1OVG - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   M64V PNP +MEPDR

Authors :   S. E. Ealick, E. M. Bennett, R. Anand, J. A. Secrist, P. W. Parker, A. E. Ha P. W. Allan, D. T. Mcpherson, E. J. Sorscher

Date :   26 Mar 03 (Deposition) - 17 Feb 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Pnp, M64V, Mepdr, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. M. Bennett, R. Anand, P. W. Allan, A. E. Hassan, J. S. Hong, D. N. Levasseur, D. T. Mcpherson, W. B. Parker, J. A. Secrist, E. J. Sorscher, T. M. Townes, W. R. Waud, S. E. Ealick
Designer Gene Therapy Using An Escherichia Coli Purine Nucleoside Phosphorylase/Prodrug System.
Chem. Biol. V. 10 1173 2003
PubMed-ID: 14700625 | Reference-DOI: 10.1016/J.CHEMBIOL.2003.11.008

Molecule 1 - PURINE NUCLEOSIDE PHOSPHORYLASE
	Chains	:	A, B, C
	EC Number	:	2.4.2.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	DEOD OR PUP OR B4384 OR Z5986 OR ECS5343
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	INOSINE PHOSPHORYLASE, PNP

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (2x)	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	MDR	3	Ligand/Ion	9-(2-DEOXY-BETA-D-RIBOFURANOSYL)-6-METHYLPURINE
2	PO4	3	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (2, 12)

No.	Name	Count	Type	Full Name
1	MDR	6	Ligand/Ion	9-(2-DEOXY-BETA-D-RIBOFURANOSYL)-6-METHYLPURINE
2	PO4	6	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:20 , ARG A:43 , ARG A:87 , GLY A:89 , SER A:90 , MDR A:245 , HOH A:278	BINDING SITE FOR RESIDUE PO4 A 248
2	AC2	SOFTWARE	GLY B:20 , ARG B:87 , GLY B:89 , SER B:90 , MDR B:246 , HOH B:263 , ARG C:43	BINDING SITE FOR RESIDUE PO4 B 249
3	AC3	SOFTWARE	ARG B:43 , GLY C:20 , ARG C:87 , GLY C:89 , SER C:90 , MDR C:247 , HOH C:277	BINDING SITE FOR RESIDUE PO4 C 250
4	AC4	SOFTWARE	HIS A:4 , ARG A:43 , SER A:90 , PHE A:159 , VAL A:178 , ASP A:204 , ILE A:206 , PO4 A:248 , HOH A:253 , HOH A:278 , HOH A:308 , HOH A:322	BINDING SITE FOR RESIDUE MDR A 245
5	AC5	SOFTWARE	SER B:90 , GLY B:92 , PHE B:159 , VAL B:178 , MET B:180 , GLU B:181 , ASP B:204 , PO4 B:249 , HIS C:4 , ARG C:43	BINDING SITE FOR RESIDUE MDR B 246
6	AC6	SOFTWARE	HIS B:4 , ARG B:43 , HOH B:294 , SER C:90 , CYS C:91 , GLY C:92 , PHE C:159 , VAL C:178 , GLU C:179 , GLU C:181 , ASP C:204 , ILE C:206 , PO4 C:250 , HOH C:313	BINDING SITE FOR RESIDUE MDR C 247

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

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

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

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PNP_UDP_1	PS01232	Purine and other phosphorylases family 1 signature.	DEOD_ECOLI	62-77	3	A:61-76 B:61-76 C:61-76

Biological Unit 1 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PNP_UDP_1	PS01232	Purine and other phosphorylases family 1 signature.	DEOD_ECOLI	62-77	6	A:61-76 B:61-76 C:61-76

(no "Exon" information available for 1OVG)

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:237
 aligned with DEOD_ECOLI | P0ABP8 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:237
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       
           DEOD_ECOLI     2 ATPHINAEMGDFADVVLMPGDPLRAKYIAETFLEDAREVNNVRGMLGFTGTYKGRKISVMGHGMGIPSCSIYTKELITDFGVKKIIRVGSCGAVLPHVKLRDVVIGMGACTDSKVNRIRFKDHDFAAIADFDMVRNAVDAAKALGIDARVGNLFSADLFYSPDGEMFDVMEKYGILGVEMEAAGIYGVAAEFGAKALTICTVSDHIRTHEQTTAAERQTTFNDMIKIALESVLLGDK 238
               SCOP domains d1ovga_ A: Purine nucleoside phosphorylase, PNP                                                                                                                                                                                               SCOP domains
               CATH domains 1ovgA00 A:1-237  [code=3.40.50.1580, no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeee...hhhhhhhhhhheeeeeeehhhhh.eeeeee..eeeeee....hhhhhhhhhhhhhhhhh..eeeeeeeeee.........eeeeeeeee..hhhhhhh.........hhhhhhhhhhhhhhh....eeeeeee.........hhhhhhhhh...eee.hhhhhhhhhhhh..eeeeeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------PNP_UDP_1       ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ovg A   1 ATPHINAEMGDFADVVLMPGDPLRAKYIAETFLEDAREVNNVRGMLGFTGTYKGRKISVMGHGVGIPSCSIYTKELITDFGVKKIIRVGSCGAVLPHVKLRDVVIGMGACTDSKVNRIRFKDHDFAAIADFDMVRNAVDAAKALGIDARVGNLFSADLFYSPDGEMFDVMEKYGILGVEMEAAGIYGVAAEFGAKALTICTVSDHIRTHEQTTAAERQTTFNDMIKIALESVLLGDK 237
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

Chain B from PDB  Type:PROTEIN  Length:237
 aligned with DEOD_ECOLI | P0ABP8 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:237
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       
           DEOD_ECOLI     2 ATPHINAEMGDFADVVLMPGDPLRAKYIAETFLEDAREVNNVRGMLGFTGTYKGRKISVMGHGMGIPSCSIYTKELITDFGVKKIIRVGSCGAVLPHVKLRDVVIGMGACTDSKVNRIRFKDHDFAAIADFDMVRNAVDAAKALGIDARVGNLFSADLFYSPDGEMFDVMEKYGILGVEMEAAGIYGVAAEFGAKALTICTVSDHIRTHEQTTAAERQTTFNDMIKIALESVLLGDK 238
               SCOP domains d1ovgb_ B: Purine nucleoside phosphorylase, PNP                                                                                                                                                                                               SCOP domains
               CATH domains 1ovgB00 B:1-237  [code=3.40.50.1580, no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeee..hhhhhhhhhhhhheeeeeeehhhhh.eeeeee..eeeeee....hhhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeeee..hhhhhhh......ee.hhhhhhhhhhhhhhh...eeeeeeee........hhhhhhhhhh...eee.hhhhhhhhhhhh..eeeeeeeeeee........hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------PNP_UDP_1       ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ovg B   1 ATPHINAEMGDFADVVLMPGDPLRAKYIAETFLEDAREVNNVRGMLGFTGTYKGRKISVMGHGVGIPSCSIYTKELITDFGVKKIIRVGSCGAVLPHVKLRDVVIGMGACTDSKVNRIRFKDHDFAAIADFDMVRNAVDAAKALGIDARVGNLFSADLFYSPDGEMFDVMEKYGILGVEMEAAGIYGVAAEFGAKALTICTVSDHIRTHEQTTAAERQTTFNDMIKIALESVLLGDK 237
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

Chain C from PDB  Type:PROTEIN  Length:237
 aligned with DEOD_ECOLI | P0ABP8 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:237
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       
           DEOD_ECOLI     2 ATPHINAEMGDFADVVLMPGDPLRAKYIAETFLEDAREVNNVRGMLGFTGTYKGRKISVMGHGMGIPSCSIYTKELITDFGVKKIIRVGSCGAVLPHVKLRDVVIGMGACTDSKVNRIRFKDHDFAAIADFDMVRNAVDAAKALGIDARVGNLFSADLFYSPDGEMFDVMEKYGILGVEMEAAGIYGVAAEFGAKALTICTVSDHIRTHEQTTAAERQTTFNDMIKIALESVLLGDK 238
               SCOP domains d1ovgc_ C: Purine nucleoside phosphorylase, PNP                                                                                                                                                                                               SCOP domains
               CATH domains 1ovgC00 C:1-237  [code=3.40.50.1580, no name defined]                                                                                                                                                                                         CATH domains
           Pfam domains (1) -------------PNP_UDP_1-1ovgC01 C:14-233                                                                                                                                                                                                  ---- Pfam domains (1)
           Pfam domains (2) -------------PNP_UDP_1-1ovgC02 C:14-233                                                                                                                                                                                                  ---- Pfam domains (2)
           Pfam domains (3) -------------PNP_UDP_1-1ovgC03 C:14-233                                                                                                                                                                                                  ---- Pfam domains (3)
         Sec.struct. author ..............eeee..hhhhhhhhhhhhheeeeeeehhhhh.eeeeee..eeeeee....hhhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeeee..hhhhhhh.........hhhhhhhhhhhhhhhh...eeeeeee.........hhhhhhhhh...eee.hhhhhhhhhhhhh.eeeeeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------PNP_UDP_1       ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ovg C   1 ATPHINAEMGDFADVVLMPGDPLRAKYIAETFLEDAREVNNVRGMLGFTGTYKGRKISVMGHGVGIPSCSIYTKELITDFGVKKIIRVGSCGAVLPHVKLRDVVIGMGACTDSKVNRIRFKDHDFAAIADFDMVRNAVDAAKALGIDARVGNLFSADLFYSPDGEMFDVMEKYGILGVEMEAAGIYGVAAEFGAKALTICTVSDHIRTHEQTTAAERQTTFNDMIKIALESVLLGDK 237
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

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) (23833)

Fold: Phosphorylase/hydrolase-like (558)

Superfamily: Purine and uridine phosphorylases (283)

Family: Purine and uridine phosphorylases (224)

Protein domain: Purine nucleoside phosphorylase, PNP (93)

Escherichia coli [TaxId: 562] (24)

1a	d1ovga_	A:
1b	d1ovgb_	B:
1c	d1ovgc_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1580, no name defined] (194)

Escherichia coli. Organism_taxid: 562. (30)

1a	1ovgA00	A:1-237
1b	1ovgB00	B:1-237
1c	1ovgC00	C:1-237

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PUP (121)

Family: PNP_UDP_1 (121)

Escherichia coli (strain K12) (27)

1a	PNP_UDP_1-1ovgC01	C:14-233
1b	PNP_UDP_1-1ovgC02	C:14-233
1c	PNP_UDP_1-1ovgC03	C:14-233

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (DEOD_ECOLI | P0ABP8)

molecular function
	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:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0004731	purine-nucleoside phosphorylase activity	Catalysis of the reaction: purine nucleoside + phosphate = purine + alpha-D-ribose 1-phosphate.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0016757	transferase activity, transferring glycosyl groups	Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
	GO:0016763	transferase activity, transferring pentosyl groups	Catalysis of the transfer of a pentosyl group from one compound (donor) to another (acceptor).
biological process
	GO:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0006139	nucleobase-containing compound metabolic process	Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
	GO:0009116	nucleoside metabolic process	The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine).
	GO:0006152	purine nucleoside catabolic process	The chemical reactions and pathways resulting in the breakdown of purine nucleoside, one of a family of organic molecules consisting of a purine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).
	GO:0019686	purine nucleoside interconversion	The chemical reactions and pathways by which a purine nucleoside is synthesized from another purine nucleoside.
	GO:0042278	purine nucleoside metabolic process	The chemical reactions and pathways involving one of a family of organic molecules consisting of a purine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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Biological Unit
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Description

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Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

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