PDBsum entry 2scp

Binding protein

PDB id

2scp

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Contents

			Protein chains

					174 a.a. *

			Metals

					_CA ×6

			Waters ×213

* Residue conservation analysis

PDB id:

2scp

Links

Name:

Binding protein

Title:

Structure of a sarcoplasmic calcium-binding protein from nereis diversicolor refined at 2.0 angstroms resolution

Structure:

Sarcoplasmic calcium-binding protein. Chain: a, b. Engineered: yes

Source:

Neanthes diversicolor. Organism_taxid: 6352

Biol. unit:

Dimer (from PQS)

Resolution:

2.00Å

R-factor:

0.180

Authors:

W.J.Cook,S.Vijay-Kumar

Key ref:

S.Vijay-Kumar and W.J.Cook (1992). Structure of a sarcoplasmic calcium-binding protein from Nereis diversicolor refined at 2.0 A resolution. J Mol Biol, 224, 413-426. PubMed id: 1560459

Date:

22-Aug-91

Release date:

31-Oct-93

Supersedes:

1scp

PROCHECK

	Headers

	References

Protein chains

P04571 (SCP_HEDDI) - Sarcoplasmic calcium-binding protein from Hediste diversicolor

Seq: Struc:					174 a.a. 174 a.a.

Key:

PfamA domain

Secondary structure

CATH domain

	J Mol Biol 224:413-426 (1992)
PubMed id: 1560459

Structure of a sarcoplasmic calcium-binding protein from Nereis diversicolor refined at 2.0 A resolution.
S.Vijay-Kumar, W.J.Cook.

ABSTRACT

The crystal structure of a sarcoplasmic Ca(2+)-binding protein (SCP) from the sandworm Nereis diversicolor has been determined and refined at 2.0 A resolution using restrained least-squares techniques. The two molecules in the crystallographic asymmetric unit, which are related by a non-crystallographic 2-fold axis, were refined independently. The refined model includes all 174 residues and three calcium ions for each molecule, as well as 213 water molecules. The root-mean-square difference in co-ordinates for backbone atoms and calcium ions of the two molecules is 0.51 A. The final crystallographic R-factor, based on 18,959 reflections in the range 2.0 A less than or equal to d less than or equal to 7.0 A, with intensities exceeding 2.0 sigma, is 0.182. Bond lengths and bond angles in the molecules have root-mean-square deviations from ideal values of 0.013 A and 2.2 degrees, respectively. SCP has four distinct domains with the typical helix-loop-helix (EF-hand) Ca(2+)-binding motif, although the second Ca(2+)-binding domain is not functional due to amino acid changes in the loop. The structure shows several unique features compared to other Ca(2+)-binding proteins with four EF-hand domains. The overall structure is highly compact and globular with a predominant hydrophobic core, unlike the extended dumbbell-shaped structure of calmodulin or troponin C. A hydrophobic tail at the COOH terminus adds to the structural stability by packing against a hydrophobic pocket created by the folding of the NH2 and COOH-terminal Ca(2+)-binding domain pairs. The first and second domains show different helix-packing arrangements from any previously described for Ca(2+)-binding proteins.

Literature references that cite this PDB file's key reference

PubMed id

Reference

19720824

S.Dobney, D.Chiasson, P.Lam, S.P.Smith, and W.A.Snedden (2009).
The calmodulin-related calcium sensor CML42 plays a role in trichome branching.

J Biol Chem, 284, 31647-31657.

16700049

C.A.Bottoms, T.A.White, and J.J.Tanner (2006).
Exploring structurally conserved solvent sites in protein families.

Proteins, 64, 404-421.

15819893

G.Rabah, R.Popescu, J.A.Cox, Y.Engelborghs, and C.T.Craescu (2005).
Solution structure and internal dynamics of NSCP, a compact calcium-binding protein.

FEBS J, 272, 2022-2036.

PDB code:

1q80

16147998

J.N.Wingard, J.Chan, I.Bosanac, F.Haeseleer, K.Palczewski, M.Ikura, and J.B.Ames (2005).
Structural analysis of Mg2+ and Ca2+ binding to CaBP1, a neuron-specific regulator of calcium channels.

J Biol Chem, 280, 37461-37470.

12755706

H.Tossavainen, P.Permi, A.Annila, I.Kilpeläinen, and T.Drakenberg (2003).
NMR solution structure of calerythrin, an EF-hand calcium-binding protein from Saccharopolyspora erythraea.

Eur J Biochem, 270, 2505-2512.

PDB code:

1nya

11909870

R.A.Maxwell, W.H.Welch, F.M.Horodyski, K.M.Schegg, and D.A.Schooley (2002).
Juvenile hormone diol kinase. II. Sequencing, cloning, and molecular modeling of juvenile hormone-selective diol kinase from Manduca sexta.

J Biol Chem, 277, 21882-21890.

11266596

H.Aitio, T.Laakso, T.Pihlajamaa, M.Torkkeli, I.Kilpeläinen, T.Drakenberg, R.Serimaa, and A.Annila (2001).
Characterization of apo and partially saturated states of calerythrin, an EF-hand protein from S. erythraea: a molten globule when deprived of Ca(2+).

Protein Sci, 10, 74-82.

11733019

M.Palczewska, P.Groves, A.Ambrus, A.Kaleta, K.E.Kövér, G.Batta, and J.Kuźnicki (2001).
Structural and biochemical characterization of neuronal calretinin domain I-II (residues 1-100). Comparison to homologous calbindin D28k domain I-II (residues 1-93).

Eur J Biochem, 268, 6229-6237.

10739258

A.Sillen, J.F.Díaz, and Y.Engelborghs (2000).
A step toward the prediction of the fluorescence lifetimes of tryptophan residues in proteins based on structural and spectral data.

Protein Sci, 9, 158-169.

10842334

P.Christova, J.A.Cox, and C.T.Craescu (2000).
Ion-induced conformational and stability changes in Nereis sarcoplasmic calcium binding protein: evidence that the APO state is a molten globule.

Proteins, 40, 177-184.

10822252

P.M.Hwang, and H.J.Vogel (2000).
Structures of the platelet calcium- and integrin-binding protein and the alphaIIb-integrin cytoplasmic domain suggest a mechanism for calcium-regulated recognition; homology modelling and NMR studies.

J Mol Recognit, 13, 83-92.

PDB codes:

1dgu 1dgv

11152121

T.Berggård, E.Thulin, K.S.Akerfeldt, and S.Linse (2000).
Fragment complementation of calbindin D28k.

Protein Sci, 9, 2094-2108.

10631973

H.Aitio, A.Annila, S.Heikkinen, E.Thulin, T.Drakenberg, and I.Kilpeläinen (1999).
NMR assignments, secondary structure, and global fold of calerythrin, an EF-hand calcium-binding protein from Saccharopolyspora erythraea.

Protein Sci, 8, 2580-2588.

10591109

K.L.Yap, J.B.Ames, M.B.Swindells, and M.Ikura (1999).
Diversity of conformational states and changes within the EF-hand protein superfamily.

Proteins, 37, 499-507.

9519411

S.P.Smith, and G.S.Shaw (1998).
A novel calcium-sensitive switch revealed by the structure of human S100B in the calcium-bound form.

Structure, 6, 211-222.

PDB code:

1uwo

9041633

P.Groves, S.Linse, E.Thulin, and S.Forsén (1997).
A calbindin D9k mutant containing a novel structural extension: 1H nuclear magnetic resonance studies.

Protein Sci, 6, 323-330.

9385641

S.Linse, E.Thulin, L.K.Gifford, D.Radzewsky, J.Hagan, R.R.Wilk, and K.S.Akerfeldt (1997).
Domain organization of calbindin D28k as determined from the association of six synthetic EF-hand fragments.

Protein Sci, 6, 2385-2396.

7896823

A.C.da Silva, J.Kendrick-Jones, and F.C.Reinach (1995).
Determinants of ion specificity on EF-hands sites. Conversion of the Ca2+/Mg2+ site of smooth muscle myosin regulatory light chain into a Ca(2+)-specific site.

J Biol Chem, 270, 6773-6778.

7592474

C.J.Morris, Y.M.Kim, K.E.Perkins, and M.E.Lidstrom (1995).
Identification and nucleotide sequences of mxaA, mxaC, mxaK, mxaL, and mxaD genes from Methylobacterium extorquens AM1.

J Bacteriol, 177, 6825-6831.

7899550

J.J.Falke, S.K.Drake, A.L.Hazard, and O.B.Peersen (1994).
Molecular tuning of ion binding to calcium signaling proteins.

Q Rev Biophys, 27, 219-290.

8341712

S.Raghunathan, R.J.Chandross, B.P.Cheng, A.Persechini, S.E.Sobottka, and R.H.Kretsinger (1993).
The linker of des-Glu84-calmodulin is bent.

Proc Natl Acad Sci U S A, 90, 6869-6873.

PDB code:

1deg

1423614

T.N.Davis (1992).
What's new with calcium?

Cell, 71, 557-564.

1511682

Y.Luan-Rilliet, M.Milos, and J.A.Cox (1992).
Thermodynamics of cation binding to Nereis sarcoplasmic calcium-binding protein. Direct binding studies, microcalorimetry and conformational changes.

Eur J Biochem, 208, 133-138.

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.