2HY1 - JenaLib

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Title :   CRYSTAL STRUCTURE OF RV0805

Authors :   A. R. Shenoy, M. Capuder, P. Draskovic, D. Lamba, S. S. Visweswariah, M.

Date :   04 Aug 06 (Deposition) - 26 Dec 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.93

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Metallophosphoesterase, Camp, Phosphodiesterase, Bi-Nuclear Active Site, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. R. Shenoy, M. Capuder, P. Draskovic, D. Lamba, S. S. Visweswariah, M. Podobnik
Structural And Biochemical Analysis Of The Rv0805 Cyclic Nucleotide Phosphodiesterase From Mycobacterium Tuberculosis.
J. Mol. Biol. V. 365 211 2007
PubMed-ID: 17059828 | Reference-DOI: 10.1016/J.JMB.2006.10.005
(for further references see the PDB file header)

Molecule 1 - RV0805
	Chains	:	A
	EC Number	:	3.1.4.17
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PPROEXHTC
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	CATALYTIC CORE (RESIDUES 1-278)
	Gene	:	RV0805
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	83332
	Strain	:	H37RV
	Synonym	:	ICC PROTEIN

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	FE	1	Ligand/Ion	FE (III) ION
2	MN	1	Ligand/Ion	MANGANESE (II) ION
3	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	FE	-1	Ligand/Ion	FE (III) ION
2	MN	-1	Ligand/Ion	MANGANESE (II) ION
3	PO4	2	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:21 , HIS A:23 , ASP A:63 , HIS A:209 , MN A:555 , PO4 A:666 , HOH A:768	BINDING SITE FOR RESIDUE FE A 444
2	AC2	SOFTWARE	ASP A:63 , ASN A:97 , HIS A:169 , HIS A:207 , FE A:444 , PO4 A:666 , HOH A:768	BINDING SITE FOR RESIDUE MN A 555
3	AC3	SOFTWARE	HIS A:23 , ASP A:63 , ASN A:97 , HIS A:98 , HIS A:207 , HIS A:209 , FE A:444 , MN A:555 , HOH A:768	BINDING SITE FOR RESIDUE PO4 A 666

(no "SS Bond" information available for 2HY1)

(no "Cis Peptide Bond" information available for 2HY1)

(no "SAP(SNP)/Variant" information available for 2HY1)

(no "PROSITE Motif" information available for 2HY1)

(no "Exon" information available for 2HY1)

Asymmetric 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:227
 aligned with CPDA_MYCTO | P9WP64 from UniProtKB/Swiss-Prot  Length:318

    Alignment length:256
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259      
           CPDA_MYCTO    10 PRPDYVLLHISDTHLIGGDRRLYGAVDADDRLGELLEQLNQSGLRPDAIVFTGDLADKGEPAAYRKLRGLVEPFAAQLGAELVWVMGNHDDRAELRKFLLDEAPSMAPLDRVCMIDGLRIIVLDTSVPGHHHGEIRASQLGWLAEELATPAPDGTILALHHPPIPSVLDMAVTVELRDQAALGRVLRGTDVRAILAGHLHYSTNATFVGIPVSVASATCYTQDLTVAAGGTRGRDGAQGCNLVHVYPDTVVHSVIP 265
               SCOP domains d2hy1a1 A:10-265           Rv0805 cyclic nucleotide phosphodiesterase                                                                                                                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee......----------hhhhhhhhhhhhhhhhh....eeee........hhhhhhhhhhhhhhhhhhhh.eeee......hhhhhhhhh...........eeeee..eeeee.............hhhhhhhhhhhhh......eeee.........hhhhhh....hhhhhhhhhh...eeeeee......eeeee..eeeee.....-------------------.eeeeee....eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hy1 A  10 PRPDYVLLHISDTHLI----------DADDRLGELLEQLNQSGLRPDAIVFTGDLADKGEPAAYRKLRGLVEPFAAQLGAELVWVMGNHDDRAELRKFLLDEAPSMAPLDRVCMIDGLRIIVLDTSVPGHHHGEIRASQLGWLAEELATPAPDGTILALHHPPIPSVLDMAVTVELRDQAALGRVLRGTDVRAILAGHLHYSTNATFVGIPVSVASATC-------------------GCNLVHVYPDTVVHSVIP 265
                                    19     |   -      | 39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219        |-         -       249       259      
                                          25         36                                                                                                                                                                                             228                 248

Chain A from PDB  Type:PROTEIN  Length:227
 aligned with CPDA_MYCTU | P9WP65 from UniProtKB/Swiss-Prot  Length:318

    Alignment length:256
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259      
           CPDA_MYCTU    10 PRPDYVLLHISDTHLIGGDRRLYGAVDADDRLGELLEQLNQSGLRPDAIVFTGDLADKGEPAAYRKLRGLVEPFAAQLGAELVWVMGNHDDRAELRKFLLDEAPSMAPLDRVCMIDGLRIIVLDTSVPGHHHGEIRASQLGWLAEELATPAPDGTILALHHPPIPSVLDMAVTVELRDQAALGRVLRGTDVRAILAGHLHYSTNATFVGIPVSVASATCYTQDLTVAAGGTRGRDGAQGCNLVHVYPDTVVHSVIP 265
               SCOP domains d2hy1a1 A:10-265           Rv0805 cyclic nucleotide phosphodiesterase                                                                                                                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee......----------hhhhhhhhhhhhhhhhh....eeee........hhhhhhhhhhhhhhhhhhhh.eeee......hhhhhhhhh...........eeeee..eeeee.............hhhhhhhhhhhhh......eeee.........hhhhhh....hhhhhhhhhh...eeeeee......eeeee..eeeee.....-------------------.eeeeee....eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hy1 A  10 PRPDYVLLHISDTHLI----------DADDRLGELLEQLNQSGLRPDAIVFTGDLADKGEPAAYRKLRGLVEPFAAQLGAELVWVMGNHDDRAELRKFLLDEAPSMAPLDRVCMIDGLRIIVLDTSVPGHHHGEIRASQLGWLAEELATPAPDGTILALHHPPIPSVLDMAVTVELRDQAALGRVLRGTDVRAILAGHLHYSTNATFVGIPVSVASATC-------------------GCNLVHVYPDTVVHSVIP 265
                                    19     |   -      | 39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219        |-         -       249       259      
                                          25         36                                                                                                                                                                                             228                 248

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Metallo-dependent phosphatases (115)

Superfamily: Metallo-dependent phosphatases (115)

Family: GpdQ-like (8)

Protein domain: Rv0805 cyclic nucleotide phosphodiesterase (3)

Mycobacterium tuberculosis [TaxId: 1773] (3)

d2hy1a1

A:10-265

(no "CATH Domain" information available for 2HY1)

(no "Pfam Domain" information available for 2HY1)

Asymmetric Unit(hide GO term definitions)

Chain A (CPDA_MYCTU | P9WP65)

molecular function
	GO:0008663	2',3'-cyclic-nucleotide 2'-phosphodiesterase activity	Catalysis of the reaction: nucleoside 2',3'-cyclic phosphate + H2O = nucleoside 3'-phosphate.
	GO:0004115	3',5'-cyclic-AMP phosphodiesterase activity	Catalysis of the reaction: adenosine 3',5'-cyclic phosphate + H2O = adenosine 5'-phosphate.
	GO:0008199	ferric iron binding	Interacting selectively and non-covalently with ferric iron, Fe(III).
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) 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:0016791	phosphatase activity	Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
	GO:0042301	phosphate ion binding	Interacting selectively and non-covalently with phosphate.
	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:0006198	cAMP catabolic process	The chemical reactions and pathways resulting in the breakdown of the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
	GO:0042545	cell wall modification	The series of events leading to chemical and structural alterations of an existing cell wall that can result in loosening, increased extensibility or disassembly.
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	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:0005618	cell wall	The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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.
	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 (CPDA_MYCTO | P9WP64)

molecular function
	GO:0004115	3',5'-cyclic-AMP phosphodiesterase activity	Catalysis of the reaction: adenosine 3',5'-cyclic phosphate + H2O = adenosine 5'-phosphate.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	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.
cellular component
	GO:0005618	cell wall	The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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.
	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 Unit
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