Role of a remote leucine residue in the catalytic function of polyol dehydrogenase

Manish Kumar Tiwari, Vipin C. Kalia, Yun Chan Kang, Jung Kul Lee

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

Studies on the protein-metal binding sites have mainly focused on the residues immediately surrounding the reacting substrate, cofactors, and metal ions. The contribution of residues in remote layers to the highly optimized microenvironments of catalytic active sites is not well understood. To improve our understanding, the present study examined the role of remote residues on the structure and function of zinc-dependent polyol dehydrogenases. We used an integrated computational and biochemical approach to determine the role of L136 in the third shell of the L-arabinitol 4-dehydrogenase (LAD) from Neurospora crassa. Substitution of L136 with charged (Asp, Lys, or His) and bulky (Trp) side chain amino acids abolished enzyme activity. Whereas the L136A mutant exhibited a 95% decrease in catalytic efficiency (k cat /K m ), the L136C mutant exhibited a 39% decrease in k cat /K m . Additionally, molecular docking and dynamic simulations on the mutant (L136A, L136C, L136H, and L136P) complexes showed the loss of crucial H-bonds between G77 and the corresponding mutated residue. It is evident from theoretical and biochemical studies that the L136 is part of the extensive hydrogen bonding network coupled to the reaction catalyzed at the active site. We propose that L136, critically positioned behind the active site residues H78 and E79 in the third shell of LAD, plays a crucial role in modulating catalysis or substrate binding by stabilizing the GHE motif in the LAD active site.

Original languageEnglish
Pages (from-to)3255-3263
Number of pages9
JournalMolecular BioSystems
Volume10
Issue number12
DOIs
Publication statusPublished - 2014 Dec 1

Fingerprint

L-Iditol 2-Dehydrogenase
L-arabinitol 4-dehydrogenase
Leucine
Catalytic Domain
Cats
Molecular Docking Simulation
Metals
Neurospora crassa
Molecular Dynamics Simulation
Hydrogen Bonding
Catalysis
Protein Binding
Zinc
Theoretical Models
Binding Sites
Ions
Amino Acids
Enzymes

ASJC Scopus subject areas

  • Biotechnology
  • Molecular Biology

Cite this

Role of a remote leucine residue in the catalytic function of polyol dehydrogenase. / Tiwari, Manish Kumar; Kalia, Vipin C.; Kang, Yun Chan; Lee, Jung Kul.

In: Molecular BioSystems, Vol. 10, No. 12, 01.12.2014, p. 3255-3263.

Research output: Contribution to journalArticle

Tiwari, Manish Kumar ; Kalia, Vipin C. ; Kang, Yun Chan ; Lee, Jung Kul. / Role of a remote leucine residue in the catalytic function of polyol dehydrogenase. In: Molecular BioSystems. 2014 ; Vol. 10, No. 12. pp. 3255-3263.
@article{14ee69f0bf234d04a7ba5cd03f6f836c,
title = "Role of a remote leucine residue in the catalytic function of polyol dehydrogenase",
abstract = "Studies on the protein-metal binding sites have mainly focused on the residues immediately surrounding the reacting substrate, cofactors, and metal ions. The contribution of residues in remote layers to the highly optimized microenvironments of catalytic active sites is not well understood. To improve our understanding, the present study examined the role of remote residues on the structure and function of zinc-dependent polyol dehydrogenases. We used an integrated computational and biochemical approach to determine the role of L136 in the third shell of the L-arabinitol 4-dehydrogenase (LAD) from Neurospora crassa. Substitution of L136 with charged (Asp, Lys, or His) and bulky (Trp) side chain amino acids abolished enzyme activity. Whereas the L136A mutant exhibited a 95{\%} decrease in catalytic efficiency (k cat /K m ), the L136C mutant exhibited a 39{\%} decrease in k cat /K m . Additionally, molecular docking and dynamic simulations on the mutant (L136A, L136C, L136H, and L136P) complexes showed the loss of crucial H-bonds between G77 and the corresponding mutated residue. It is evident from theoretical and biochemical studies that the L136 is part of the extensive hydrogen bonding network coupled to the reaction catalyzed at the active site. We propose that L136, critically positioned behind the active site residues H78 and E79 in the third shell of LAD, plays a crucial role in modulating catalysis or substrate binding by stabilizing the GHE motif in the LAD active site.",
author = "Tiwari, {Manish Kumar} and Kalia, {Vipin C.} and Kang, {Yun Chan} and Lee, {Jung Kul}",
year = "2014",
month = "12",
day = "1",
doi = "10.1039/c4mb00459k",
language = "English",
volume = "10",
pages = "3255--3263",
journal = "Molecular BioSystems",
issn = "1742-206X",
publisher = "Royal Society of Chemistry",
number = "12",

}

TY - JOUR

T1 - Role of a remote leucine residue in the catalytic function of polyol dehydrogenase

AU - Tiwari, Manish Kumar

AU - Kalia, Vipin C.

AU - Kang, Yun Chan

AU - Lee, Jung Kul

PY - 2014/12/1

Y1 - 2014/12/1

N2 - Studies on the protein-metal binding sites have mainly focused on the residues immediately surrounding the reacting substrate, cofactors, and metal ions. The contribution of residues in remote layers to the highly optimized microenvironments of catalytic active sites is not well understood. To improve our understanding, the present study examined the role of remote residues on the structure and function of zinc-dependent polyol dehydrogenases. We used an integrated computational and biochemical approach to determine the role of L136 in the third shell of the L-arabinitol 4-dehydrogenase (LAD) from Neurospora crassa. Substitution of L136 with charged (Asp, Lys, or His) and bulky (Trp) side chain amino acids abolished enzyme activity. Whereas the L136A mutant exhibited a 95% decrease in catalytic efficiency (k cat /K m ), the L136C mutant exhibited a 39% decrease in k cat /K m . Additionally, molecular docking and dynamic simulations on the mutant (L136A, L136C, L136H, and L136P) complexes showed the loss of crucial H-bonds between G77 and the corresponding mutated residue. It is evident from theoretical and biochemical studies that the L136 is part of the extensive hydrogen bonding network coupled to the reaction catalyzed at the active site. We propose that L136, critically positioned behind the active site residues H78 and E79 in the third shell of LAD, plays a crucial role in modulating catalysis or substrate binding by stabilizing the GHE motif in the LAD active site.

AB - Studies on the protein-metal binding sites have mainly focused on the residues immediately surrounding the reacting substrate, cofactors, and metal ions. The contribution of residues in remote layers to the highly optimized microenvironments of catalytic active sites is not well understood. To improve our understanding, the present study examined the role of remote residues on the structure and function of zinc-dependent polyol dehydrogenases. We used an integrated computational and biochemical approach to determine the role of L136 in the third shell of the L-arabinitol 4-dehydrogenase (LAD) from Neurospora crassa. Substitution of L136 with charged (Asp, Lys, or His) and bulky (Trp) side chain amino acids abolished enzyme activity. Whereas the L136A mutant exhibited a 95% decrease in catalytic efficiency (k cat /K m ), the L136C mutant exhibited a 39% decrease in k cat /K m . Additionally, molecular docking and dynamic simulations on the mutant (L136A, L136C, L136H, and L136P) complexes showed the loss of crucial H-bonds between G77 and the corresponding mutated residue. It is evident from theoretical and biochemical studies that the L136 is part of the extensive hydrogen bonding network coupled to the reaction catalyzed at the active site. We propose that L136, critically positioned behind the active site residues H78 and E79 in the third shell of LAD, plays a crucial role in modulating catalysis or substrate binding by stabilizing the GHE motif in the LAD active site.

UR - http://www.scopus.com/inward/record.url?scp=84908461952&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84908461952&partnerID=8YFLogxK

U2 - 10.1039/c4mb00459k

DO - 10.1039/c4mb00459k

M3 - Article

C2 - 25292207

AN - SCOPUS:84908461952

VL - 10

SP - 3255

EP - 3263

JO - Molecular BioSystems

JF - Molecular BioSystems

SN - 1742-206X

IS - 12

ER -