1JPV - JenaLib

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Title :   CRYSTAL STRUCTURE OF 5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE COMPLEXED WITH SO4

Authors :   T. C. Appleby, I. I. Mathews, M. Porcelli, G. Cacciapuoti, S. E. Ealick

Date :   03 Aug 01 (Deposition) - 26 Oct 01 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Alpha-Beta Protein, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. C. Appleby, I. I. Mathews, M. Porcelli, G. Cacciapuoti, S. E. Ealick
Three-Dimensional Structure Of A Hyperthermophilic 5'-Deoxy-5'-Methylthioadenosine Phosphorylase From Sulfolobus Solfataricus.
J. Biol. Chem. V. 276 39232 2001
PubMed-ID: 11489901 | Reference-DOI: 10.1074/JBC.M105694200
(for further references see the PDB file header)

Molecule 1 - 5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE
	Chains	:	A, B, C
	EC Number	:	2.4.2.28
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	SULFOLOBUS SOLFATARICUS
	Organism Taxid	:	2287
	Synonym	:	MTA PHOSPHORYLASE; MTAP

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	SO4	6	Ligand/Ion	SULFATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:21 , ARG A:43 , ARG A:86 , GLY A:88 , THR A:89 , HOH A:535	BINDING SITE FOR RESIDUE SO4 A 1250
2	AC2	SOFTWARE	GLY B:21 , ARG B:86 , TYR B:87 , GLY B:88 , THR B:89 , HOH B:510 , HOH B:523 , ARG C:43	BINDING SITE FOR RESIDUE SO4 B 2250
3	AC3	SOFTWARE	ARG B:43 , GLY C:21 , ARG C:86 , GLY C:88 , THR C:89	BINDING SITE FOR RESIDUE SO4 C 3250

Asymmetric Unit

No.	Residues
1	A:125	-	C:125
2	B:125	-	B:125

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

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

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.	PNPH_SULSO	61-76	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.	PNPH_SULSO	61-76	6	A:61-76 B:61-76 C:61-76

(no "Exon" information available for 1JPV)

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:235
 aligned with PNPH_SULSO | P50389 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:235
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231     
           PNPH_SULSO     2 NPVHILAKKGEVAERVLVVGDPGRARLLSTLLQNPKLTNENRGFLVYTGKYNGETVSIATHGIGGPSIAIVLEELAMLGANVFIRYGTTGALVPYINLGEYIIVTGASYNQGGLFYQYLRDNACVASTPDFELTNKLVTSFSKRNLKYYVGNVFSSDAFYAEDEEFVKKWSSRGNIAVEMECATLFTLSKVKGWKSATVLVVSDNLAKGGIWITKEELEKSVMDGAKAVLDTLTS 236
               SCOP domains d1jpva_ A: 5'-deoxy-5'-methylthioadenosine phosphorylase                                                                                                                                                                                    SCOP domains
               CATH domains 1jpvA00 A:2-236  [code=3.40.50.1580, no name defined]                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeee.hhhhhhhhhh..eeeeeeehhhhh.eeeeee..eeeeeee...hhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeee...hhhhhhhhh.........hhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhh..eeeee.hhhhhhhhhhhhh.eeeeeeeeeee........hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------PNP_UDP_1       ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jpv A   2 NPVHILAKKGEVAERVLVVGDPGRARLLSTLLQNPKLTNENRGFLVYTGKYNGETVSIATHGIGGPSIAIVLEELAMLGANVFIRYGTTGALVPYINLGEYIIVTGASYNQGGLFYQYLRDNACVASTPDFELTNKLVTSFSKRNLKYYVGNVFSSDAFYAEDEEFVKKWSSRGNIAVEMECATLFTLSKVKGWKSATVLVVSDNLAKGGIWITKEELEKSVMDGAKAVLDTLTS 236
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231

Chain B from PDB  Type:PROTEIN  Length:234
 aligned with PNPH_SULSO | P50389 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:234
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232    
           PNPH_SULSO     3 PVHILAKKGEVAERVLVVGDPGRARLLSTLLQNPKLTNENRGFLVYTGKYNGETVSIATHGIGGPSIAIVLEELAMLGANVFIRYGTTGALVPYINLGEYIIVTGASYNQGGLFYQYLRDNACVASTPDFELTNKLVTSFSKRNLKYYVGNVFSSDAFYAEDEEFVKKWSSRGNIAVEMECATLFTLSKVKGWKSATVLVVSDNLAKGGIWITKEELEKSVMDGAKAVLDTLTS 236
               SCOP domains d1jpvb_ B: 5'-deoxy-5'-methylthioadenosine phosphorylase                                                                                                                                                                                   SCOP domains
               CATH domains 1jpvB00 B:3-236  [code=3.40.50.1580, no name defined]                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............eeeee.hhhhhhhhhhhheeeeeeehhhhh.eeeeee..eeeeeee...hhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeee...hhhhhhhhh.........hhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhh..eeeee.hhhhhhhhhhhhh.eeeeeeeeeee........hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------PNP_UDP_1       ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jpv B   3 PVHILAKKGEVAERVLVVGDPGRARLLSTLLQNPKLTNENRGFLVYTGKYNGETVSIATHGIGGPSIAIVLEELAMLGANVFIRYGTTGALVPYINLGEYIIVTGASYNQGGLFYQYLRDNACVASTPDFELTNKLVTSFSKRNLKYYVGNVFSSDAFYAEDEEFVKKWSSRGNIAVEMECATLFTLSKVKGWKSATVLVVSDNLAKGGIWITKEELEKSVMDGAKAVLDTLTS 236
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232

Chain C from PDB  Type:PROTEIN  Length:234
 aligned with PNPH_SULSO | P50389 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:234
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232    
           PNPH_SULSO     3 PVHILAKKGEVAERVLVVGDPGRARLLSTLLQNPKLTNENRGFLVYTGKYNGETVSIATHGIGGPSIAIVLEELAMLGANVFIRYGTTGALVPYINLGEYIIVTGASYNQGGLFYQYLRDNACVASTPDFELTNKLVTSFSKRNLKYYVGNVFSSDAFYAEDEEFVKKWSSRGNIAVEMECATLFTLSKVKGWKSATVLVVSDNLAKGGIWITKEELEKSVMDGAKAVLDTLTS 236
               SCOP domains d1jpvc_ C: 5'-deoxy-5'-methylthioadenosine phosphorylase                                                                                                                                                                                   SCOP domains
               CATH domains 1jpvC00 C:3-236  [code=3.40.50.1580, no name defined]                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............eeeee.hhhhhhhhhh..eeeeeeehhhhh.eeeeee..eeeeeee...hhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeee...hhhhhhhhh.........hhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhh.eeeee.hhhhhhhhhhhhh.eeeeeeeeeee........hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------PNP_UDP_1       ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jpv C   3 PVHILAKKGEVAERVLVVGDPGRARLLSTLLQNPKLTNENRGFLVYTGKYNGETVSIATHGIGGPSIAIVLEELAMLGANVFIRYGTTGALVPYINLGEYIIVTGASYNQGGLFYQYLRDNACVASTPDFELTNKLVTSFSKRNLKYYVGNVFSSDAFYAEDEEFVKKWSSRGNIAVEMECATLFTLSKVKGWKSATVLVVSDNLAKGGIWITKEELEKSVMDGAKAVLDTLTS 236
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232

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: 5'-deoxy-5'-methylthioadenosine phosphorylase (18)

Sulfolobus solfataricus [TaxId: 2287] (9)

1a	d1jpva_	A:
1b	d1jpvb_	B:
1c	d1jpvc_	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)

Sulfolobus solfataricus. Organism_taxid: 2287. (9)

1a	1jpvA00	A:2-236
1b	1jpvB00	B:3-236
1c	1jpvC00	C:3-236

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (PNPH_SULSO | P50389)

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: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: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).

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1jpv)

Biological Unit
	Complete Structure
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	1jpv
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	2.4.2.28
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UniProtKB/Swiss-Prot
	PNPH_SULSO \| P50389	:	1jds 1jdt 1jdu 1jdv 1jdz 1je0 1je1 1jp7

1jds	NATIVE COMPLEX
1jdt	COMPLEXED WITH PHOSPHATE
1jdu	COMPLEXED WITH GUANOSINE AND SULFATE
1jdv	COMPLEXED WITH PHOSPHATE (SPACE GROUP: C2221)
1jdz	COMPLEXED WITH FORMYCIN B AND SULFATE
1je0	COMPLEXED WITH ADENOSINE AND SULFATE
1je1	COMPLEXED WITH MTA AND SULFATE
1jp7	COMPLEXED WITH SO4

Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (0, 0)

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Gene Ontology (6, 6)

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