4BYA - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - model 1, sites (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   CALMODULIN, C-TERMINAL DOMAIN, M144H MUTANT

Authors :   Y. S. Moroz, Y. Wu, N. A. J. Van Nuland, I. V. Korendovych

Date :   18 Jul 13 (Deposition) - 18 Jun 14 (Release) - 16 Dec 15 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)
NMR Structure *: A  (1x)

Keywords :   Calmodulin, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. S. Moroz, T. T. Dunston, O. V. Makhlynets, O. V. Moroz, Y. Wu, J. H. Yoon, A. B. Olsen, J. M. Mclaughlin, K. L. Mack, P. M. Gosavi, N. A. J. Van Nuland, I. V. Korendovych
New Tricks For Old Proteins: Single Mutations In A Nonenzymatic Protein Give Rise To Various Enzymatic Activities.
J. Am. Chem. Soc. V. 137 14905 2015
PubMed-ID: 26555770 | Reference-DOI: 10.1021/JACS.5B07812

Molecule 1 - CALMODULIN, C-TERMINAL DOMAIN, M144H MUTANT
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PEXP5-NT/TOPO
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	PLYSS
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINAL DOMAIN, RESIDUES 76-144
	Mutation	:	YES
	Organism Common	:	BANTAM, CHICKENS
	Organism Scientific	:	GALLUS GALLUS
	Organism Taxid	:	9031

		1
NMR Structure (20x)	:	A
NMR Structure * (1x)	:	A

Summary Information (see also Sequences/Alignments below)

NMR Structure (1, 2)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION

NMR Structure * (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

NMR Structure (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:20 , ASP A:22 , ASN A:24 , TYR A:26 , GLU A:31	BINDING SITE FOR RESIDUE CA A 76
2	AC2	SOFTWARE	ASP A:56 , ASP A:58 , ASP A:60 , GLN A:62 , ASN A:64 , GLU A:67	BINDING SITE FOR RESIDUE CA A 77

(no "SS Bond" information available for 4BYA)

(no "Cis Peptide Bond" information available for 4BYA)

(no "SAP(SNP)/Variant" information available for 4BYA)

NMR Structure (2, 5)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	CALM_CHICK	8-43 44-79 81-116 117-149	3	- A:3-5 A:7-42 A:43-75
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	CALM_CHICK	21-33 57-69 94-106 130-142	2	- - A:20-32 A:56-68

NMR Structure * (2, 5)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	CALM_CHICK	8-43 44-79 81-116 117-149	3	- A:3-5 A:7-42 A:43-75
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	CALM_CHICK	21-33 57-69 94-106 130-142	2	- - A:20-32 A:56-68

NMR Structure (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2a	ENSGALT00000016279	2a	ENSGALE00000108322	chr3:28345291-28345260	32	F2Z4K8_CHICK	1-11	11	0	-	-
1.3b	ENSGALT00000016279	3b	ENSGALE00000108320	chr3:28340224-28340081	144	F2Z4K8_CHICK	11-59	49	1	A:1-2	2
1.4	ENSGALT00000016279	4	ENSGALE00000108321	chr3:28340004-28339898	107	F2Z4K8_CHICK	59-94	36	1	A:3-28	26
1.5a	ENSGALT00000016279	5a	ENSGALE00000108319	chr3:28339027-28338892	136	F2Z4K8_CHICK	95-140	46	1	A:29-73 (gaps)	46
1.6a	ENSGALT00000016279	6a	ENSGALE00000108317	chr3:28337689-28337661	29	F2Z4K8_CHICK	140-148	9	1	A:73-75	3

NMR Structure

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:75
 aligned with CALM_CHICK | P62149 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:111
                                    48        58        68        78        88        98       108       118       128       138       148 
           CALM_CHICK    39 SLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK 149
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..------------------------------------......hhhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhhhhhhhhhh.......hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) EF_HAEF_HAND_2  PDB: A:3-5 UniProt: 44-79-EF_HAND_2  PDB: A:7-42              EF_HAND_2  PDB: A:43-75           PROSITE (1)
                PROSITE (2) ------------------EF_HAND_1    ------------------------EF_HAND_1    -----------------------EF_HAND_1    ------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 4bya A   1 SL------------------------------------MKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQHMTAK  75
                             |       -         -         -        |4        14        24        34        44        54        64        74 
                             2                                    3

Chain A from PDB  Type:PROTEIN  Length:75
 aligned with F2Z4K8_CHICK | F2Z4K8 from UniProtKB/TrEMBL  Length:142

    Alignment length:112
                                    40        50        60        70        80        90       100       110       120       130       140  
         F2Z4K8_CHICK    31 SLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEVQLFTYFFVY 142
               SCOP domains ---------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..------------------------------------......hhhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhhhhhhhhhh.......hhh-hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3b  PDB: A:1-2        -----------------------------------Exon 1.5a  PDB: A:29-73 (gaps) UniProt: 95-140-- Transcript 1 (1)
           Transcript 1 (2) ----------------------------Exon 1.4  PDB: A:3-28 UniProt: 59-94---------------------------------------------1.6 Transcript 1 (2)
                 4bya A   1 SL------------------------------------MKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYE-EFVQHMTAK  75
                             |       -         -         -        |4        14        24        34        44        54        64 | |    73  
                             2                                    3                                                             66 |        
                                                                                                                                  67

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 4BYA)

(no "CATH Domain" information available for 4BYA)

(no "Pfam Domain" information available for 4BYA)

NMR Structure(hide GO term definitions)

Chain A (F2Z4K8_CHICK | F2Z4K8)

molecular function
	GO:0031997	N-terminal myristoylation domain binding	Interacting selectively and non-covalently with the N-terminus of a protein that has the potential to be, or has been, modified by N-terminal myristoylation. Binding affinity is typically altered by myristoylation; for example, N-terminal myristoylation of HIV Nef increases its affinity for calmodulin.
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0044325	ion channel binding	Interacting selectively and non-covalently with one or more specific sites on an ion channel, a protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient.
	GO:0043274	phospholipase binding	Interacting selectively and non-covalently with any phospholipase, enzymes that catalyze of the hydrolysis of a glycerophospholipid.
	GO:0019904	protein domain specific binding	Interacting selectively and non-covalently with a specific domain of a protein.
	GO:0019901	protein kinase binding	Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
	GO:0072542	protein phosphatase activator activity	Increases the activity of a protein phosphatase, an enzyme which catalyzes of the removal of a phosphate group from a protein substrate molecule.
	GO:0031996	thioesterase binding	Interacting selectively and non-covalently with any thioesterase enzyme.
	GO:0031432	titin binding	Interacting selectively and non-covalently with titin, any of a family of giant proteins found in striated and smooth muscle. In striated muscle, single titin molecules span half the sarcomere, with their N- and C-termini in the Z-disc and M-line, respectively.
biological process
	GO:0005513	detection of calcium ion	The series of events in which a calcium ion stimulus is received by a cell and converted into a molecular signal.
	GO:0030801	positive regulation of cyclic nucleotide metabolic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving cyclic nucleotides.
	GO:0051343	positive regulation of cyclic-nucleotide phosphodiesterase activity	Any process that activates or increases the frequency, rate or extent of cyclic nucleotide phosphodiesterase activity, the catalysis of the reaction: nucleotide 3',5'-cyclic phosphate + H2O = nucleotide 5'-phosphate.
	GO:0032516	positive regulation of phosphoprotein phosphatase activity	Any process that activates or increases the activity of a phosphoprotein phosphatase.
	GO:0035307	positive regulation of protein dephosphorylation	Any process that activates or increases the frequency, rate or extent of removal of phosphate groups from a protein.
	GO:0060316	positive regulation of ryanodine-sensitive calcium-release channel activity	Any process that increases the activity of a ryanodine-sensitive calcium-release channel. The ryanodine-sensitive calcium-release channel catalyzes the transmembrane transfer of a calcium ion by a channel that opens when a ryanodine class ligand has been bound by the channel complex or one of its constituent parts.
	GO:0055117	regulation of cardiac muscle contraction	Any process that modulates the frequency, rate or extent of cardiac muscle contraction.
	GO:0032465	regulation of cytokinesis	Any process that modulates the frequency, rate or extent of the division of the cytoplasm of a cell and its separation into two daughter cells.
	GO:0002027	regulation of heart rate	Any process that modulates the frequency or rate of heart contraction.
	GO:0010880	regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum	Any process that modulates the rate, frequency or extent of release of sequestered calcium ion into cytosol by the sarcoplasmic reticulum, the process in which the release of sequestered calcium ion by sarcoplasmic reticulum into cytosol occurs via calcium release channels.
	GO:0051592	response to calcium ion	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a calcium ion stimulus.
	GO:0021762	substantia nigra development	The progression of the substantia nigra over time from its initial formation until its mature state. The substantia nigra is the layer of gray substance that separates the posterior parts of the cerebral peduncles (tegmentum mesencephali) from the anterior parts; it normally includes a posterior compact part with many pigmented cells (pars compacta) and an anterior reticular part whose cells contain little pigment (pars reticularis).
cellular component
	GO:0034704	calcium channel complex	An ion channel complex through which calcium ions pass.
	GO:0005813	centrosome	A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0030017	sarcomere	The repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs.
	GO:0005876	spindle microtubule	Any microtubule that is part of a mitotic or meiotic spindle; anchored at one spindle pole.
	GO:0000922	spindle pole	Either of the ends of a spindle, where spindle microtubules are organized; usually contains a microtubule organizing center and accessory molecules, spindle microtubules and astral microtubules.
	GO:0031982	vesicle	Any small, fluid-filled, spherical organelle enclosed by membrane.

Chain A (CALM_CHICK | P62149)

molecular function
	GO:0031997	N-terminal myristoylation domain binding	Interacting selectively and non-covalently with the N-terminus of a protein that has the potential to be, or has been, modified by N-terminal myristoylation. Binding affinity is typically altered by myristoylation; for example, N-terminal myristoylation of HIV Nef increases its affinity for calmodulin.
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0044325	ion channel binding	Interacting selectively and non-covalently with one or more specific sites on an ion channel, a protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0017022	myosin binding	Interacting selectively and non-covalently with any part of a myosin complex; myosins are any of a superfamily of molecular motor proteins that bind to actin and use the energy of ATP hydrolysis to generate force and movement along actin filaments.
	GO:0043274	phospholipase binding	Interacting selectively and non-covalently with any phospholipase, enzymes that catalyze of the hydrolysis of a glycerophospholipid.
	GO:0019904	protein domain specific binding	Interacting selectively and non-covalently with a specific domain of a protein.
	GO:0019901	protein kinase binding	Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
	GO:0072542	protein phosphatase activator activity	Increases the activity of a protein phosphatase, an enzyme which catalyzes of the removal of a phosphate group from a protein substrate molecule.
	GO:0031996	thioesterase binding	Interacting selectively and non-covalently with any thioesterase enzyme.
	GO:0031432	titin binding	Interacting selectively and non-covalently with titin, any of a family of giant proteins found in striated and smooth muscle. In striated muscle, single titin molecules span half the sarcomere, with their N- and C-termini in the Z-disc and M-line, respectively.
biological process
	GO:0005513	detection of calcium ion	The series of events in which a calcium ion stimulus is received by a cell and converted into a molecular signal.
	GO:0030801	positive regulation of cyclic nucleotide metabolic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving cyclic nucleotides.
	GO:0051343	positive regulation of cyclic-nucleotide phosphodiesterase activity	Any process that activates or increases the frequency, rate or extent of cyclic nucleotide phosphodiesterase activity, the catalysis of the reaction: nucleotide 3',5'-cyclic phosphate + H2O = nucleotide 5'-phosphate.
	GO:0032516	positive regulation of phosphoprotein phosphatase activity	Any process that activates or increases the activity of a phosphoprotein phosphatase.
	GO:0035307	positive regulation of protein dephosphorylation	Any process that activates or increases the frequency, rate or extent of removal of phosphate groups from a protein.
	GO:0060316	positive regulation of ryanodine-sensitive calcium-release channel activity	Any process that increases the activity of a ryanodine-sensitive calcium-release channel. The ryanodine-sensitive calcium-release channel catalyzes the transmembrane transfer of a calcium ion by a channel that opens when a ryanodine class ligand has been bound by the channel complex or one of its constituent parts.
	GO:0055117	regulation of cardiac muscle contraction	Any process that modulates the frequency, rate or extent of cardiac muscle contraction.
	GO:0032465	regulation of cytokinesis	Any process that modulates the frequency, rate or extent of the division of the cytoplasm of a cell and its separation into two daughter cells.
	GO:0002027	regulation of heart rate	Any process that modulates the frequency or rate of heart contraction.
	GO:0010880	regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum	Any process that modulates the rate, frequency or extent of release of sequestered calcium ion into cytosol by the sarcoplasmic reticulum, the process in which the release of sequestered calcium ion by sarcoplasmic reticulum into cytosol occurs via calcium release channels.
	GO:0051592	response to calcium ion	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a calcium ion stimulus.
	GO:0021762	substantia nigra development	The progression of the substantia nigra over time from its initial formation until its mature state. The substantia nigra is the layer of gray substance that separates the posterior parts of the cerebral peduncles (tegmentum mesencephali) from the anterior parts; it normally includes a posterior compact part with many pigmented cells (pars compacta) and an anterior reticular part whose cells contain little pigment (pars reticularis).
cellular component
	GO:0034704	calcium channel complex	An ion channel complex through which calcium ions pass.
	GO:0005813	centrosome	A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0030017	sarcomere	The repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs.
	GO:0005876	spindle microtubule	Any microtubule that is part of a mitotic or meiotic spindle; anchored at one spindle pole.
	GO:0000922	spindle pole	Either of the ends of a spindle, where spindle microtubules are organized; usually contains a microtubule organizing center and accessory molecules, spindle microtubules and astral microtubules.
	GO:0031982	vesicle	Any small, fluid-filled, spherical organelle enclosed by membrane.

NMR Structure
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(no "Related Entries Specified in the PDB File" available for 4BYA)

Description

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Ligands, Modified Residues, Ions (1, 2)

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SS Bonds (0, 0)

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