blázquez (2009).
Molecular interactions between light and hormone signaling to control plant growth.
  Plant Mol Biol, 69, 409-417.  
  19820338 D.Patel, and K.A.Franklin (2009).
Temperature-regulation of plant architecture.
  Plant Signal Behav, 4, 577-579.  
18807199 E.Benková, and J.Hejátko (2009).
Hormone interactions at the root apical meristem.
  Plant Mol Biol, 69, 383-396.  
19558423 F.F.Millenaar, M.van Zanten, M.C.Cox, R.Pierik, L.A.Voesenek, and A.J.Peeters (2009).
Differential petiole growth in Arabidopsis thaliana: photocontrol and hormonal regulation.
  New Phytol, 184, 141-152.  
19300494 G.Krouk, D.Tranchina, L.Lejay, A.A.Cruikshank, D.Shasha, G.M.Coruzzi, and R.A.Gutiérrez (2009).
A systems approach uncovers restrictions for signal interactions regulating genome-wide responses to nutritional cues in Arabidopsis.
  PLoS Comput Biol, 5, e1000326.  
19306104 H.Chen, and L.Xiong (2009).
The short-rooted vitamin B(6)-deficient mutant pdx1 has impaired local auxin biosynthesis.
  Planta, 229, 1303-1310.  
  19820306 H.Chen, and L.Xiong (2009).
Localized auxin biosynthesis and postembryonic root development in Arabidopsis.
  Plant Signal Behav, 4, 752-754.  
19360022 H.Wolters, and G.Jürgens (2009).
Survival of the flexible: hormonal growth control and adaptation in plant development.
  Nat Rev Genet, 10, 305-317.  
19251652 J.E.Moreno, Y.Tao, J.Chory, and C.L.Ballaré (2009).
Ecological modulation of plant defense via phytochrome control of jasmonate sensitivity.
  Proc Natl Acad Sci U S A, 106, 4935-4940.  
19716335 J.Hua (2009).
From freezing to scorching, transcriptional responses to temperature variations in plants.
  Curr Opin Plant Biol, 12, 568-573.  
19713425 J.Preston, K.Tatematsu, Y.Kanno, T.Hobo, M.Kimura, Y.Jikumaru, R.Yano, Y.Kamiya, and E.Nambara (2009).
Temporal expression patterns of hormone metabolism genes during imbibition of Arabidopsis thaliana seeds: a comparative study on dormant and non-dormant accessions.
  Plant Cell Physiol, 50, 1786-1800.  
19154004 J.W.Chandler (2009).
Local auxin production: a small contribution to a big field.
  Bioessays, 31, 60-70.  
18951837 K.A.Franklin (2009).
Light and temperature signal crosstalk in plant development.
  Curr Opin Plant Biol, 12, 63-68.  
  20457562 K.J.Halliday, J.F.Martínez-García, and E.M.Josse (2009).
Integration of light and auxin signaling.
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19246387 K.Ruzicka, M.Simásková, J.Duclercq, J.Petrásek, E.Zazímalová, S.Simon, J.Friml, M.C.Van Montagu, and E.Benková (2009).
Cytokinin regulates root meristem activity via modulation of the polar auxin transport.
  Proc Natl Acad Sci U S A, 106, 4284-4289.  
19249207 M.A.Koini, L.Alvey, T.Allen, C.A.Tilley, N.P.Harberd, G.C.Whitelam, and K.A.Franklin (2009).
High temperature-mediated adaptations in plant architecture require the bHLH transcription factor PIF4.
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Towards a functional understanding of cell growth dynamics in shoot meristem stem-cell niche.
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The control of shoot branching: an example of plant information processing.
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Cell polarity in plants: Linking PIN polarity generation mechanisms to morphogenic auxin gradients.
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sparse inflorescence1 encodes a monocot-specific YUCCA-like gene required for vegetative and reproductive development in maize.
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TAA1-mediated auxin biosynthesis is essential for hormone crosstalk and plant development.
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Plant biology: in their neighbour's shadow.
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A new path to auxin.
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New auxin analogs with growth-promoting effects in intact plants reveal a chemical strategy to improve hormone delivery.
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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.