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PDBsum entry 1hwy

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1hwy
Jmol
Contents
Protein chains
(+ 0 more) 501 a.a. *
Ligands
PO4 ×24
AKG ×6
NAD ×12
Waters ×36
* Residue conservation analysis
PDB id:
1hwy
Name: Oxidoreductase
Title: Bovine glutamate dehydrogenase complexed with NAD and 2-oxog
Structure: Glutamate dehydrogenase. Chain: a, b, c, d, e, f. Synonym: gdh. Ec: 1.4.1.3
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: liver. Organelle: mitochondria. Cellular_location: inner mitochondrial matrix
Biol. unit: Hexamer (from PQS)
Resolution:
3.20Å     R-factor:   0.230     R-free:   0.290
Authors: T.J.Smith,P.E.Peterson,T.Schmidt,J.Fang,C.A.Stanley
Key ref:
T.J.Smith et al. (2001). Structures of bovine glutamate dehydrogenase complexes elucidate the mechanism of purine regulation. J Mol Biol, 307, 707-720. PubMed id: 11254391 DOI: 10.1006/jmbi.2001.4499
Date:
10-Jan-01     Release date:   31-Jan-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00366  (DHE3_BOVIN) -  Glutamate dehydrogenase 1, mitochondrial
Seq:
Struc:
 
Seq:
Struc:
558 a.a.
501 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 17 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.1.4.1.3  - Glutamate dehydrogenase (NAD(P)(+)).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-glutamate + H2O + NAD(P)(+) = 2-oxoglutarate + NH3 + NAD(P)H
L-glutamate
+ H(2)O
+
NAD(P)(+)
Bound ligand (Het Group name = NAD)
matches with 91.67% similarity
=
2-oxoglutarate
Bound ligand (Het Group name = AKG)
corresponds exactly
+ NH(3)
+ NAD(P)H
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     mitochondrion   3 terms 
  Biological process     tricarboxylic acid metabolic process   6 terms 
  Biochemical function     nucleotide binding     7 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.2001.4499 J Mol Biol 307:707-720 (2001)
PubMed id: 11254391  
 
 
Structures of bovine glutamate dehydrogenase complexes elucidate the mechanism of purine regulation.
T.J.Smith, P.E.Peterson, T.Schmidt, J.Fang, C.A.Stanley.
 
  ABSTRACT  
 
Glutamate dehydrogenase is found in all organisms and catalyses the oxidative deamination of l-glutamate to 2-oxoglutarate. However, only animal GDH utilizes both NAD(H) or NADP(H) with comparable efficacy and exhibits a complex pattern of allosteric inhibition by a wide variety of small molecules. The major allosteric inhibitors are GTP and NADH and the two main allosteric activators are ADP and NAD(+). The structures presented here have refined and modified the previous structural model of allosteric regulation inferred from the original boGDH.NADH.GLU.GTP complex. The boGDH.NAD(+).alpha-KG complex structure clearly demonstrates that the second coenzyme-binding site lies directly under the "pivot helix" of the NAD(+) binding domain. In this complex, phosphates are observed to occupy the inhibitory GTP site and may be responsible for the previously observed structural stabilization by polyanions. The boGDH.NADPH.GLU.GTP complex shows the location of the additional phosphate on the active site coenzyme molecule and the GTP molecule bound to the GTP inhibitory site. As expected, since NADPH does not bind well to the second coenzyme site, no evidence of a bound molecule is observed at the second coenzyme site under the pivot helix. Therefore, these results suggest that the inhibitory GTP site is as previously identified. However, ADP, NAD(+), and NADH all bind under the pivot helix, but a second GTP molecule does not. Kinetic analysis of a hyperinsulinism/hyperammonemia mutant strongly suggests that ATP can inhibit the reaction by binding to the GTP site. Finally, the fact that NADH, NAD(+), and ADP all bind to the same site requires a re-analysis of the previous models for NADH inhibition.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Refined structure of the bound GTP molecule in the NADH delta GLU delta GTP complex. (a) Schematic of the bound GTP mol- ecule and its contact with the enzyme at the base of the antenna. The view here is approximately from the antenna towards the NAD binding domain. Note the contacts between the purine ring and E292 and K289. (b) 6-Fold averaged omit map of the bound GTP.
Figure 5.
Figure 5. Structure of the active site ligands in the NAD+ delta a-KG complex. (a) Schematic diagram of the NAD+ and a-KG molecules bound in the active site. The orien- tation is the same as that used in Figure 2. (b) 6-Fold averaged, omit electron density of the bound ligands (black lines) with their atomic models included.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 307, 707-720) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21428913 P.C.Engel (2011).
Making biochemistry count: life among the amino acid dehydrogenases.
  Biochem Soc Trans, 39, 425-429.  
20936362 A.A.Palladino, and C.A.Stanley (2010).
The hyperinsulinism/hyperammonemia syndrome.
  Rev Endocr Metab Disord, 11, 171-178.  
  20857847 C.Diao, S.Chen, X.Xiao, T.Wang, X.Sun, O.Wang, H.Song, Y.Zhang, M.Yu, Q.Zhang, and H.Wang (2010).
Two unrelated Chinese patients with hyperinsulinism /hyperammonemia (HI/HA) syndrome due to mutations in glutamate dehydrogenase gene.
  J Pediatr Endocrinol Metab, 23, 733-738.  
  20944214 G.W.Han, C.Bakolitsa, M.D.Miller, A.Kumar, D.Carlton, R.J.Najmanovich, P.Abdubek, T.Astakhova, H.L.Axelrod, C.Chen, H.J.Chiu, T.Clayton, D.Das, M.C.Deller, L.Duan, D.Ernst, J.Feuerhelm, J.C.Grant, A.Grzechnik, L.Jaroszewski, K.K.Jin, H.A.Johnson, H.E.Klock, M.W.Knuth, P.Kozbial, S.S.Krishna, D.Marciano, D.McMullan, A.T.Morse, E.Nigoghossian, L.Okach, R.Reyes, C.L.Rife, N.Sefcovic, H.J.Tien, C.B.Trame, H.van den Bedem, D.Weekes, Q.Xu, K.O.Hodgson, J.Wooley, M.A.Elsliger, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2010).
Structures of the first representatives of Pfam family PF06938 (DUF1285) reveal a new fold with repeated structural motifs and possible involvement in signal transduction.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 1218-1225.
PDB codes: 2ra9 2re3
21070950 G.Wisedchaisri, D.M.Dranow, T.J.Lie, J.B.Bonanno, Y.Patskovsky, S.A.Ozyurt, J.M.Sauder, S.C.Almo, S.R.Wasserman, S.K.Burley, J.A.Leigh, and T.Gonen (2010).
Structural underpinnings of nitrogen regulation by the prototypical nitrogen-responsive transcriptional factor NrpR.
  Structure, 18, 1512-1521.
PDB code: 3nek
20697932 J.R.Treberg, M.E.Brosnan, and J.T.Brosnan (2010).
The simultaneous determination of NAD(H) and NADP(H) utilization by glutamate dehydrogenase.
  Mol Cell Biochem, 344, 253-259.  
19858196 M.M.Islam, M.Nautiyal, R.M.Wynn, J.A.Mobley, D.T.Chuang, and S.M.Hutson (2010).
Branched-chain amino acid metabolon: interaction of glutamate dehydrogenase with the mitochondrial branched-chain aminotransferase (BCATm).
  J Biol Chem, 285, 265-276.  
20665690 S.A.Wacker, M.J.Bradley, J.Marion, and E.Bell (2010).
Ligand-induced changes in the conformational stability and flexibility of glutamate dehydrogenase and their role in catalysis and regulation.
  Protein Sci, 19, 1820-1829.  
19393024 K.Kanavouras, N.Borompokas, H.Latsoudis, A.Stagourakis, I.Zaganas, and A.Plaitakis (2009).
Mutations in human GLUD2 glutamate dehydrogenase affecting basal activity and regulation.
  J Neurochem, 109, 167-173.  
19531491 M.Li, C.J.Smith, M.T.Walker, and T.J.Smith (2009).
Novel inhibitors complexed with glutamate dehydrogenase: allosteric regulation by control of protein dynamics.
  J Biol Chem, 284, 22988-23000.
PDB codes: 3etd 3ete 3etg
19564688 N.Volkmann (2009).
Confidence intervals for fitting of atomic models into low-resolution densities.
  Acta Crystallogr D Biol Crystallogr, 65, 679-689.  
19816556 O.N.Demerdash, M.D.Daily, and J.C.Mitchell (2009).
Structure-based predictive models for allosteric hot spots.
  PLoS Comput Biol, 5, e1000531.  
18442970 C.Frieden (2008).
A lifetime of kinetics.
  J Biol Chem, 283, 19873-19878.  
18433062 C.J.Liao, K.H.Chin, C.H.Lin, P.S.Tsai, P.C.Lyu, C.C.Young, A.H.Wang, and S.H.Chou (2008).
Crystal structure of DFA0005 complexed with alpha-ketoglutarate: a novel member of the ICL/PEPM superfamily from alkali-tolerant Deinococcus ficus.
  Proteins, 73, 362-371.
PDB code: 2ze3
18957586 C.Vamsee-Krishna, and P.S.Phale (2008).
Carbon source-dependent modulation of NADP-glutamate dehydrogenases in isophthalate-degrading Pseudomonas aeruginosa strain PP4, Pseudomonas strain PPD and Acinetobacter lwoffii strain ISP4.
  Microbiology, 154, 3329-3337.  
18078298 S.Bigdeli, A.H.Talasaz, P.Ståhl, H.H.Persson, M.Ronaghi, R.W.Davis, and M.Nemat-Gorgani (2008).
Conformational flexibility of a model protein upon immobilization on self-assembled monolayers.
  Biotechnol Bioeng, 100, 19-27.  
18819805 T.J.Smith, and C.A.Stanley (2008).
Untangling the glutamate dehydrogenase allosteric nightmare.
  Trends Biochem Sci, 33, 557-564.  
17531094 A.Del Sol, M.J.Araúzo-Bravo, D.Amoros, and R.Nussinov (2007).
Modular architecture of protein structures and allosteric communications: potential implications for signaling proteins and regulatory linkages.
  Genome Biol, 8, R92.  
17850332 J.B.Carrigan, and P.C.Engel (2007).
Probing the determinants of coenzyme specificity in Peptostreptococcus asaccharolyticus glutamate dehydrogenase by site-directed mutagenesis.
  FEBS J, 274, 5167-5174.  
17253646 K.Kanavouras, V.Mastorodemos, N.Borompokas, C.Spanaki, and A.Plaitakis (2007).
Properties and molecular evolution of human GLUD2 (neural and testicular tissue-specific) glutamate dehydrogenase.
  J Neurosci Res, 85, 1101-1109.  
17924438 K.Kanavouras, V.Mastorodemos, N.Borompokas, C.Spanaki, and A.Plaitakis (2007).
Properties and molecular evolution of human GLUD2 (neural and testicular tissue-specific) glutamate dehydrogenase.
  J Neurosci Res, 85, 3398-3406.  
17949437 M.Hamelin, J.Mary, M.Vostry, B.Friguet, and H.Bakala (2007).
Glycation damage targets glutamate dehydrogenase in the rat liver mitochondrial matrix during aging.
  FEBS J, 274, 5949-5961.  
18044977 M.Li, A.Allen, and T.J.Smith (2007).
High throughput screening reveals several new classes of glutamate dehydrogenase inhibitors.
  Biochemistry, 46, 15089-15102.  
17507377 M.M.Choi, E.A.Kim, S.J.Yang, S.Y.Choi, S.W.Cho, and J.W.Huh (2007).
Amino acid changes within antenna helix are responsible for different regulatory preferences of human glutamate dehydrogenase isozymes.
  J Biol Chem, 282, 19510-19517.  
16685657 C.Delnatte, D.Sanlaville, J.F.Mougenot, J.R.Vermeesch, C.Houdayer, M.C.Blois, D.Genevieve, O.Goulet, J.P.Fryns, F.Jaubert, M.Vekemans, S.Lyonnet, S.Romana, C.Eng, and D.Stoppa-Lyonnet (2006).
Contiguous gene deletion within chromosome arm 10q is associated with juvenile polyposis of infancy, reflecting cooperation between the BMPR1A and PTEN tumor-suppressor genes.
  Am J Hum Genet, 78, 1066-1074.  
16476731 C.Li, A.Allen, J.Kwagh, N.M.Doliba, W.Qin, H.Najafi, H.W.Collins, F.M.Matschinsky, C.A.Stanley, and T.J.Smith (2006).
Green tea polyphenols modulate insulin secretion by inhibiting glutamate dehydrogenase.
  J Biol Chem, 281, 10214-10221.  
16574664 C.Li, A.Matter, A.Kelly, T.J.Petty, H.Najafi, C.MacMullen, Y.Daikhin, I.Nissim, A.Lazarow, J.Kwagh, H.W.Collins, B.Y.Hsu, I.Nissim, M.Yudkoff, F.M.Matschinsky, and C.A.Stanley (2006).
Effects of a GTP-insensitive mutation of glutamate dehydrogenase on insulin secretion in transgenic mice.
  J Biol Chem, 281, 15064-15072.  
17173671 E.Jaspard (2006).
A computational analysis of the three isoforms of glutamate dehydrogenase reveals structural features of the isoform EC 1.4.1.4 supporting a key role in ammonium assimilation by plants.
  Biol Direct, 1, 38.  
17032644 T.J.Vickers, G.Orsomando, R.D.de la Garza, D.A.Scott, S.O.Kang, A.D.Hanson, and S.M.Beverley (2006).
Biochemical and genetic analysis of methylenetetrahydrofolate reductase in Leishmania metabolism and virulence.
  J Biol Chem, 281, 38150-38158.  
15573397 D.La, B.Sutch, and D.R.Livesay (2005).
Predicting protein functional sites with phylogenetic motifs.
  Proteins, 58, 309-320.  
15578726 V.Mastorodemos, I.Zaganas, C.Spanaki, M.Bessa, and A.Plaitakis (2005).
Molecular basis of human glutamate dehydrogenase regulation under changing energy demands.
  J Neurosci Res, 79, 65-73.  
12414808 S.Aghajanian, M.Hovsepyan, K.F.Geoghegan, B.A.Chrunyk, and P.C.Engel (2003).
A thermally sensitive loop in clostridial glutamate dehydrogenase detected by limited proteolysis.
  J Biol Chem, 278, 1067-1074.  
12193607 H.Y.Yoon, E.H.Cho, H.Y.Kwon, S.Y.Choi, and S.W.Cho (2002).
Importance of glutamate 279 for the coenzyme binding of human glutamate dehydrogenase.
  J Biol Chem, 277, 41448-41454.  
12022886 H.Y.Yoon, E.Y.Lee, and S.W.Cho (2002).
Cassette mutagenesis and photoaffinity labeling of adenine binding domain of ADP regulatory site within human glutamate dehydrogenase.
  Biochemistry, 41, 6817-6823.  
11950837 I.Zaganas, and A.Plaitakis (2002).
Single amino acid substitution (G456A) in the vicinity of the GTP binding domain of human housekeeping glutamate dehydrogenase markedly attenuates GTP inhibition and abolishes the cooperative behavior of the enzyme.
  J Biol Chem, 277, 26422-26428.  
11746417 A.Plaitakis, and I.Zaganas (2001).
Regulation of human glutamate dehydrogenases: implications for glutamate, ammonia and energy metabolism in brain.
  J Neurosci Res, 66, 899-908.  
  11600502 E.Y.Lee, H.Y.Yoon, J.Y.Ahn, S.Y.Choi, and S.W.Cho (2001).
Identification of the GTP binding site of human glutamate dehydrogenase by cassette mutagenesis and photoaffinity labeling.
  J Biol Chem, 276, 47930-47936.  
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.