Crystal Structure of Haloalkane Dehalogenase LinB from
Sphingomonas paucimobilis UT26 at 0.95 A Resolution: Dynamics
of Catalytic Residues

J 2004

Crystal Structure of Haloalkane Dehalogenase LinB from Sphingomonas paucimobilis UT26 at 0.95 A Resolution: Dynamics of Catalytic Residues

OAKLEY, Aaron, Martin KLVAŇA, Michal OTYEPKA, Yuji NAGATA, Matthew WILCE et. al.

Základní údaje

Originální název

Crystal Structure of Haloalkane Dehalogenase LinB from Sphingomonas paucimobilis UT26 at 0.95 A Resolution: Dynamics of Catalytic Residues

Název česky

Krystalová struktura haloalkán dehalogenázy LinB z Sphingomonas paucimobilis UT26 při rozlišení 0,94 A: funkční a katalytické zbytky.

Autoři

OAKLEY, Aaron (36 Austrálie), Martin KLVAŇA (203 Česká republika), Michal OTYEPKA (203 Česká republika), Yuji NAGATA (392 Japonsko), Matthew WILCE (36 Austrálie) a Jiří DAMBORSKÝ (203 Česká republika, garant)

Vydání

Biochemistry, USA, 2004, 0006-2960

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10600 1.6 Biological sciences

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 4.008

Kód RIV

RIV/00216224:14310/04:00010578

Organizační jednotka

Přírodovědecká fakulta

UT WoS

000188504800005

Klíčová slova anglicky

Crystal structure; Haloalkane Dehalogenase; LinB

Štítky

Crystal Structure, haloalkane dehalogenase, LINB

Změněno: 19. 3. 2010 12:17, prof. Mgr. Jiří Damborský, Dr.

Anotace

ORIG CZ

V originále

We present the structure of LinB, a 33 kDa haloalkane dehalogenase from Sphingomonas paucimobilis UT26, at 0.95 A resolution. The data have allowed us to directly observe the anisotropic motions of the catalytic residues. In particular, the side-chain of the catalytic nucleophile, Asp108, displays a high degree of disorder. It has been modeled in two conformations, one similar to that observed previously (conformation A) and one strained (conformation B) that approached the catalytic base (His272). The strain in the conformation B was mainly in the Ca-Cb-Cg angle (126) that deviated by 13.4 from the "ideal" bond angle of 112.6. Based on these observations, we propose a role for the charge state of the catalytic histidine in determining the geometry of the catalytic residues. We hypothesized that double-protonation of the catalytic base (His272) reduces the distance between the side-chain of this residue and that of the Asp108. The results of molecular dynamics simulations were consistent with the structural data showing that the His272 side chain nitrogen atoms does indeed reduce the distance between the side chains of the residues in question, although the simulations failed to demonstrate the same degree of strain in Asp108 Ca-Cb-Cg angle. Instead, the changes in the molecular dynamics structures were distributed over several bond and dihedral angles. Quantum mechanics calculations on LinB with 1-chloro-2,2-dimethylpropane as a substrate were performed to determine which active site conformations and protonation states were most likely to result in catalysis. It was shown that His272 singly protonated at Nd1 and Asp108 in conformation A gave the most exothermic reaction (dH = -22 kcal/mol). With His272 doubly protonated at Nd1 and Ne2, the reactions were only slightly exothermic or were endothermic. In all calculations starting with Asp108 in the conformation B, the Asp108 Ca-Cb-Cg angle changed during the reaction and the Asp108 moved to the conformation A. The results presented here indicate that the positions of the catalytic residues and charge state of the catalytic base are important for determining reaction energetics in LinB.

Česky

Zkoumali jsme strukturu LinB 33 kDa haloalkándehalogenázy z bakterie Sphingomonas paucimobilis UT26,při rozlišení 0.95 A. Námi ziskaná data přímo poukázaly anizotropní pohyb katalytických zbytků.

Návaznosti

MSM 143100005, záměr

Název: Strukturně-funkční vztahy biomolekul a jejich role v metabolismu

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Strukturně-funkční vztahy biomolekul a jejich role v metabolismu

Citovat

OAKLEY, Aaron, Martin KLVAŇA, Michal OTYEPKA, Yuji NAGATA, Matthew WILCE a Jiří DAMBORSKÝ. Crystal Structure of Haloalkane Dehalogenase LinB from Sphingomonas paucimobilis UT26 at 0.95 A Resolution: Dynamics of Catalytic Residues. Biochemistry. USA, 2004, roč. 43, č. 43, s. 870-878, 8 s. ISSN 0006-2960.

@article{561694,
   author = {Oakley, Aaron and Klvaňa, Martin and Otyepka, Michal and Nagata, Yuji and Wilce, Matthew and Damborský, Jiří},
   article_number = {43},
   keywords = {Crystal structure; Haloalkane Dehalogenase; LinB},
   language = {eng},
   issn = {0006-2960},
   journal = {Biochemistry},
   title = {Crystal Structure of Haloalkane Dehalogenase LinB from Sphingomonas paucimobilis UT26 at 0.95 A Resolution: Dynamics of Catalytic Residues},
   url = {http://ncbr.chemi.muni.cz/~jiri/abstracts/biochem04a.html},
   volume = {43},
   year = {2004}
}

TY  - JOUR
ID  - 561694
AU  - Oakley, Aaron - Klvaňa, Martin - Otyepka, Michal - Nagata, Yuji - Wilce, Matthew - Damborský, Jiří
PY  - 2004
TI  - Crystal Structure of Haloalkane Dehalogenase LinB from Sphingomonas paucimobilis UT26 at 0.95 A Resolution: Dynamics of Catalytic Residues
JF  - Biochemistry
VL  - 43
IS  - 43
SP  - 870-878
EP  - 870-878
PB  - USA
SN  - 00062960
KW  - Crystal structure
KW  - Haloalkane Dehalogenase
KW  - LinB
UR  - http://ncbr.chemi.muni.cz/~jiri/abstracts/biochem04a.html
N2  - We present the structure of LinB, a 33 kDa haloalkane dehalogenase from Sphingomonas paucimobilis UT26, at 0.95 A resolution. The data have allowed us to directly observe the anisotropic motions of the catalytic residues. In particular, the side-chain of the catalytic nucleophile, Asp108, displays a high degree of disorder. It has been modeled in two conformations, one similar to that observed previously (conformation A) and one strained (conformation B) that approached the catalytic base (His272). The strain in the conformation B was mainly in the Ca-Cb-Cg angle (126) that deviated by 13.4 from the "ideal" bond angle of 112.6. Based on these observations, we propose a role for the charge state of the catalytic histidine in determining the geometry of the catalytic residues. We hypothesized that double-protonation of the catalytic base (His272) reduces the distance between the side-chain of this residue and that of the Asp108. The results of molecular dynamics simulations were consistent with the structural data showing that the His272 side chain nitrogen atoms does indeed reduce the distance between the side chains of the residues in question, although the simulations failed to demonstrate the same degree of strain in Asp108 Ca-Cb-Cg angle. Instead, the changes in the molecular dynamics structures were distributed over several bond and dihedral angles. Quantum mechanics calculations on LinB with 1-chloro-2,2-dimethylpropane as a substrate were performed to determine which active site conformations and protonation states were most likely to result in catalysis. It was shown that His272 singly protonated at Nd1 and Asp108 in conformation A gave the most exothermic reaction (dH = -22 kcal/mol). With His272 doubly protonated at Nd1 and Ne2, the reactions were only slightly exothermic or were endothermic. In all calculations starting with Asp108 in the conformation B, the Asp108 Ca-Cb-Cg angle changed during the reaction and the Asp108 moved to the conformation A. The results presented here indicate that the positions of the catalytic residues and charge state of the catalytic base are important for determining reaction energetics in LinB.
ER  -

OAKLEY, Aaron, Martin KLVAŇA, Michal OTYEPKA, Yuji NAGATA, Matthew WILCE a Jiří DAMBORSKÝ. Crystal Structure of Haloalkane Dehalogenase LinB from Sphingomonas paucimobilis UT26 at 0.95 A Resolution: Dynamics of Catalytic Residues. \textit{Biochemistry}. USA, 2004, roč.~43, č.~43, s.~870-878, 8 s. ISSN~0006-2960.

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