1JDT - JenaLib

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Title :   CRYSTAL STRUCTURE OF 5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE COMPLEXED WITH MTA AND SULFATE ION

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

Date :   15 Jun 01 (Deposition) - 26 Oct 01 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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'-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 (2, 6)

No.	Name	Count	Type	Full Name
1	MTA	3	Ligand/Ion	5'-DEOXY-5'-METHYLTHIOADENOSINE
2	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 12)

No.	Name	Count	Type	Full Name
1	MTA	6	Ligand/Ion	5'-DEOXY-5'-METHYLTHIOADENOSINE
2	SO4	6	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:21 , ARG A:25 , ARG A:43 , ARG A:86 , GLY A:88 , THR A:89 , GLU A:182 , MTA A:1260	BINDING SITE FOR RESIDUE SO4 A 1250
2	AC2	SOFTWARE	GLY B:21 , ARG B:25 , ARG B:86 , GLY B:88 , THR B:89 , MTA B:2260 , ARG C:43	BINDING SITE FOR RESIDUE SO4 B 2250
3	AC3	SOFTWARE	ARG B:43 , GLY C:21 , ARG C:25 , ARG C:86 , GLY C:88 , THR C:89 , MTA C:3260	BINDING SITE FOR RESIDUE SO4 C 3250
4	AC4	SOFTWARE	HIS A:5 , ARG A:43 , THR A:89 , THR A:90 , GLY A:91 , PHE A:160 , GLU A:163 , VAL A:179 , GLU A:180 , MET A:181 , GLU A:182 , ASP A:205 , SO4 A:1250	BINDING SITE FOR RESIDUE MTA A 1260
5	AC5	SOFTWARE	ARG B:86 , THR B:89 , THR B:90 , GLY B:91 , PHE B:160 , GLU B:163 , VAL B:179 , GLU B:180 , MET B:181 , GLU B:182 , SER B:204 , ASP B:205 , SO4 B:2250 , HIS C:5 , ARG C:43	BINDING SITE FOR RESIDUE MTA B 2260
6	AC6	SOFTWARE	HIS B:5 , ARG B:43 , ILE C:64 , ARG C:86 , THR C:89 , THR C:90 , GLY C:91 , PHE C:160 , GLU C:163 , VAL C:179 , GLU C:180 , MET C:181 , GLU C:182 , SER C:204 , ASP C:205 , LEU C:207 , SO4 C:3250	BINDING SITE FOR RESIDUE MTA C 3260

Asymmetric Unit

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

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

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

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 1JDT)

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:231
 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 d1jdta_ A: 5'-deoxy-5'-methylthioadenosine phosphorylase                                                                                                                                                                                    SCOP domains
               CATH domains 1jdtA00 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.......hhhhhhhhhh..eeeee.hhhhhhhhhhhhh.eeeeeeeeeee...----.hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------PNP_UDP_1       ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jdt A   2 NPVHILAKKGEVAERVLVVGDPGRARLLSTLLQNPKLTNENRGFLVYTGKYNGETVSIATHGIGGPSIAIVLEELAMLGANVFIRYGTTGALVPYINLGEYIIVTGASYNQGGLFYQYLRDNACVASTPDFELTNKLVTSFSKRNLKYYVGNVFSSDAFYAEDEEFVKKWSSRGNIAVEMECATLFTLSKVKGWKSATVLVVSDNLAK----ITKEELEKSVMDGAKAVLDTLTS 236
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       | -  |    221       231     
                                                                                                                                                                                                                                         209  214

Chain B from PDB  Type:PROTEIN  Length:231
 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 d1jdtb_ B: 5'-deoxy-5'-methylthioadenosine phosphorylase                                                                                                                                                                                    SCOP domains
               CATH domains 1jdtB00 B:2-236  [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.......hhhhhhhhhh..eeeee.hhhhhhhhhhhhh.eeeeeeeeeee...----.hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------PNP_UDP_1       ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jdt B   2 NPVHILAKKGEVAERVLVVGDPGRARLLSTLLQNPKLTNENRGFLVYTGKYNGETVSIATHGIGGPSIAIVLEELAMLGANVFIRYGTTGALVPYINLGEYIIVTGASYNQGGLFYQYLRDNACVASTPDFELTNKLVTSFSKRNLKYYVGNVFSSDAFYAEDEEFVKKWSSRGNIAVEMECATLFTLSKVKGWKSATVLVVSDNLAK----ITKEELEKSVMDGAKAVLDTLTS 236
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       | -  |    221       231     
                                                                                                                                                                                                                                         209  214

Chain C from PDB  Type:PROTEIN  Length:226
 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 d1jdtc_ C: 5'-deoxy-5'-methylthioadenosine phosphorylase                                                                                                                                                                                    SCOP domains
               CATH domains 1jdtC00 C: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...---------hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------PNP_UDP_1       ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jdt C   2 NPVHILAKKGEVAERVLVVGDPGRARLLSTLLQNPKLTNENRGFLVYTGKYNGETVSIATHGIGGPSIAIVLEELAMLGANVFIRYGTTGALVPYINLGEYIIVTGASYNQGGLFYQYLRDNACVASTPDFELTNKLVTSFSKRNLKYYVGNVFSSDAFYAEDEEFVKKWSSRGNIAVEMECATLFTLSKVKGWKSATVLVVSDNLAK---------LEKSVMDGAKAVLDTLTS 236
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       | -       221       231     
                                                                                                                                                                                                                                         209       219

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(

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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	d1jdta_	A:
1b	d1jdtb_	B:
1c	d1jdtc_	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	1jdtA00	A:2-236
1b	1jdtB00	B:2-236
1c	1jdtC00	C:2-236

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

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

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

Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (0, 0)

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