PDBsum entry 1d1c

Contractile protein

PDB id: 1d1c

Contents

Protein chain

744 a.a. *

Ligands

NMQ

Metals

_MG

Waters ×591

* Residue conservation analysis

PDB id:

1d1c

Name:

Contractile protein

Title:

Dictyostelium myosin s1dc (motor domain fragment) complexed with n- methyl-o-nitrophenyl aminoethyldiphosphate beryllium trifluoride.

Structure:

Myosin. Chain: a. Fragment: s1dc motor domain. Engineered: yes. Mutation: yes

Source:

Dictyostelium discoideum. Organism_taxid: 44689. Expressed in: dictyostelium discoideum. Expression_system_taxid: 44689

Resolution:

2.30Å R-factor: 0.181

Authors:

A.M.Gulick,C.B.Bauer,J.B.Thoden,E.Pate,R.G.Yount,I.Rayment

Key ref:

A.M.Gulick et al. (2000). X-ray structures of the Dictyostelium discoideum myosin motor domain with six non-nucleotide analogs. J Biol Chem, 275, 398-408. PubMed id: 10617631 DOI: 10.1074/jbc.275.1.398

Date:

15-Sep-99 Release date: 12-Jan-00

Protein chain

P08799  (MYS2_DICDI) -  Myosin-2 heavy chain from Dictyostelium discoideum

Seq: 2116 a.a.

Struc: 744 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1074/jbc.275.1.398

J Biol Chem 275:398-408 (2000)

PubMed id: 10617631

X-ray structures of the Dictyostelium discoideum myosin motor domain with six non-nucleotide analogs.

A.M.Gulick, C.B.Bauer, J.B.Thoden, E.Pate, R.G.Yount, I.Rayment.

ABSTRACT

The three-dimensional structures of the truncated myosin head from Dictyostelium discoideum myosin II complexed with dinitrophenylaminoethyl-, dinitrophenylaminopropyl-, o-nitrophenylaminoethyl-, m-nitrophenylaminoethyl-, p-nitrophenylaminoethyl-, and o-nitrophenyl-N-methyl-aminoethyl-diphosphate.beryllium fluoride have been determined to better than 2.3-A resolution. The structure of the protein and nucleotide binding pocket in these complexes is very similar to that of S1dC.ADP.BeF(x) (Fisher, A. J., Smith, C. A., Thoden, J., Smith, R., Sutoh, K., Holden, H. M., and Rayment, I. (1995) Biochemistry 34, 8960-8972). The position of the triphosphate-like moiety is essentially identical in all complexes. Furthermore, the alkyl-amino group plays the same role as the ribose by linking the triphosphate to the adenine binding pocket; however, none of the phenyl groups lie in the same position as adenine in S1dC.MgADP.BeF(x), even though several of these nucleotide analogs are functionally equivalent to ATP. Rather the former location of adenine is occupied by water in the nanolog complexes, and the phenyl groups are organized in a manner that attempts to optimize their hydrogen bonding interactions with this constellation of solvent molecules. A comparison of the kinetic and structural properties of the nanologs relative to ATP suggests that the ability of a substrate to sustain tension and to generate movement correlates with a well defined interaction with the active site water structure observed in S1dC.MgADP.BeF(x).

Selected figure(s)

Figure 1.
Fig. 1. Electron density for the nucleotide analogs. Stereodiagrams are shown for the active site contents of the complexes of the six nanologs with S1dC as follows: a, o-NPhAE; b, m-NPhAE; c, p-NPhAE; d, o,p-NPhAE; e, o,p-DNPhAP; f, N-methyl-NPhAE. The nanologs and Mg2+ atoms were removed from the coordinate file, and the structure was submitted to one round of least squares refinement with TNT (31). The subsequent omit map, created with coefficients of the form F[o] F[c], was contoured at 2.5 and used to create the figures. The residues that form the P-loop which wraps around the triphosphate region of the nucleotide, Ser181-Asn188, are shown as ball and stick. Additionally, the N-terminal region that forms the binding pocket for the nucleotide (Asn127-Pro133) is included. The side chains for Asn127, Phe^129, and Arg131 are represented with ball and stick atoms. The atoms are colored by atom type for the nanologs as follows: carbon, gray; oxygen, red; nitrogen, blue; beryllium, green; fluorine, yellow; phosphorus, magenta; and magnesium, orange. All protein atoms are colored gray. Figs. 1-4 were prepared with the programs Molscript and Molded (18, 54).

Figure 2.
Fig. 2. Location of the nanolog molecule within the active site. The orientations of the nanolog molecules compared with ADP·BeF[x] are shown. a shows the adenine base of ADP located in the base pocket that is formed by residues Asn127-Tyr135. The coordinates for this figure were taken from 1MMD (17). c, the ATP nucleotide molecule is shown as ball and stick with yellow bonds. The colors of specific atoms are as in Fig. 1. The nanolog molecules are superimposed on the molecule of ADP·BeF[x] and are represented in solid colors. b, o-NPhAE, m-NPhAE, and p-NPhAE are shown in orange, cyan, and magenta, respectively. c, o,p-DNPhAE, o,p-DNPhAP, and N-methyl-NPhAE are shown in purple, red, and green, respectively. The protein backbones were aligned with the program LSQKAB implemented in the CCP4 program package (33, 41) where all carbons were included in the calculation.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2000, 275, 398-408) copyright 2000.

Figures were selected by an automated process.