1YK9 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A MUTANT FORM OF THE MYCOBACTERIAL ADENYLYL CYCLASE RV1625C

Authors :   A. D. Ketkar, A. R. Shenoy, U. A. Ramagopal, S. S. Visweswariah, K. Suguna, Tb Structural Genomics Consortium (Tbsgc)

Date :   17 Jan 05 (Deposition) - 24 Jan 06 (Release) - 20 May 08 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym./Biol. Unit : A

Keywords :   Beta-Alpha-Beta Sandwich, Structural Genomics, Psi, Protein Structure Initiative, Tb Structural Genomics Consortium, Tbsgc, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. D. Ketkar, A. R. Shenoy, U. A. Ramagopal, S. S. Visweswariah, K. Suguna
A Structural Basis For The Role Of Nucleotide Specifying Residues In Regulating The Oligomerization Of The Rv1625C Adenylyl Cyclase From M. Tuberculosis
J. Mol. Biol. V. 356 904 2006
PubMed-ID: 16403515 | Reference-DOI: 10.1016/J.JMB.2005.12.017
(for further references see the PDB file header)

Molecule 1 - ADENYLATE CYCLASE
	Chains	:	A
	EC Number	:	4.6.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PRSET
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	RV1625C CATALYTIC DOMAIN
	Gene	:	RV1625C
	Mutation	:	YES
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	1773
	Synonym	:	ATP PYROPHOSPHATE-LYASE, ADENYLYL CYCLASE

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1YK9)

(no "Site" information available for 1YK9)

(no "SS Bond" information available for 1YK9)

Asymmetric/Biological Unit

No.	Residues
1	Asp A:335	-	Pro A:336

(no "SAP(SNP)/Variant" information available for 1YK9)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GUANYLATE_CYCLASE_2	PS50125	Guanylate cyclase domain profile.	CYA1_MYCBO	251-378	1	A:251-378
				CYA1_MYCTO	251-378	1	A:251-378
				CYA1_MYCTU	251-378	1	A:251-378
2	GUANYLATE_CYCLASE_1	PS00452	Guanylate cyclase signature.	CYA1_MYCBO	355-378	1	A:355-378
				CYA1_MYCTO	355-378	1	A:355-378
				CYA1_MYCTU	355-378	1	A:355-378

(no "Exon" information available for 1YK9)

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:184
 aligned with CYA1_MYCBO | P0A4Y1 from UniProtKB/Swiss-Prot  Length:443

    Alignment length:184
                                   254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424    
           CYA1_MYCBO   245 DKYDEASVLFADIVGFTERASSTAPADLVRFLDRLYSAFDELVDQHGLEKIKVSGDSYMVVSGVPRPRPDHTQALADFALDMTNVAAQLKDPRGNPVPLRVGLATGPVVAGVVGSRRFFYDVWGDAVNVASRMESTDSVGQIQVPDEVYERLKDDFVLRERGHINVKGKGVMRTWYLIGRKVAA 428
               SCOP domains d1yk9a_ A: automated matches                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Guanylate_cyc-1yk9A01 A:245-423                                                                                                                                                    ----- Pfam domains
         Sec.struct. author .....eeeeeeee................hhhhhhhh..hhhhh....ee.......eeee........hhhhhhhhhhhhhhhhh............eeeeeeee.eee...........eeehhhhhhhhhhhh.....ee.hhhhhhh....eeeee...............eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------GUANYLATE_CYCLASE_2  PDB: A:251-378 UniProt: 251-378                                                                            -------------------------------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (5)
                PROSITE (6) --------------------------------------------------------------------------------------------------------------GUANYLATE_CYCLASE_1     -------------------------------------------------- PROSITE (6)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yk9 A 245 DKYDEASVLFADIVGFTERASSTAPADLVRFLDRLYSAFDELVDQHGLEKIEVSGDSYMVVSGVPRPRPDHTQALADFALDMTNVAAQLKDPRGNPVPLRVGLATGPVVAGVVGSRRFRYCVWGDAVNVASRMESTDSVGQIQVPDEVYERLKDDFVLRERGHINVKGKGVMRTWYLIGRKVAA 428
                                   254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424

Chain A from PDB  Type:PROTEIN  Length:184
 aligned with CYA1_MYCTO | P9WQ34 from UniProtKB/Swiss-Prot  Length:443

    Alignment length:184
                                   254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424    
           CYA1_MYCTO   245 DKYDEASVLFADIVGFTERASSTAPADLVRFLDRLYSAFDELVDQHGLEKIKVSGDSYMVVSGVPRPRPDHTQALADFALDMTNVAAQLKDPRGNPVPLRVGLATGPVVAGVVGSRRFFYDVWGDAVNVASRMESTDSVGQIQVPDEVYERLKDDFVLRERGHINVKGKGVMRTWYLIGRKVAA 428
               SCOP domains d1yk9a_ A: automated matches                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Guanylate_cyc-1yk9A01 A:245-423                                                                                                                                                    ----- Pfam domains
         Sec.struct. author .....eeeeeeee................hhhhhhhh..hhhhh....ee.......eeee........hhhhhhhhhhhhhhhhh............eeeeeeee.eee...........eeehhhhhhhhhhhh.....ee.hhhhhhh....eeeee...............eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------GUANYLATE_CYCLASE_2  PDB: A:251-378 UniProt: 251-378                                                                            -------------------------------------------------- PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) --------------------------------------------------------------------------------------------------------------GUANYLATE_CYCLASE_1     -------------------------------------------------- PROSITE (5)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yk9 A 245 DKYDEASVLFADIVGFTERASSTAPADLVRFLDRLYSAFDELVDQHGLEKIEVSGDSYMVVSGVPRPRPDHTQALADFALDMTNVAAQLKDPRGNPVPLRVGLATGPVVAGVVGSRRFRYCVWGDAVNVASRMESTDSVGQIQVPDEVYERLKDDFVLRERGHINVKGKGVMRTWYLIGRKVAA 428
                                   254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424

Chain A from PDB  Type:PROTEIN  Length:184
 aligned with CYA1_MYCTU | P9WQ35 from UniProtKB/Swiss-Prot  Length:443

    Alignment length:184
                                   254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424    
           CYA1_MYCTU   245 DKYDEASVLFADIVGFTERASSTAPADLVRFLDRLYSAFDELVDQHGLEKIKVSGDSYMVVSGVPRPRPDHTQALADFALDMTNVAAQLKDPRGNPVPLRVGLATGPVVAGVVGSRRFFYDVWGDAVNVASRMESTDSVGQIQVPDEVYERLKDDFVLRERGHINVKGKGVMRTWYLIGRKVAA 428
               SCOP domains d1yk9a_ A: automated matches                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Guanylate_cyc-1yk9A01 A:245-423                                                                                                                                                    ----- Pfam domains
         Sec.struct. author .....eeeeeeee................hhhhhhhh..hhhhh....ee.......eeee........hhhhhhhhhhhhhhhhh............eeeeeeee.eee...........eeehhhhhhhhhhhh.....ee.hhhhhhh....eeeee...............eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ------GUANYLATE_CYCLASE_2  PDB: A:251-378 UniProt: 251-378                                                                            -------------------------------------------------- PROSITE (3)
                PROSITE (4) --------------------------------------------------------------------------------------------------------------GUANYLATE_CYCLASE_1     -------------------------------------------------- PROSITE (4)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yk9 A 245 DKYDEASVLFADIVGFTERASSTAPADLVRFLDRLYSAFDELVDQHGLEKIEVSGDSYMVVSGVPRPRPDHTQALADFALDMTNVAAQLKDPRGNPVPLRVGLATGPVVAGVVGSRRFRYCVWGDAVNVASRMESTDSVGQIQVPDEVYERLKDDFVLRERGHINVKGKGVMRTWYLIGRKVAA 428
                                   254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424

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: Alpha and beta proteins (a+b) (23004)

Fold: Ferredoxin-like (1795)

Superfamily: Nucleotide cyclase (51)

Family: automated matches (7)

Protein domain: automated matches (7)

Mycobacterium tuberculosis (1)

d1yk9a_

(no "CATH Domain" information available for 1YK9)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Nucleot_cyclase (14)

Family: Guanylate_cyc (8)

Mycobacterium tuberculosis (4)

Guanylate_cyc-1yk9A01

A:245-423

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CYA1_MYCBO | P0A4Y1)

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: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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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.
	GO:0016849	phosphorus-oxygen lyase activity	Catalysis of the cleavage of a phosphorus-oxygen bond by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond.
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:0009190	cyclic nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a cyclic nucleotide, a nucleotide in which the phosphate group is in diester linkage to two positions on the sugar residue.
	GO:0035556	intracellular signal transduction	The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain A (CYA1_MYCTU | P9WQ35)

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: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:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0030145	manganese ion binding	Interacting selectively and non-covalently with manganese (Mn) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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.
	GO:0016849	phosphorus-oxygen lyase activity	Catalysis of the cleavage of a phosphorus-oxygen bond by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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:0009190	cyclic nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a cyclic nucleotide, a nucleotide in which the phosphate group is in diester linkage to two positions on the sugar residue.
	GO:0035556	intracellular signal transduction	The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain A (CYA1_MYCTO | P9WQ34)

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: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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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.
	GO:0016849	phosphorus-oxygen lyase activity	Catalysis of the cleavage of a phosphorus-oxygen bond by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond.
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:0009190	cyclic nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a cyclic nucleotide, a nucleotide in which the phosphate group is in diester linkage to two positions on the sugar residue.
	GO:0035556	intracellular signal transduction	The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric/Biological Unit
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	Sites
(no "Sites" information available for 1yk9)

	Cis Peptide Bonds
		Asp A:335 - Pro A:336	[ RasMol ]

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	1yk9
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	CYA1_MYCTO \| P9WQ34
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	CYA1_MYCTU \| P9WQ35
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	CYA1_MYCTO \| P9WQ34	:	4p2f 4p2m 4p2x
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(no "Related Entries Specified in the PDB File" available for 1YK9)

Description

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Ligands, Modified Residues, Ions (0, 0)

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SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

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SCOP Domains (1, 1)

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Pfam Domains (1, 1)

Gene Ontology (17, 43)

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