2COL - JenaLib

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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE ANALYSIS OF CYAA/C-CAM WITH PYROPHOSPHATE

Authors :   Q. Guo, W. J. Tang, Y. Shen

Date :   18 May 05 (Deposition) - 24 Jan 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym./Biol. Unit : A,B

Keywords :   Lyase, Calcium Binding, Lyase/Metal Binding Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Q. Guo, Y. Shen, Y. S. Lee, C. S. Gibbs, M. Mrksich, W. J. Tang
Structural Basis For The Interaction Of Bordetella Pertussis Adenylyl Cyclase Toxin With Calmodulin
Embo J. V. 24 3190 2005
PubMed-ID: 16138079 | Reference-DOI: 10.1038/SJ.EMBOJ.7600800
(for further references see the PDB file header)

Molecule 1 - BIFUNCTIONAL HEMOLYSIN-ADENYLATE CYCLASE
	Chains	:	A
	EC Number	:	4.6.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	BORDETELLA PERTUSSIS
	Organism Taxid	:	520
	Synonym	:	ADENYLYL CYCALSE, CYCLOLYSIN, ACT, AC-HLY

Molecule 2 - CALMODULIN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	AFRICAN CLAWED FROG
	Organism Scientific	:	XENOPUS LAEVIS
	Organism Taxid	:	8355

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 5)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	MG	2	Ligand/Ion	MAGNESIUM ION
3	POP	1	Ligand/Ion	PYROPHOSPHATE 2-

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP B:129 , ASP B:131 , ASP B:133 , GLN B:135 , GLU B:140 , HOH B:803	BINDING SITE FOR RESIDUE CA B 800
2	AC2	SOFTWARE	ASP B:93 , ASP B:95 , ASN B:97 , TYR B:99 , GLU B:104	BINDING SITE FOR RESIDUE CA B 801
3	AC3	SOFTWARE	ASP A:188 , ASP A:190 , HIS A:298 , HOH A:964	BINDING SITE FOR RESIDUE MG A 907
4	AC4	SOFTWARE	ASP A:188 , ILE A:189 , VAL A:296 , GLN A:297 , HIS A:298	BINDING SITE FOR RESIDUE MG A 908
5	AC5	SOFTWARE	LYS A:58 , LYS A:65 , ASP A:190 , HOH A:964	BINDING SITE FOR RESIDUE POP A 893

(no "SS Bond" information available for 2COL)

(no "Cis Peptide Bond" information available for 2COL)

(no "SAP(SNP)/Variant" information available for 2COL)

Asymmetric/Biological Unit (2, 4)

	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	2	- - B:80-115 B:116-145
				CAM2A_XENLA	8-43 44-79 81-116 117-149	2	- - B:80-115 B:116-145
				CALM1_XENLA	8-43 44-79 81-116 117-149	2	- - B:80-115 B:116-145
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	CAM2B_XENLA	21-33 57-69 94-106 130-142	2	- - B:93-105 B:129-141
				CAM2A_XENLA	21-33 57-69 94-106 130-142	2	- - B:93-105 B:129-141
				CALM1_XENLA	21-33 57-69 94-106 130-142	2	- - B:93-105 B:129-141

(no "Exon" information available for 2COL)

Asymmetric/Biological Unit

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:349
 aligned with CYAA_BORP1 | J7QLC0 from UniProtKB/Swiss-Prot  Length:1706

    Alignment length:356
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356      
           CYAA_BORP1     7 AGYANAADRESGIPAAVLDGIKAVAKEKNATLMFRLVNPHSTSLIAEGVATKGLGVHAKSSDWGLQAGYIPVNPNLSKLFGRAPEVIARADNDVNSSLAHGHTAVDLTLSKERLDYLRQAGLVTGMADGVVASNHAGYEQFEFRVKETSDGRYAVQYRRKGGDDFEAVKVIGNAAGIPLTADIDMFAIMPHLSNFRDSARSSVTSGDSVTDYLARTRRAASEATGGLDRERIDLLWKIARAGARSAVGTEARRQFRYDGDMNIGVITDFELEVRNALNRRAHAVGAQDVVQHGTEQNNPFPEADEKIFVVSATGESQMLTRGQLKEYIGQQRGEGYVFYENRAYGVAGKSLFDDGL 362
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhh..hhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhh.ee...............................hhhhhhhhhhhhhhhhhh..eeee.eehhhhhhhhhhh..............hhhhh.eeeeee......eeeeeee......ee.eeee......ee....eeeeee.hhhhhhhhhhhhh...hhhhhhhhhh..-------.hhhhhhhhhhhhhhhhhhhh.hhhhhh..ee..ee....hhhhhhhhhhhhhhhhhh.........hhhhh........eeee.....eeeehhhhhhhhhhhhhhh...................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2col A   7 AGYANAADRESGIPAAVLDGIKAVAKEKNATLMFRLVNPHSTSLIAEGVATKGLGVHAKSSDWGLQAGYIPVNPNLSKLFGRAPEVIARADNDVNSSLAHGHTAVDLTLSKERLDYLRQAGLVTGMADGVVASNHAGYEQFEFRVKETSDGRYAVQYRRKGGDDFEAVKVIGNAAGIPLTADIDMFAIMPHLSNFRDSARSSVTSGDSVTDYLARTRRA-------LDRERIDLLWKIARAGARSAVGTEARRQFRYDGDMNIGVITDFELEVRNALNRRAHAVGAQDVVQHGTEQNNPFPEADEKIFVVSATGESQMLTRGQLKEYIGQQRGEGYVFYENRAYGVAGKSLFDDGL 362
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216        |-      |236       246       256       266       276       286       296       306       316       326       336       346       356      
                                                                                                                                                                                                                                                    225     233

Chain A from PDB  Type:PROTEIN  Length:349
 aligned with CYAA_BORPE | P0DKX7 from UniProtKB/Swiss-Prot  Length:1706

    Alignment length:356
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356      
           CYAA_BORPE     7 AGYANAADRESGIPAAVLDGIKAVAKEKNATLMFRLVNPHSTSLIAEGVATKGLGVHAKSSDWGLQAGYIPVNPNLSKLFGRAPEVIARADNDVNSSLAHGHTAVDLTLSKERLDYLRQAGLVTGMADGVVASNHAGYEQFEFRVKETSDGRYAVQYRRKGGDDFEAVKVIGNAAGIPLTADIDMFAIMPHLSNFRDSARSSVTSGDSVTDYLARTRRAASEATGGLDRERIDLLWKIARAGARSAVGTEARRQFRYDGDMNIGVITDFELEVRNALNRRAHAVGAQDVVQHGTEQNNPFPEADEKIFVVSATGESQMLTRGQLKEYIGQQRGEGYVFYENRAYGVAGKSLFDDGL 362
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhh..hhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhh.ee...............................hhhhhhhhhhhhhhhhhh..eeee.eehhhhhhhhhhh..............hhhhh.eeeeee......eeeeeee......ee.eeee......ee....eeeeee.hhhhhhhhhhhhh...hhhhhhhhhh..-------.hhhhhhhhhhhhhhhhhhhh.hhhhhh..ee..ee....hhhhhhhhhhhhhhhhhh.........hhhhh........eeee.....eeeehhhhhhhhhhhhhhh...................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2col A   7 AGYANAADRESGIPAAVLDGIKAVAKEKNATLMFRLVNPHSTSLIAEGVATKGLGVHAKSSDWGLQAGYIPVNPNLSKLFGRAPEVIARADNDVNSSLAHGHTAVDLTLSKERLDYLRQAGLVTGMADGVVASNHAGYEQFEFRVKETSDGRYAVQYRRKGGDDFEAVKVIGNAAGIPLTADIDMFAIMPHLSNFRDSARSSVTSGDSVTDYLARTRRA-------LDRERIDLLWKIARAGARSAVGTEARRQFRYDGDMNIGVITDFELEVRNALNRRAHAVGAQDVVQHGTEQNNPFPEADEKIFVVSATGESQMLTRGQLKEYIGQQRGEGYVFYENRAYGVAGKSLFDDGL 362
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216        |-      |236       246       256       266       276       286       296       306       316       326       336       346       356      
                                                                                                                                                                                                                                                    225     233

Chain B from PDB  Type:PROTEIN  Length:67
 aligned with CALM1_XENLA | P0DP33 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:67
                                    89        99       109       119       129       139       
          CALM1_XENLA    80 TDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMM 146
               SCOP domains d2colb_ B: automated matches                                        SCOP domains
               CATH domains 2colB00 B:79-145 EF-hand                                            CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhhh.......hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -EF_HAND_2  PDB: B:80-115            EF_HAND_2  PDB: B:116-145      PROSITE (3)
                PROSITE (4) ------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) ------------------------------------------------------------------- PROSITE (5)
                PROSITE (6) --------------EF_HAND_1    -----------------------EF_HAND_1    ---- PROSITE (6)
                 Transcript ------------------------------------------------------------------- Transcript
                 2col B  79 TDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMM 145
                                    88        98       108       118       128       138

Chain B from PDB  Type:PROTEIN  Length:67
 aligned with CAM2A_XENLA | P0DP34 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:67
                                    89        99       109       119       129       139       
          CAM2A_XENLA    80 TDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMM 146
               SCOP domains d2colb_ B: automated matches                                        SCOP domains
               CATH domains 2colB00 B:79-145 EF-hand                                            CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhhh.......hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -EF_HAND_2  PDB: B:80-115            EF_HAND_2  PDB: B:116-145      PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) ------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) --------------EF_HAND_1    -----------------------EF_HAND_1    ---- PROSITE (5)
                 Transcript ------------------------------------------------------------------- Transcript
                 2col B  79 TDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMM 145
                                    88        98       108       118       128       138

Chain B from PDB  Type:PROTEIN  Length:67
 aligned with CAM2B_XENLA | P0DP35 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:67
                                    89        99       109       119       129       139       
          CAM2B_XENLA    80 TDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMM 146
               SCOP domains d2colb_ B: automated matches                                        SCOP domains
               CATH domains 2colB00 B:79-145 EF-hand                                            CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhhh.......hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -EF_HAND_2  PDB: B:80-115            EF_HAND_2  PDB: B:116-145      PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) --------------EF_HAND_1    -----------------------EF_HAND_1    ---- PROSITE (4)
                 Transcript ------------------------------------------------------------------- Transcript
                 2col B  79 TDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMM 145
                                    88        98       108       118       128       138

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 '\|'

Asymmetric/Biological Unit

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: automated matches (54)

African clawed frog (Xenopus laevis) [TaxId: 8355] (3)

d2colb_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Recoverin; domain 1 (474)

Homologous Superfamily: EF-hand (412)

Bordetella pertussis. Organism_taxid: 520. (2)

2colB00

B:79-145

(no "Pfam Domain" information available for 2COL)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CYAA_BORPE | P0DKX7)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004016	adenylate cyclase activity	Catalysis of the reaction: ATP = 3',5'-cyclic AMP + diphosphate.
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0008294	calcium- and calmodulin-responsive adenylate cyclase activity	Catalysis of the reaction: ATP = 3',5'-cyclic AMP + diphosphate, stimulated by calcium-bound calmodulin.
	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: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:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
	GO:0006171	cAMP biosynthetic process	The chemical reactions and pathways resulting in the formation of the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
	GO:0019835	cytolysis	The rupture of cell membranes and the loss of cytoplasm.
	GO:0044179	hemolysis in other organism	The cytolytic destruction of red blood cells, with the release of intracellular hemoglobin, in one organism by another.
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	GO:0007204	positive regulation of cytosolic calcium ion concentration	Any process that increases the concentration of calcium ions in the cytosol.
cellular component
	GO:0005623	cell	The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Chain A (CYAA_BORP1 | J7QLC0)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004016	adenylate cyclase activity	Catalysis of the reaction: ATP = 3',5'-cyclic AMP + diphosphate.
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0008294	calcium- and calmodulin-responsive adenylate cyclase activity	Catalysis of the reaction: ATP = 3',5'-cyclic AMP + diphosphate, stimulated by calcium-bound calmodulin.
	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: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:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
	GO:0006171	cAMP biosynthetic process	The chemical reactions and pathways resulting in the formation of the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
	GO:0019835	cytolysis	The rupture of cell membranes and the loss of cytoplasm.
	GO:0044179	hemolysis in other organism	The cytolytic destruction of red blood cells, with the release of intracellular hemoglobin, in one organism by another.
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Chain B (CAM2B_XENLA | P0DP35)

Chain B (CAM2A_XENLA | P0DP34)

Chain B (CALM1_XENLA | P0DP33)

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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2col)

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(no "Related Entries Specified in the PDB File" available for 2COL)

Description

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Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

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SCOP Domains (1, 1)

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Gene Ontology (17, 30)

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