PDB EDUCATION CORNER: EARLY PROTEIN STRUCTURES
Part of the RCSB-Rutgers Open House (described in this newsletter's
Message from the RCSB PDB) was a celebration marking the opening of
the Molecular Art Mural. Painted by local artist Jessica Milazzo onto
the walls of RCSB-Rutgers, this mural depicts some of the earliest
structures solved by X-ray crystallography.The mural's accompanying text notes, reprinted here, are from the RCSB
PDB's Molecule of the Month series and RCSB PDB staff.
Lysozyme protects biological organisms from the ever-present danger
of bacterial infection. This small enzyme attacks the protective cell
walls of bacteria. Bacteria build a tough skin of carbohydrate chains
to brace their delicate cell membranes against changes in osmotic
pressure. Lysozyme breaks these carbohydrate chains, which destroys
the structural integrity of the bacterial cell wall. The bacteria
then burst under their own internal pressure.
Lysozyme is present in many places that are rich with potential food
for bacterial growth. The lysozyme pictured here is from hen egg
white, where lysozyme serves to protect the proteins and fats that
will nourish the developing chick.
Lysozyme was the first enzyme structure solved.
PDB ID: 2lyz. Blake, CCF, Koenig, DF, Mair, GA, North, ACT, Phillips,
DC and Sarma, VR (1965) Structure of hen egg-white lysozyme. A three
dimensional Fourier synthesis at 2 Angstrom resolution. Nature, 206,
757-761. Blake, CCF, Johnson, LN, Mair, GA, North, ACT, Phillips, DC
and Sarma, VR (1967) Crystallographic studies of the activity of hen
egg-white lysozyme. Proc. R. Soc. London Ser. B, 167, 378-388.
Myoglobin was the first reported protein structure. It represented a
milestone in structural biology for which John Kendrew shared the
Nobel Prize in Chemistry in 1962. This structure, along with the work
on hemoglobin being carried out by Max Perutz, set the stage for
developing our emerging understanding of biology at the atomic level.
Myoglobin is a small, bright red protein. It is very common in muscle
cells, and gives meat much of its red color. Its biological function
is to store oxygen obtained from hemoglobin that is carried in the
blood for use when muscles are hard at work. The myoglobin used in the
structure shown was taken from sperm whale muscles. Marine whales and
dolphins have a great need for myoglobin, so that they can store extra
oxygen for use in their deep dives undersea.
PDB ID: 1mbn. Kendrew, JC, Bodo, G, Dintzis, HM, Parrish, RG and
Wyckoff, H (1958) A three-dimensional model of the myoglobin molecule
obtained by X-ray analysis. Nature, 181, 662-666. Watson, HC (1969)
The stereochemistry of the protein myoglobin. Prog. Stereochem., 4,
The structure of ribonuclease was the third protein - after myoglobin
and lysozyme - that was determined by X-ray crystallography. Two
independent ribonuclease structures were reported in 1967.
Ribonucleases are small enzymes that catalyze the breakdown of
single-stranded ribonucleic acid (RNA) by cleaving a phosphodiester
bond. Ribonucleases have many biological functions, such as cutting
harmful RNA into smaller components in order to remove them from the
cell. Ribonuclease's structure contains a cleft in which the RNA is
held during cleavage.
Kartha, G, Bello, J and Harker, D (1967) Tertiary structure of
ribonuclease. Nature, 213, 862-865. Wyckoff, HW, Hardman, KD,
Allewell, NM, Inagami, T, Tsernoglou, D, Johnson, LN and Richards, FM
(1967) The structure of ribonuclease-S at 6 Angstrom
resolution. J. Biol. Chem., 242, 3749-3753.
The science of protein structure began with the structure of
hemoglobin. After years of arduous work, Max Perutz and his coworkers
determined its atomic structure. Perutz's pioneering work in X-ray
crystallography of proteins - including his study of hemoglobin - won
him the Nobel Prize in 1962.
Hemoglobin is the protein that makes blood red. It is composed of four
protein chains - two alpha chains and two beta chains, each with a
ring-like heme group containing an iron atom. Oxygen binds reversibly
to these iron atoms and is transported through blood. Each of the
protein chains is similar in structure to myoglobin, the protein used
to store oxygen in muscles and other tissues.
PDB ID: 2dhb. Bolton, W and Perutz, MF (1970) Three-dimensional
Fourier synthesis of horse deoxyhaemoglobin at 2.8 Angstrom units
resolution. Nature, 228, 551-552. Perutz, MF, Rossmann, MG, Cullis,
AF, Muirhead, G and Will, G (1960) Structure of haemoglobin: a
three-dimensional Fourier synthesis at 5.5 Angstrom resolution. Nature,