Hydrogen bonding cooperativity of water to nucleotide recognition:: structure of octadecahydrated inosine 5′-monophosphate, 2(C10H12N4O8P)•18H2O at atomic resolution

被引:7
作者
Bera, AK [1 ]
Mukhopadhyay, BP [1 ]
Pal, AK [1 ]
Haldar, U [1 ]
Bhattacharya, S [1 ]
Banerjee, A [1 ]
机构
[1] Bose Inst, Div Biophys, Calcutta, W Bengal 700054, India
关键词
nucleic acid-water interaction; water mediated recognition in biology; inosine 5 '-monophosphate polyhydrated complex; variant and invariant water molecules for nucleotide recognition;
D O I
10.1023/A:1023235820633
中图分类号
O7 [晶体学];
学科分类号
0702 ; 070205 ; 0703 ; 080501 ;
摘要
The crystal structure of an octadecahydrated complex between two inosine 5'-monophosphate (IMP) has been determined at atomic resolution, which reveals the hydrogen bonding and the coordination cooperativity of water molecules to nucleotide recognition. The crystal belongs to monoclinic space group P2(1) with cell dimensions a = 8.65(1), b = 21.90(1), c = 12.37(1)A, and beta = 110.38(9)degrees. The ribose hydroxyls, purine N7, keto(O6) bonded water molecules W1, W2, W5, W6, W8 and the phosphate bridge forming water oxygens of W4, W7, W11 appear to play an invariant role in their hydrogen bonding interactions with the IMPs. The synergistic role of the water molecules W5, W6, W8 in the purine staking domain (N27 ... W5 = 2.583, N17 ... W5 = 2.563, O16 ... W8 = 2.759, O26 ... W6 = 2.723 Angstrom) have been clearly observed for the first time. The complexation of the water molecules through variable hydrogen bonding coordination indicate their functional involvement through extensive cooperative donor-acceptor network mechanism. The occurrence of hydrogen-bonded water spines, water bridges and their interplay in the structural association of IMPs could indicate the possible viability of those aquatic centers in the biological situation.
引用
收藏
页码:509 / 516
页数:8
相关论文
共 16 条
[1]   SOLVENT-ACCESSIBLE SURFACES OF NUCLEIC-ACIDS [J].
ALDEN, CJ ;
KIM, SH .
JOURNAL OF MOLECULAR BIOLOGY, 1979, 132 (03) :411-434
[2]  
DAVID MJ, 1995, DNA PROTEIN STRUCTUR
[3]  
JEFFREY GA, 1992, HYDROGEN BONDING BIO
[4]   ORDERED WATER-STRUCTURE AROUND A BETA-DNA DODECAMER - A QUANTITATIVE STUDY [J].
KOPKA, ML ;
FRATINI, AV ;
DREW, HR ;
DICKERSON, RE .
JOURNAL OF MOLECULAR BIOLOGY, 1983, 163 (01) :129-146
[5]   ROLE OF WATER-MOLECULES IN PROTEIN-NUCLEIC ACID INTERACTIONS - VISUALIZATION OF A MODEL HIGHLY HYDRATED COMPLEX STRUCTURE OF INOSINE 5'-MONOPHOSPHATE AND L-SERINE (2C(10)H(13)N(4)O(8)P-CENTER-DOT-C3H7NO3-CENTER-DOT-12H(2)O) AT ATOMIC-RESOLUTION [J].
MUKHOPADHYAY, BP ;
GHOSH, S ;
BANERJEE, A .
JOURNAL OF CHEMICAL CRYSTALLOGRAPHY, 1995, 25 (08) :477-485
[6]   CRYSTAL AND MOLECULAR-STRUCTURE OF INOSINE-5'-PHOSPHATE [J].
NAGASHIMA, N ;
WAKABAYASHI, K ;
MATZUZAKI, T ;
IITAKA, Y .
ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS, 1974, 30 (FEB15) :320-326
[8]  
ROGER LP, 1986, BIOCH NUCL ACID
[9]   DNA CONFORMATION IS DETERMINED BY ECONOMICS IN THE HYDRATION OF PHOSPHATE GROUPS [J].
SAENGER, W ;
HUNTER, WN ;
KENNARD, O .
NATURE, 1986, 324 (6095) :385-388
[10]  
Saenger W, 1984, Principles of Nucleic Acid Structure