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NMR Structure - model 1 (Jmol Viewer)

NMR Structure - model 1, sites (Jmol Viewer)

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Title :   SOLUTION STRUCTURE OF CA2+/CALMODULIN BOUND TO THE C-TERMINAL DOMAIN OF PETUNIA GLUTAMATE DECARBOXYLASE

Authors :   K. L. Yap, T. Yuan, T. K. Mal, H. J. Vogel, M. Ikura

Date :   06 Feb 03 (Deposition) - 08 Apr 03 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B,C  (20x)

Keywords :   Calmodulin-Peptide Complex, Calmodulin, Gad, Glutamate Decarboxylase, Dimer, Nmr, Binding Protein/Hydrolase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. L. Yap, T. Yuan, T. K. Mal, H. J. Vogel, M. Ikura
Structural Basis For Simultaneous Binding Of Two Carboxy-Terminal Peptides Of Plant Glutamate Decarboxylase To Calmodulin
J. Mol. Biol. V. 328 193 2003
PubMed-ID: 12684008 | Reference-DOI: 10.1016/S0022-2836(03)00271-7
(for further references see the PDB file header)

Molecule 1 - CALMODULIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PAS
	Expression System Strain	:	AR58
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	(CALM1 OR CAM1 OR CALM OR CAM) AND (CALM2 OR CAM2 OR CAMB) AND (CALM3 OR CAM3 OR CAMC)
	Organism Common	:	AFRICAN CLAWED FROG
	Organism Scientific	:	XENOPUS LAEVIS
	Organism Taxid	:	8355

Molecule 2 - GLUTAMATE DECARBOXYLASE
	Chains	:	B, C
	EC Number	:	4.1.1.15
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PGEX-2T
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINAL CALMODULIN BINDING DOMAIN (RESIDUES 470-495)
	Gene	:	GAD
	Organism Scientific	:	PETUNIA X HYBRIDA
	Organism Taxid	:	4102
	Synonym	:	GAD


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

NMR Structure (1, 4)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION

NMR Structure (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:22 , ASP A:24 , THR A:26 , GLU A:31	BINDING SITE FOR RESIDUE CA A 149
2	AC2	SOFTWARE	ASP A:58 , THR A:62 , ASP A:64 , GLU A:67	BINDING SITE FOR RESIDUE CA A 150
3	AC3	SOFTWARE	ASP A:93 , ASN A:97 , TYR A:99 , ILE A:100 , SER A:101 , GLU A:104 , GLN A:135	BINDING SITE FOR RESIDUE CA A 151
4	AC4	SOFTWARE	ASP A:129 , ASP A:131 , GLY A:132 , ASP A:133 , GLN A:135 , GLU A:140	BINDING SITE FOR RESIDUE CA A 152

(no "SS Bond" information available for 1NWD)

(no "Cis Peptide Bond" information available for 1NWD)

(no "SAP(SNP)/Variant" information available for 1NWD)

NMR Structure (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	CAM2B_XENLA	8-43 44-79 81-116 117-149	4	A:7-42 A:43-78 A:80-115 A:116-148
				CAM2A_XENLA	8-43 44-79 81-116 117-149	4	A:7-42 A:43-78 A:80-115 A:116-148
				CALM1_XENLA	8-43 44-79 81-116 117-149	4	A:7-42 A:43-78 A:80-115 A:116-148
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	CAM2B_XENLA	21-33 57-69 94-106 130-142	4	A:20-32 A:56-68 A:93-105 A:129-141
				CAM2A_XENLA	21-33 57-69 94-106 130-142	4	A:20-32 A:56-68 A:93-105 A:129-141
				CALM1_XENLA	21-33 57-69 94-106 130-142	4	A:20-32 A:56-68 A:93-105 A:129-141

(no "Exon" information available for 1NWD)

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:148
 aligned with CALM1_XENLA | P0DP33 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:148
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141        
          CALM1_XENLA     2 ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK 149
               SCOP domains d1nwda_ A: Calmodulin                                                                                                                                SCOP domains
               CATH domains ----1nwdA01 A:5-78 EF-hand                                                    1nwdA02 A:79-148 EF-hand                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhh.....eehhhhhhhhhhhhh...hhhhhhhhhhh........eehhhhhhhhh.......hhhhhhhhhhhhh.......hhhhhhhhhhhhhh...hhhhhhh............hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ------EF_HAND_2  PDB: A:7-42 UniProt: 8-43EF_HAND_2  PDB: A:43-78             -EF_HAND_2  PDB: A:80-115            EF_HAND_2  PDB: A:116-148         PROSITE (3)
                PROSITE (4) ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (5)
                PROSITE (6) -------------------EF_HAND_1    -----------------------EF_HAND_1    ------------------------EF_HAND_1    -----------------------EF_HAND_1    ------- PROSITE (6)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nwd A   1 ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK 148
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain A from PDB  Type:PROTEIN  Length:148
 aligned with CAM2A_XENLA | P0DP34 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:148
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141        
          CAM2A_XENLA     2 ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK 149
               SCOP domains d1nwda_ A: Calmodulin                                                                                                                                SCOP domains
               CATH domains ----1nwdA01 A:5-78 EF-hand                                                    1nwdA02 A:79-148 EF-hand                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhh.....eehhhhhhhhhhhhh...hhhhhhhhhhh........eehhhhhhhhh.......hhhhhhhhhhhhh.......hhhhhhhhhhhhhh...hhhhhhh............hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------EF_HAND_2  PDB: A:7-42 UniProt: 8-43EF_HAND_2  PDB: A:43-78             -EF_HAND_2  PDB: A:80-115            EF_HAND_2  PDB: A:116-148         PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) -------------------EF_HAND_1    -----------------------EF_HAND_1    ------------------------EF_HAND_1    -----------------------EF_HAND_1    ------- PROSITE (4)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nwd A   1 ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK 148
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain A from PDB  Type:PROTEIN  Length:148
 aligned with CAM2B_XENLA | P0DP35 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:148
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141        
          CAM2B_XENLA     2 ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK 149
               SCOP domains d1nwda_ A: Calmodulin                                                                                                                                SCOP domains
               CATH domains ----1nwdA01 A:5-78 EF-hand                                                    1nwdA02 A:79-148 EF-hand                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhh.....eehhhhhhhhhhhhh...hhhhhhhhhhh........eehhhhhhhhh.......hhhhhhhhhhhhh.......hhhhhhhhhhhhhh...hhhhhhh............hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------EF_HAND_2  PDB: A:7-42 UniProt: 8-43EF_HAND_2  PDB: A:43-78             -EF_HAND_2  PDB: A:80-115            EF_HAND_2  PDB: A:116-148         PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) -------------------EF_HAND_1    -----------------------EF_HAND_1    ------------------------EF_HAND_1    -----------------------EF_HAND_1    ------- PROSITE (5)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nwd A   1 ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK 148
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain B from PDB  Type:PROTEIN  Length:28
 aligned with DCE_PETHY | Q07346 from UniProtKB/Swiss-Prot  Length:500

    Alignment length:30
                                   475       485       495
            DCE_PETHY   466 GSEVHKKTDSEVQLEMITAWKKFVEEKKKK 495
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author ..--...hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
                 Transcript ------------------------------ Transcript
                 1nwd B   1 GS--HKKTDSEVQLEMITAWKKFVEEKKKK  28
                             |  |    8        18        28
                             2  3

Chain C from PDB  Type:PROTEIN  Length:28
 aligned with DCE_PETHY | Q07346 from UniProtKB/Swiss-Prot  Length:500

    Alignment length:30
                                   475       485       495
            DCE_PETHY   466 GSEVHKKTDSEVQLEMITAWKKFVEEKKKK 495
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author ..--...hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
                 Transcript ------------------------------ Transcript
                 1nwd C   1 GS--HKKTDSEVQLEMITAWKKFVEEKKKK  28
                             |  |    8        18        28
                             2  3

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 '\|'

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: EF Hand-like (739)

Superfamily: EF-hand (657)

Family: Calmodulin-like (356)

Protein domain: Calmodulin (152)

African clawed frog (Xenopus laevis) [TaxId: 8355] (13)

d1nwda_

NMR Structure

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Recoverin; domain 1 (474)

Homologous Superfamily: EF-hand (412)

African clawed frog (Xenopus laevis) (12)

1a	1nwdA01	A:5-78
1b	1nwdA02	A:79-148

(no "Pfam Domain" information available for 1NWD)

NMR Structure(hide GO term definitions)

Chain A (CAM2B_XENLA | P0DP35)

Chain A (CALM1_XENLA | P0DP33)

Chain A (CAM2A_XENLA | P0DP34)

Chain B,C (DCE_PETHY | Q07346)

molecular function
	GO:0005516	calmodulin binding	Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
	GO:0016831	carboxy-lyase activity	Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0004351	glutamate decarboxylase activity	Catalysis of the reaction: L-glutamate = 4-aminobutanoate + CO2.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0030170	pyridoxal phosphate binding	Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
biological process
	GO:0019752	carboxylic acid metabolic process	The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
	GO:0006536	glutamate metabolic process	The chemical reactions and pathways involving glutamate, the anion of 2-aminopentanedioic acid.

NMR Structure
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(no "Related Entries Specified in the PDB File" available for 1NWD)

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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