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PDBsum entry 1cl0
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Oxidoreductase PDB id
1cl0

 

 

 

 

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Contents
Protein chain
317 a.a. *
Ligands
FAD
Waters ×109
* Residue conservation analysis
PDB id:
1cl0
Name: Oxidoreductase
Title: Crystal structure of reduced thioredoxin reductase from escherichia coli.
Structure: Thioredoxin reductase. Chain: a. Engineered: yes. Other_details: fad and active site disulfide (cys 135 and cys 138) reduced by sodium dithionite after crystallization
Source: Escherichia coli. Organism_taxid: 562. Gene: trxb. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: trxb-strain
Biol. unit: Dimer (from PDB file)
Resolution:
2.50Å     R-factor:   0.200     R-free:   0.292
Authors: B.W.Lennon,C.H.Williams Jr,M.L.Ludwig
Key ref: B.W.Lennon et al. (1999). Crystal structure of reduced thioredoxin reductase from Escherichia coli: structural flexibility in the isoalloxazine ring of the flavin adenine dinucleotide cofactor. Protein Sci, 8, 2366-2379. PubMed id: 10595539 DOI: 10.1110/ps.8.11.2366
Date:
04-May-99     Release date:   03-Dec-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
P0A9P4  (TRXB_ECOLI) -  Thioredoxin reductase from Escherichia coli (strain K12)
Seq:
Struc: 		321 a.a.
317 a.a.
Key:    Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.8.1.9  - thioredoxin-disulfide reductase (NADPH).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: [thioredoxin]-dithiol + NADP+ = [thioredoxin]-disulfide + NADPH + H+
[thioredoxin]-dithiol
 +
NADP(+)
Bound ligand (Het Group name = FAD)
matches with 71.19% similarity 		= [thioredoxin]-disulfide
 + NADPH
 + H(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
DOI no: 10.1110/ps.8.11.2366 Protein Sci 8:2366-2379 (1999)
PubMed id: 10595539  
 
 
Crystal structure of reduced thioredoxin reductase from Escherichia coli: structural flexibility in the isoalloxazine ring of the flavin adenine dinucleotide cofactor.
B.W.Lennon, C.H.Williams, M.L.Ludwig.
 
  ABSTRACT  
 
Catalysis by thioredoxin reductase (TrxR) from Escherichia coli requires alternation between two domain arrangements. One of these conformations has been observed by X-ray crystallography (Waksman G, Krishna TSR, Williams CH Jr, Kuriyan J, 1994, J Mol Biol 236:800-816). This form of TrxR, denoted FO, permits the reaction of enzyme-bound reduced FAD with a redox-active disulfide on TrxR. As part of an investigation of conformational changes and intermediates in catalysis by TrxR, an X-ray structure of the FO form of TrxR with both the FAD and active site disulfide reduced has been determined. Reduction after crystallization resulted in significant local conformation changes. The isoalloxazine ring of the FAD cofactor, which is essentially planar in the oxidized enzyme, assumes a 34 degree "butterfly" bend about the N(5)-N(10) axis in reduced TrxR. Theoretical calculations reported by others predict ring bending of 15-28 degrees for reduced isoalloxazines protonated at N(1). The large bending in reduced TrxR is attributed in part to steric interactions between the isoalloxazine ring and the sulfur of Cys138, formed by reduction of the active site disulfide, and is accompanied by changes in the positions and interactions of several of the ribityl side-chain atoms of FAD. The bending angle in reduced TrxR is larger than that for any flavoprotein in the Protein Data Bank. Distributions of bending angles in published oxidized and reduced flavoenzyme structures are different from those found in studies of free flavins, indicating that the protein environment has a significant effect on bending.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19158086 H.Unno, S.Yamashita, Y.Ikeda, S.Y.Sekiguchi, N.Yoshida, T.Yoshimura, M.Kusunoki, T.Nakayama, T.Nishino, and H.Hemmi (2009).
New role of flavin as a general acid-base catalyst with no redox function in type 2 isopentenyl-diphosphate isomerase.
  J Biol Chem, 284, 9160-9167.
PDB codes: 2zru 2zrv 2zrw 2zrx 2zry 2zrz
19690371 K.G.Kirkensgaard, P.Hägglund, C.Finnie, B.Svensson, and A.Henriksen (2009).
Structure of Hordeum vulgare NADPH-dependent thioredoxin reductase 2. Unwinding the reaction mechanism.
  Acta Crystallogr D Biol Crystallogr, 65, 932-941.
PDB code: 2whd
19719175 T.D.Gruber, W.M.Westler, L.L.Kiessling, and K.T.Forest (2009).
X-ray crystallography reveals a reduced substrate complex of UDP-galactopyranose mutase poised for covalent catalysis by flavin.
  Biochemistry, 48, 9171-9173.
PDB codes: 3inr 3int
18231600 B.Meyer, and J.Kuever (2008).
Homology Modeling of Dissimilatory APS Reductases (AprBA) of Sulfur-Oxidizing and Sulfate-Reducing Prokaryotes.
  PLoS ONE, 3, e1514.  
18638483 D.S.Berkholz, H.R.Faber, S.N.Savvides, and P.A.Karplus (2008).
Catalytic cycle of human glutathione reductase near 1 A resolution.
  J Mol Biol, 382, 371-384.
PDB codes: 3djg 3djj 3dk4 3dk8 3dk9
18717593 H.H.Hernandez, O.A.Jaquez, M.J.Hamill, S.J.Elliott, and C.L.Drennan (2008).
Thioredoxin reductase from Thermoplasma acidophilum: a new twist on redox regulation.
  Biochemistry, 47, 9728-9737.
PDB code: 3cty
  18323604 N.Muraki, D.Seo, T.Shiba, T.Sakurai, and G.Kurisu (2008).
Crystallization and preliminary X-ray studies of ferredoxin-NAD(P)+ reductase from Chlorobium tepidum.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 186-189.  
18426222 T.A.White, W.H.Johnson, C.P.Whitman, and J.J.Tanner (2008).
Structural basis for the inactivation of Thermus thermophilus proline dehydrogenase by N-propargylglycine.
  Biochemistry, 47, 5573-5580.
PDB code: 2ekg
18767842 Y.T.Kao, C.Saxena, T.F.He, L.Guo, L.Wang, A.Sancar, and D.Zhong (2008).
Ultrafast dynamics of flavins in five redox states.
  J Am Chem Soc, 130, 13132-13139.  
18500802 Y.T.Kao, C.Tan, S.H.Song, N.Oztürk, J.Li, L.Wang, A.Sancar, and D.Zhong (2008).
Ultrafast dynamics and anionic active states of the flavin cofactor in cryptochrome and photolyase.
  J Am Chem Soc, 130, 7695-7701.  
18029419 A.Y.Lyubimov, K.Heard, H.Tang, N.S.Sampson, and A.Vrielink (2007).
Distortion of flavin geometry is linked to ligand binding in cholesterol oxidase.
  Protein Sci, 16, 2647-2656.
PDB codes: 3b3r 3b6d
17142294 G.van den Bogaart, V.Krasnikov, and B.Poolman (2007).
Dual-color fluorescence-burst analysis to probe protein efflux through the mechanosensitive channel MscL.
  Biophys J, 92, 1233-1240.  
17582174 T.N.Gustafsson, T.Sandalova, J.Lu, A.Holmgren, and G.Schneider (2007).
High-resolution structures of oxidized and reduced thioredoxin reductase from Helicobacter pylori.
  Acta Crystallogr D Biol Crystallogr, 63, 833-843.
PDB codes: 2q0k 2q0l
17209558 W.Zhang, M.Zhang, W.Zhu, Y.Zhou, S.Wanduragala, D.Rewinkel, J.J.Tanner, and D.F.Becker (2007).
Redox-induced changes in flavin structure and roles of flavin N(5) and the ribityl 2'-OH group in regulating PutA--membrane binding.
  Biochemistry, 46, 483-491.
PDB code: 2fzm
16430210 A.Nagpal, M.P.Valley, P.F.Fitzpatrick, and A.M.Orville (2006).
Crystal structures of nitroalkane oxidase: insights into the reaction mechanism from a covalent complex of the flavoenzyme trapped during turnover.
  Biochemistry, 45, 1138-1150.
PDB codes: 2c0u 2c12
  17142893 I.Leiros, E.Wang, T.Rasmussen, E.Oksanen, H.Repo, S.B.Petersen, P.Heikinheimo, and E.Hough (2006).
The 2.1 A structure of Aerococcus viridans L-lactate oxidase (LOX).
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 1185-1190.
PDB code: 2j6x
16537445 X.Zhu, P.Wentworth, R.A.Kyle, R.A.Lerner, and I.A.Wilson (2006).
Cofactor-containing antibodies: crystal structure of the original yellow antibody.
  Proc Natl Acad Sci U S A, 103, 3581-3585.
PDB code: 2fl5
16301794 M.Akif, K.Suhre, C.Verma, and S.C.Mande (2005).
Conformational flexibility of Mycobacterium tuberculosis thioredoxin reductase: crystal structure and normal-mode analysis.
  Acta Crystallogr D Biol Crystallogr, 61, 1603-1611.
PDB code: 2a87
15213381 R.Kort, H.Komori, S.Adachi, K.Miki, and A.Eker (2004).
DNA apophotolyase from Anacystis nidulans: 1.8 A structure, 8-HDF reconstitution and X-ray-induced FAD reduction.
  Acta Crystallogr D Biol Crystallogr, 60, 1205-1213.
PDB codes: 1owl 1owm 1own 1owo 1owp
15066170 W.Eisenreich, K.Kemter, A.Bacher, S.B.Mulrooney, C.H.Williams, and F.Müller (2004).
13C-, 15N- and 31P-NMR studies of oxidized and reduced low molecular mass thioredoxin reductase and some mutant proteins.
  Eur J Biochem, 271, 1437-1452.  
11842205 G.Fritz, A.Roth, A.Schiffer, T.Büchert, G.Bourenkov, H.D.Bartunik, H.Huber, K.O.Stetter, P.M.Kroneck, and U.Ermler (2002).
Structure of adenylylsulfate reductase from the hyperthermophilic Archaeoglobus fulgidus at 1.6-A resolution.
  Proc Natl Acad Sci U S A, 99, 1836-1841.
PDB codes: 1jnr 1jnz
12351822 R.Artali, G.Bombieri, F.Meneghetti, G.Gilardi, S.J.Sadeghi, D.Cavazzini, and G.L.Rossi (2002).
Comparison of the refined crystal structures of wild-type (1.34 A) flavodoxin from Desulfovibrio vulgaris and the S35C mutant (1.44 A) at 100 K.
  Acta Crystallogr D Biol Crystallogr, 58, 1787-1792.
PDB codes: 1j8q 1j9e 1j9g
11761324 C.J.Rizzo (2001).
Further computational studies on the conformation of 1,5-dihydrolumiflavin.
  Antioxid Redox Signal, 3, 737-746.  
11544348 D.Ritz, and J.Beckwith (2001).
Roles of thiol-redox pathways in bacteria.
  Annu Rev Microbiol, 55, 21-48.  
11340659 G.Cavelier, and L.M.Amzel (2001).
Mechanism of NAD(P)H:quinone reductase: Ab initio studies of reduced flavin.
  Proteins, 43, 420-432.  
11169101 O.Carmel-Harel, R.Stearman, A.P.Gasch, D.Botstein, P.O.Brown, and G.Storz (2001).
Role of thioredoxin reductase in the Yap1p-dependent response to oxidative stress in Saccharomyces cerevisiae.
  Mol Microbiol, 39, 595-605.  
11514662 O.Dym, and D.Eisenberg (2001).
Sequence-structure analysis of FAD-containing proteins.
  Protein Sci, 10, 1712-1728.  
10869173 P.Trickey, J.Basran, L.Y.Lian, Z.Chen, J.D.Barton, M.J.Sutcliffe, N.S.Scrutton, and F.S.Mathews (2000).
Structural and biochemical characterization of recombinant wild type and a C30A mutant of trimethylamine dehydrogenase from methylophilus methylotrophus (sp. W(3)A(1)).
  Biochemistry, 39, 7678-7688.
PDB codes: 1djn 1djq
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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