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PDBsum entry 1e20
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protein ligands metals links
Flavoprotein PDB id
1e20

 

 

 

 

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Contents
Protein chain
185 a.a. *
Ligands
FMN
BME
Metals
_NI
Waters ×92
* Residue conservation analysis
PDB id:
1e20
Name: Flavoprotein
Title: The fmn binding protein athal3
Structure: Halotolerance protein hal3. Chain: a. Synonym: hal3. Engineered: yes
Source: Arabidopsis thaliana. Mouse-ear cress. Organism_taxid: 3702. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Homo-Trimer (from PDB file)
Resolution:
2.02Å     R-factor:   0.210     R-free:   0.260
Authors: A.Albert,M.Martinez-Ripoll,A.Espinosa-Ruiz,L.Yenush,F.A.Culianez- Macia,R.Serrano
Key ref:
A.Albert et al. (2000). The X-ray structure of the FMN-binding protein AtHal3 provides the structural basis for the activity of a regulatory subunit involved in signal transduction. Structure, 8, 961-969. PubMed id: 10986463 DOI: 10.1016/S0969-2126(00)00187-8
Date:
12-May-00     Release date:   11-Sep-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Q9SWE5  (HAL3A_ARATH) -  Phosphopantothenoylcysteine decarboxylase from Arabidopsis thaliana
Seq:
Struc: 		209 a.a.
185 a.a.
Key:    Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.4.1.1.36  - phosphopantothenoylcysteine decarboxylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway: 		Coenzyme A Biosynthesis (late stages)
      Reaction: N-[(R)-4-phosphopantothenoyl]-L-cysteine + H+ = (R)- 4'-phosphopantetheine + CO2
N-[(R)-4-phosphopantothenoyl]-L-cysteine
 + H(+)
 = (R)- 4'-phosphopantetheine
 +
CO2
Bound ligand (Het Group name = BME)
matches with 40.00% similarity
      Cofactor: FMN
FMN
Bound ligand (Het Group name = FMN) corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
DOI no: 10.1016/S0969-2126(00)00187-8 Structure 8:961-969 (2000)
PubMed id: 10986463  
 
 
The X-ray structure of the FMN-binding protein AtHal3 provides the structural basis for the activity of a regulatory subunit involved in signal transduction.
A.Albert, M.Martínez-Ripoll, A.Espinosa-Ruiz, L.Yenush, F.A.Culiáñez-Macià, R.Serrano.
 
  ABSTRACT  
 
BACKGROUND: The Arabidopsis thaliana HAL3 gene product encodes for an FMN-binding protein (AtHal3) that is related to plant growth and salt and osmotic tolerance. AtHal3 shows sequence homology to ScHal3, a regulatory subunit of the Saccharomyces cerevisae serine/threonine phosphatase PPz1. It has been proposed that AtHal3 and ScHal3 have similar roles in cellular physiology, as Arabidopsis transgenic plants that overexpress AtHal3 and yeast cells that overexpress ScHal3 display similar phenotypes of improved salt tolerance. The enzymatic activity of AtHal3 has not been investigated. However, the AtHal3 sequence is homologous to that of EpiD, a flavoprotein from Staphylococcus epidermidis that recognizes a peptidic substrate and subsequently catalyzes the alpha, beta-dehydrogenation of its C-terminal cysteine residue. RESULTS: The X-ray structure of AtHal3 at 2 A resolution reveals that the biological unit is a trimer. Each protomer adopts an alpha/beta Rossmann fold consisting of a six-stranded parallel beta sheet flanked by two layers of alpha helices. The FMN-binding site of AtHal3 contains all the structural requirements of the flavoenzymes that catalyze dehydrogenation reactions. Comparison of the amino acid sequences of AtHal3, ScHal3 and EpiD reveals that a significant number of residues involved in trimer formation, the active site, and FMN binding are conserved. This observation suggests that ScHal3 and EpiD might also be trimers, having a similar structure and function to AtHal3. CONCLUSIONS: Structural comparisons of AtHal3 with other FMN-binding proteins show that AtHal3 defines a new subgroup of this protein family that is involved in signal transduction. Analysis of the structure of AtHal3 indicates that this protein is designed to interact with another cellular component and to subsequently catalyze the alpha,beta-dehydrogenation of a peptidyl cysteine. Structural data from AtHal3, together with physiological and biochemical information from ScHal3 and EpiD, allow us to propose a model for the recognition and regulation of AtHal3/ScHal3 cellular partners.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. The AtHal3 active site. (a) Stereoview detail of the molecular surface using a probe of 1.4 Å [39]. A peptidyl cysteine residue is modeled inside the cavity. (b) Proposed mechanism for the a,b-dehydrogenation of a peptidyl cysteine residue in the active site of AtHal3.
 
  The above figure is reprinted by permission from Cell Press: Structure (2000, 8, 961-969) copyright 2000.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20821290 D.Chao, and H.Lin (2010).
The tricks plants use to reach appropriate light.
  Sci China Life Sci, 53, 916-926.  
19543273 S.Y.Sun, D.Y.Chao, X.M.Li, M.Shi, J.P.Gao, M.Z.Zhu, H.Q.Yang, S.Luan, and H.X.Lin (2009).
OsHAL3 mediates a new pathway in the light-regulated growth of rice.
  Nat Cell Biol, 11, 845-851.  
16371361 T.Kupke, and W.Schwarz (2006).
4'-phosphopantetheine biosynthesis in Archaea.
  J Biol Chem, 281, 5435-5444.  
15192104 A.Ruiz, I.Muñoz, R.Serrano, A.González, E.Simón, and J.Ariño (2004).
Functional characterization of the Saccharomyces cerevisiae VHS3 gene: a regulatory subunit of the Ppz1 protein phosphatase with novel, phosphatase-unrelated functions.
  J Biol Chem, 279, 34421-34430.  
15459342 E.S.Rangarajan, Y.Li, P.Iannuzzi, A.Tocilj, L.W.Hung, A.Matte, and M.Cygler (2004).
Crystal structure of a dodecameric FMN-dependent UbiX-like decarboxylase (Pad1) from Escherichia coli O157: H7.
  Protein Sci, 13, 3006-3016.
PDB code: 1sbz
15292171 I.Muñoz, A.Ruiz, M.Marquina, A.Barceló, A.Albert, and J.Ariño (2004).
Functional characterization of the yeast Ppz1 phosphatase inhibitory subunit Hal3: a mutagenesis study.
  J Biol Chem, 279, 42619-42627.  
14679228 Y.H.Ding, and J.G.Ferry (2004).
Flavin mononucleotide-binding flavoprotein family in the domain Archaea.
  J Bacteriol, 186, 90-97.  
12876343 M.Blaesse, T.Kupke, R.Huber, and S.Steinbacher (2003).
Structure of MrsD, an FAD-binding protein of the HFCD family.
  Acta Crystallogr D Biol Crystallogr, 59, 1414-1421.
PDB code: 1p3y
12906824 N.Manoj, E.Strauss, T.P.Begley, and S.E.Ealick (2003).
Structure of human phosphopantothenoylcysteine synthetase at 2.3 A resolution.
  Structure, 11, 927-936.
PDB code: 1p9o
14501115 N.Manoj, and S.E.Ealick (2003).
Unusual space-group pseudosymmetry in crystals of human phosphopantothenoylcysteine decarboxylase.
  Acta Crystallogr D Biol Crystallogr, 59, 1762-1766.
PDB code: 1qzu
12906818 N.O'Toole, and M.Cygler (2003).
The final player in the coenzyme A biosynthetic pathway.
  Structure, 11, 899-900.  
11923312 M.Daugherty, B.Polanuyer, M.Farrell, M.Scholle, A.Lykidis, V.de Crécy-Lagard, and A.Osterman (2002).
Complete reconstitution of the human coenzyme A biosynthetic pathway via comparative genomics.
  J Biol Chem, 277, 21431-21439.  
11923307 P.Hernández-Acosta, D.G.Schmid, G.Jung, F.A.Culiáñez-Macià, and T.Kupke (2002).
Molecular characterization of the Arabidopsis thaliana flavoprotein AtHAL3a reveals the general reaction mechanism of 4'-phosphopantothenoylcysteine decarboxylases.
  J Biol Chem, 277, 20490-20498.  
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 code is shown on the right.

 

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