 |
PDBsum entry 1hc4
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Oxygen transport
|
PDB id
|
|
|
|
1hc4
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
|
J Mol Biol
209:249-279
(1989)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
Crystal structure of hexameric haemocyanin from Panulirus interruptus refined at 3.2 A resolution.
|
|
A.Volbeda,
W.G.Hol.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
The use of non-crystallographic symmetry restraints in the refinement of the
haemocyanin hexamer from Panulirus interruptus at 3.2 A resolution has resulted
in a final model with a very reasonable geometry and a crystallographic R-factor
of 20.1%, using 59,193 observed structure factor amplitudes between 8.0 and 3.2
A. The mean co-ordinate error is approximately 0.35 A. The six subunits appear
to be related by symmetry operations that differ slightly from 32 point group
symmetry. The six subunits have essentially maintained the same structure. The
hexamer, with point group 32, is best described as a trimer of "tight dimers".
The contacts between the subunits in such a dimer are more numerous, and better
conserved during evolution than contacts in a trimer. The interface of a tight
dimer is separated by an internal cavity into two "contact areas". The contact
area nearest to the centre of the hexamer is most extensive and consists mainly
of residues that are quite conserved among arthropodan haemocyanins. All these
residues are provided by the second domain of each subunit. Hence, this second
domain may play a crucial role in the allosteric functioning of this oxygen
transport protein. The dinuclear copper oxygen-binding site resides in the
centre of domain 2. This oxygen-binding centre is not fully accessible from the
solvent. Three large cavities occur, however, within each subunit at the
interfaces of the three domains. All three cavities contain ordered water
molecules, and two of them are accessible from the surrounding solvent. These
cavities may play a role in facilitating fast movement of dioxygen towards the
binding site, which is situated in a highly conserved, rather hydrophobic core.
A detailed definition of the geometry of the copper site is, of course, not
possible at the limited resolution of 3.2 A. Nevertheless, it is possible to
conclude that each copper is co-ordinated by two, more or less tightly bound,
histidine ligands and one more distant histidine residue. The six histidine
residues utilize their N epsilon atoms for copper co-ordination, while their N
delta atoms are engaged in hydrogen bonds with conserved residues or water
molecules. The two distant histidine ligands are located in apical positions and
are on opposite sides with respect to the plane approximately defined by the
four more tightly bound histidine ligands and the two copper ions. The
copper-to-copper distance is 3.5 to 3.6 A in four of the subunits, but this
distance deviates considerably in two others.(ABSTRACT TRUNCATED AT 400 WORDS)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
A.de la Lande,
J.Maddaluno,
O.Parisel,
T.A.Darden,
and
J.P.Piquemal
(2010).
Study of the docking of competitive inhibitors at a model of tyrosinase active site: insights from joint broken-symmetry/Spin-Flip DFT computations and ELF topological analysis.
|
| |
Interdiscip Sci,
2,
3.
|
|
|
|
|
|
|
S.Scherbaum,
B.Ertas,
W.Gebauer,
and
T.Burmester
(2010).
Characterization of hemocyanin from the peacock mantis shrimp Odontodactylus scyllarus (Malacostraca: Hoplocarida).
|
| |
J Comp Physiol B,
180,
1235-1245.
|
|
|
|
|
|
|
J.Yoon,
S.Fujii,
and
E.I.Solomon
(2009).
Geometric and electronic structure differences between the type 3 copper sites of the multicopper oxidases and hemocyanin/tyrosinase.
|
| |
Proc Natl Acad Sci U S A,
106,
6585-6590.
|
|
|
|
|
|
|
K.S.Ryu,
J.O.Lee,
T.H.Kwon,
H.H.Choi,
H.S.Park,
S.K.Hwang,
Z.W.Lee,
K.B.Lee,
Y.H.Han,
Y.S.Choi,
Y.H.Jeon,
C.Cheong,
and
S.Kim
(2009).
The presence of monoglucosylated N196-glycan is important for the structural stability of storage protein, arylphorin.
|
| |
Biochem J,
421,
87-96.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
V.Amore,
M.Belardinelli,
L.Guerra,
F.Buonocore,
A.M.Fausto,
N.Ubero-Pascal,
and
R.Fochetti
(2009).
Do all stoneflies nymphs have respiratory proteins? Further data on the presence of hemocyanin in the larval stages of plecoptera species.
|
| |
Insect Mol Biol,
18,
203-211.
|
|
|
|
|
|
|
Y.Li,
Y.Wang,
H.Jiang,
and
J.Deng
(2009).
Crystal structure of Manduca sexta prophenoloxidase provides insights into the mechanism of type 3 copper enzymes.
|
| |
Proc Natl Acad Sci U S A,
106,
17002-17006.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
E.Mijangos,
J.Reedijk,
and
L.Gasque
(2008).
Copper(ii) complexes of a polydentate imidazole-based ligand. pH effect on magnetic coupling and catecholase activity.
|
| |
Dalton Trans,
(),
1857-1863.
|
|
|
|
|
|
|
K.H.Marti,
I.M.Ondík,
G.Moritz,
and
M.Reiher
(2008).
Density matrix renormalization group calculations on relative energies of transition metal complexes and clusters.
|
| |
J Chem Phys,
128,
014104.
|
|
|
|
|
|
|
S.Hirota,
T.Kawahara,
M.Beltramini,
P.Di Muro,
R.S.Magliozzo,
J.Peisach,
L.S.Powers,
N.Tanaka,
S.Nagao,
and
L.Bubacco
(2008).
Molecular basis of the bohr effect in arthropod hemocyanin.
|
| |
J Biol Chem,
283,
31941-31948.
|
|
|
|
|
|
|
C.Singleton,
and
N.E.Le Brun
(2007).
Atx1-like chaperones and their cognate P-type ATPases: copper-binding and transfer.
|
| |
Biometals,
20,
275-289.
|
|
|
|
|
|
|
K.Born,
P.Comba,
A.Daubinet,
A.Fuchs,
and
H.Wadepohl
(2007).
Catecholase activity of dicopper(II)-bispidine complexes: stabilities and structures of intermediates, kinetics and reaction mechanism.
|
| |
J Biol Inorg Chem,
12,
36-48.
|
|
|
|
|
|
|
S.Parvez,
M.Kang,
H.S.Chung,
and
H.Bae
(2007).
Naturally occurring tyrosinase inhibitors: mechanism and applications in skin health, cosmetics and agriculture industries.
|
| |
Phytother Res,
21,
805-816.
|
|
|
|
|
|
|
Y.Kawamura-Konishi,
M.Tsuji,
S.Hatana,
M.Asanuma,
D.Kakuta,
T.Kawano,
E.B.Mukouyama,
H.Goto,
and
H.Suzuki
(2007).
Purification, characterization, and molecular cloning of tyrosinase from Pholiota nameko.
|
| |
Biosci Biotechnol Biochem,
71,
1752-1760.
|
|
|
|
|
|
|
A.W.Tepper,
L.Bubacco,
and
G.W.Canters
(2006).
Paramagnetic properties of the halide-bound derivatives of oxidised tyrosinase investigated by 1H NMR spectroscopy.
|
| |
Chemistry,
12,
7668-7675.
|
|
|
|
|
|
|
I.A.Koval,
P.Gamez,
C.Belle,
K.Selmeczi,
and
J.Reedijk
(2006).
Synthetic models of the active site of catechol oxidase: mechanistic studies.
|
| |
Chem Soc Rev,
35,
814-840.
|
|
|
|
|
|
|
P.E.Siegbahn
(2006).
The performance of hybrid DFT for mechanisms involving transition metal complexes in enzymes.
|
| |
J Biol Inorg Chem,
11,
695-701.
|
|
|
|
|
|
|
R.Fochetti,
M.Belardinelli,
L.Guerra,
F.Buonocore,
A.M.Fausto,
and
C.Caporale
(2006).
Cloning and structural analysis of a haemocyanin from the Stonefly Perla grandis.
|
| |
Protein J,
25,
443-454.
|
|
|
|
|
|
|
Y.Matoba,
T.Kumagai,
A.Yamamoto,
H.Yoshitsu,
and
M.Sugiyama
(2006).
Crystallographic evidence that the dinuclear copper center of tyrosinase is flexible during catalysis.
|
| |
J Biol Chem,
281,
8981-8990.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
I.A.Koval,
C.Belle,
K.Selmeczi,
C.Philouze,
E.Saint-Aman,
A.M.Schuitema,
P.Gamez,
J.L.Pierre,
and
J.Reedijk
(2005).
Catecholase activity of a mu-hydroxodicopper(II) macrocyclic complex: structures, intermediates and reaction mechanism.
|
| |
J Biol Inorg Chem,
10,
739-750.
|
|
|
|
|
|
|
M.Beltramini,
N.Colangelo,
F.Giomi,
L.Bubacco,
P.Di Muro,
N.Hellmann,
E.Jaenicke,
and
H.Decker
(2005).
Quaternary structure and functional properties of Penaeus monodon hemocyanin.
|
| |
FEBS J,
272,
2060-2075.
|
|
|
|
|
|
|
S.Shleev,
J.Tkac,
A.Christenson,
T.Ruzgas,
A.I.Yaropolov,
J.W.Whittaker,
and
L.Gorton
(2005).
Direct electron transfer between copper-containing proteins and electrodes.
|
| |
Biosens Bioelectron,
20,
2517-2554.
|
|
|
|
|
|
|
V.S.Sprakel,
M.C.Feiters,
W.Meyer-Klaucke,
M.Klopstra,
J.Brinksma,
B.L.Feringa,
K.D.Karlin,
and
R.J.Nolte
(2005).
Oxygen binding and activation by the complexes of PY2- and TPA-appended diphenylglycoluril receptors with copper and other metals.
|
| |
Dalton Trans,
(),
3522-3534.
|
|
|
|
|
|
|
E.Jaenicke,
and
H.Decker
(2004).
Functional changes in the family of type 3 copper proteins during evolution.
|
| |
Chembiochem,
5,
163-169.
|
|
|
|
|
|
|
F.J.Stevens
(2004).
Hypothetical structure of human serum amyloid A protein.
|
| |
Amyloid,
11,
71-80.
|
|
|
|
|
|
|
F.Spinozzi,
E.Maccioni,
C.V.Teixeira,
H.Amenitsch,
R.Favilla,
M.Goldoni,
P.Di Muro,
B.Salvato,
P.Mariani,
and
M.Beltramini
(2003).
Synchrotron SAXS studies on the structural stability of Carcinus aestuarii hemocyanin in solution.
|
| |
Biophys J,
85,
2661-2672.
|
|
|
|
|
|
|
L.Bubacco,
M.Van Gastel,
E.J.Groenen,
E.Vijgenboom,
and
G.W.Canters
(2003).
Spectroscopic characterization of the electronic changes in the active site of Streptomyces antibioticus tyrosinase upon binding of transition state analogue inhibitors.
|
| |
J Biol Chem,
278,
7381-7389.
|
|
|
|
|
|
|
A.W.Tepper,
L.Bubacco,
and
G.W.Canters
(2002).
Structural basis and mechanism of the inhibition of the type-3 copper protein tyrosinase from Streptomyces antibioticus by halide ions.
|
| |
J Biol Chem,
277,
30436-30444.
|
|
|
|
|
|
|
E.Borghi,
P.L.Solari,
M.Beltramini,
L.Bubacco,
P.Di Muro,
and
B.Salvato
(2002).
Oxidized derivatives of Octopus vulgaris and Carcinus aestuarii hemocyanins at pH 7.5 and related models by x-ray absorption spectroscopy.
|
| |
Biophys J,
82,
3254-3268.
|
|
|
|
|
|
|
G.Battaini,
E.Monzani,
L.Casella,
E.Lonardi,
A.W.Tepper,
G.W.Canters,
and
L.Bubacco
(2002).
Tyrosinase-catalyzed oxidation of fluorophenols.
|
| |
J Biol Chem,
277,
44606-44612.
|
|
|
|
|
|
|
C.Gerdemann,
C.Eicken,
A.Magrini,
H.E.Meyer,
A.Rompel,
F.Spener,
and
B.Krebs
(2001).
Isozymes of Ipomoea batatas catechol oxidase differ in catalase-like activity.
|
| |
Biochim Biophys Acta,
1548,
94.
|
|
|
|
|
|
|
M.Perbandt,
V.Chandra,
K.R.Rajashankar,
K.Idakieva,
K.Parvanova,
W.Rypniewski,
S.Stoeva,
W.Voelter,
N.Genov,
and
C.Betzel
(2001).
Preliminary X-ray diffraction studies of the external functional unit RtH2-e from the Rapana thomasiana.
|
| |
Acta Crystallogr D Biol Crystallogr,
57,
1663-1665.
|
|
|
|
|
|
|
S.Jaron,
and
N.J.Blackburn
(2001).
Characterization of a half-apo derivative of peptidylglycine monooxygenase. Insight into the reactivity of each active site copper.
|
| |
Biochemistry,
40,
6867-6875.
|
|
|
|
|
|
|
A.Molon,
P.Di Muro,
L.Bubacco,
V.Vasilyev,
B.Salvato,
M.Beltramini,
W.Conze,
N.Hellmann,
and
H.Decker
(2000).
Molecular heterogeneity of the hemocyanin isolated from the king crab Paralithodes camtschaticae.
|
| |
Eur J Biochem,
267,
7046-7057.
|
|
|
|
|
|
|
H.Decker,
and
F.Tuczek
(2000).
Tyrosinase/catecholoxidase activity of hemocyanins: structural basis and molecular mechanism.
|
| |
Trends Biochem Sci,
25,
392-397.
|
|
|
|
|
|
|
J.G.Grossmann,
S.A.Ali,
A.Abbasi,
Z.H.Zaidi,
S.Stoeva,
W.Voelter,
and
S.S.Hasnain
(2000).
Low-resolution molecular structures of isolated functional units from arthropodan and molluscan hemocyanin.
|
| |
Biophys J,
78,
977-981.
|
|
|
|
|
|
|
J.K.Holm,
L.Hemmingsen,
L.Bubacco,
B.Salvato,
and
R.Bauer
(2000).
Interaction and coordination geometries for Ag(I) in the two metal sites of hemocyanin.
|
| |
Eur J Biochem,
267,
1754-1760.
|
|
|
|
|
|
|
C.Eicken,
B.Krebs,
and
J.C.Sacchettini
(1999).
Catechol oxidase - structure and activity.
|
| |
Curr Opin Struct Biol,
9,
677-683.
|
|
|
|
|
|
|
P.Fariselli,
A.Bottoni,
F.Bernardi,
and
R.Casadio
(1999).
Quantum mechanical analysis of oxygenated and deoxygenated states of hemocyanin: theoretical clues for a plausible allosteric model of oxygen binding.
|
| |
Protein Sci,
8,
1546-1550.
|
|
|
|
|
|
|
S.Jaron,
and
N.J.Blackburn
(1999).
Does superoxide channel between the copper centers in peptidylglycine monooxygenase? A new mechanism based on carbon monoxide reactivity.
|
| |
Biochemistry,
38,
15086-15096.
|
|
|
|
|
|
|
B.Salvato,
M.Santamaria,
M.Beltramini,
G.Alzuet,
and
L.Casella
(1998).
The enzymatic properties of Octopus vulgaris hemocyanin: o-diphenol oxidase activity.
|
| |
Biochemistry,
37,
14065-14077.
|
|
|
|
|
|
|
H.Decker,
and
T.Rimke
(1998).
Tarantula hemocyanin shows phenoloxidase activity.
|
| |
J Biol Chem,
273,
25889-25892.
|
|
|
|
|
|
|
T.Klabunde,
C.Eicken,
J.C.Sacchettini,
and
B.Krebs
(1998).
Crystal structure of a plant catechol oxidase containing a dicopper center.
|
| |
Nat Struct Biol,
5,
1084-1090.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
G.Alzuet,
L.Bubacco,
L.Casella,
G.P.Rocco,
B.Salvato,
and
M.Beltramini
(1997).
The binding of azide to copper-containing and cobalt-containing forms of hemocyanin from the mediterranean crab Carcinus aestuarii.
|
| |
Eur J Biochem,
247,
688-694.
|
|
|
|
|
|
|
G.Durstewitz,
and
N.B.Terwilliger
(1997).
Developmental changes in hemocyanin expression in the Dungeness crab, Cancer magister.
|
| |
J Biol Chem,
272,
4347-4350.
|
|
|
|
|
|
|
H.C.Massey,
J.Kejzlarová-Lepesant,
R.L.Willis,
A.B.Castleberry,
and
H.Benes
(1997).
The Drosophila Lsp-1 beta gene. A structural and phylogenetic analysis.
|
| |
Eur J Biochem,
245,
199-207.
|
|
|
|
|
|
|
L.J.Martins,
C.P.Hill,
and
W.R.Ellis
(1997).
Structures of wild-type chloromet and L103N hydroxomet Themiste zostericola myohemerythrins at 1.8 A resolution.
|
| |
Biochemistry,
36,
7044-7049.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
P.A.Jekel,
B.Neuteboom,
and
J.J.Beintema
(1996).
Primary structure of hemocyanin from Palinurus vulgaris.
|
| |
Comp Biochem Physiol B Biochem Mol Biol,
115,
243-246.
|
|
|
|
|
|
|
P.A.Jekel,
F.G.Perton,
and
J.J.Beintema
(1996).
Dimerization of an antigenic peptide leads to strong interaction with its antibody.
|
| |
Biochim Biophys Acta,
1291,
195-198.
|
|
|
|
|
|
|
S.Della Longa,
I.Ascone,
A.Bianconi,
A.Bonfigli,
A.C.Castellano,
O.Zarivi,
and
M.Miranda
(1996).
The dinuclear copper site structure of Agaricus bisporus tyrosinase in solution probed by X-ray absorption spectroscopy.
|
| |
J Biol Chem,
271,
21025-21030.
|
|
|
|
|
|
|
T.Burmester,
and
K.Scheller
(1996).
Common origin of arthropod tyrosinase, arthropod hemocyanin, insect hexamerin, and dipteran arylphorin receptor.
|
| |
J Mol Evol,
42,
713-728.
|
|
|
|
|
|
|
A.Buzy,
J.Gagnon,
J.Lamy,
P.Thibault,
E.Forest,
and
G.Hudry-Clergeon
(1995).
Complete amino acid sequence of the Aa6 subunit of the scorpion Androctonus australis hemocyanin determined by Edman degradation and mass spectrometry.
|
| |
Eur J Biochem,
233,
93.
|
|
|
|
|
|
|
F.G.Perton,
W.Baron,
A.J.Scheffer,
and
J.J.Beintema
(1995).
Production and characterization of monoclonal antibodies against Panulirus interruptus hemocyanin.
|
| |
Biol Chem Hoppe Seyler,
376,
243-247.
|
|
|
|
|
|
|
M.Beltramini,
L.Bubacco,
L.Casella,
G.Alzuet,
M.Gullotti,
and
B.Salvato
(1995).
The oxidation of hemocyanin. Kinetics, reaction mechanism and characterization of met-hemocyanin product.
|
| |
Eur J Biochem,
232,
98.
|
|
|
|
|
|
|
T.Kawabata,
Y.Yasuhara,
M.Ochiai,
S.Matsuura,
and
M.Ashida
(1995).
Molecular cloning of insect pro-phenol oxidase: a copper-containing protein homologous to arthropod hemocyanin.
|
| |
Proc Natl Acad Sci U S A,
92,
7774-7778.
|
|
|
|
|
|
|
F.de Haas,
F.G.Perton,
J.F.van Breemen,
J.H.Dijkema,
J.J.Beintema,
and
E.F.van Bruggen
(1994).
Identification of two antibody-interaction sites on the surface of Panulirus interruptus hemocyanin.
|
| |
Eur J Biochem,
222,
155-161.
|
|
|
|
|
|
|
K.A.Magnus,
B.Hazes,
H.Ton-That,
C.Bonaventura,
J.Bonaventura,
and
W.G.Hol
(1994).
Crystallographic analysis of oxygenated and deoxygenated states of arthropod hemocyanin shows unusual differences.
|
| |
Proteins,
19,
302-309.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
R.Sterner,
and
H.Decker
(1994).
Inversion of the Bohr effect upon oxygen binding to 24-meric tarantula hemocyanin.
|
| |
Proc Natl Acad Sci U S A,
91,
4835-4839.
|
|
|
|
|
|
|
S.Della Longa,
A.Bianconi,
L.Palladino,
B.Simonelli,
A.Congiu Castellano,
E.Borghi,
M.Barteri,
M.Beltramini,
G.P.Rocco,
and
B.Salvato
(1993).
An x-ray absorption near edge structure spectroscopy study of metal coordination in Co(II)-substituted Carcinus maenas hemocyanin.
|
| |
Biophys J,
65,
2680-2691.
|
|
|
|
|
|
|
B.Hazes,
and
W.G.Hol
(1992).
Comparison of the hemocyanin beta-barrel with other Greek key beta-barrels: possible importance of the "beta-zipper" in protein structure and folding.
|
| |
Proteins,
12,
278-298.
|
|
|
|
|
|
|
B.Neuteboom,
P.A.Jekel,
and
J.J.Beintema
(1992).
Primary structure of hemocyanin subunit c from Panulirus interruptus.
|
| |
Eur J Biochem,
206,
243-249.
|
|
|
|
|
|
|
J.Markl,
T.Burmester,
H.Decker,
A.Savel-Niemann,
J.R.Harris,
M.Süling,
U.Naumann,
and
K.Scheller
(1992).
Quaternary and subunit structure of Calliphora arylphorin as deduced from electron microscopy, electrophoresis, and sequence similarities with arthropod hemocyanin.
|
| |
J Comp Physiol [B],
162,
665-680.
|
|
|
|
|
|
|
M.Beltramini,
L.Bubacco,
B.Salvato,
L.Casella,
M.Gullotti,
and
S.Garofani
(1992).
The aromatic circular dichroism spectrum as a probe for conformational changes in the active site environment of hemocyanins.
|
| |
Biochim Biophys Acta,
1120,
24-32.
|
|
|
|
|
|
|
J.A.Tainer,
V.A.Roberts,
and
E.D.Getzoff
(1991).
Metal-binding sites in proteins.
|
| |
Curr Opin Biotechnol,
2,
582-591.
|
|
|
|
|
|
|
K.A.Magnus,
E.E.Lattman,
A.Volbeda,
and
W.G.Hol
(1991).
Hexamers of subunit II from Limulus hemocyanin (a 48-mer) have the same quaternary structure as whole Panulirus hemocyanin molecules.
|
| |
Proteins,
9,
240-247.
|
|
|
|
|
|
|
K.I.Miller,
E.Schabtach,
and
K.E.van Holde
(1990).
Arrangement of subunits and domains within the Octopus dofleini hemocyanin molecule.
|
| |
Proc Natl Acad Sci U S A,
87,
1496-1500.
|
|
|
|
|
|
The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
|
|
Links
