1V4N - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   STRUCTURE OF 5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE HOMOLOGUE FROM SULFOLOBUS TOKODAII

Authors :   Y. Kitago, Y. Yasutake, N. Sakai, M. Tsujimura, M. Yao, N. Watanabe, Y. Kawarabayasi, I. Tanaka

Date :   14 Nov 03 (Deposition) - 04 Jan 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.45

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Transferase, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Kitago, Y. Yasutake, N. Sakai, M. Tsujimura, M. Yao, N. Watanabe, Y. Kawarabayasi, I. Tanaka
Crystal Structure Of Sulfolobus Tokodaii Mtap
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - 271AA LONG HYPOTHETICAL 5'-METHYLTHIOADENOSINE PHOSPHORYLASE
	Chains	:	A, B, C
	EC Number	:	2.4.2.28
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-23A
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	ST0485
	Organism Scientific	:	SULFOLOBUS TOKODAII
	Organism Taxid	:	111955
	Synonym	:	MTAP

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1V4N)

(no "Site" information available for 1V4N)

Asymmetric/Biological Unit

No.	Residues
1	A:139	-	A:206
2	A:201	-	A:262
3	A:260	-	A:263
4	B:139	-	B:206
5	B:201	-	B:262
6	B:260	-	B:263
7	C:139	-	C:206
8	C:201	-	C:262
9	C:260	-	C:263

Asymmetric/Biological Unit

No.	Residues
1	Gly A:126	-	Pro A:127
2	Gly A:168	-	Pro A:169
3	Val A:194	-	Pro A:195
4	Gly B:126	-	Pro B:127
5	Gly B:168	-	Pro B:169
6	Val B:194	-	Pro B:195
7	Gly C:126	-	Pro C:127
8	Gly C:168	-	Pro C:169
9	Val C:194	-	Pro C:195

(no "SAP(SNP)/Variant" information available for 1V4N)

(no "PROSITE Motif" information available for 1V4N)

(no "Exon" information available for 1V4N)

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:266
 aligned with F9VN03_SULTO | F9VN03 from UniProtKB/TrEMBL  Length:270

    Alignment length:266
                                                                                                                                                                                                                                                                                                  270 
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265    | 
         F9VN03_SULTO     6 EKASIGIIGGSGLYDPQILTNVKEIKVYTPYGEPSDNIILGELEGRKVAFLPRHGRGHRIPPHKINYRANIWALKSLGVKWVIAVSAVGSLRLDYKPGDFVVPNQFIDMTKGRTYTFFDGPTVAHVSMADPFCEHLRSIILDSAKDLGITTHDKGTYICIEGPRFSTRAESIVWKEVFKADIIGMTLVPEVNLACEAEMCYSVIGMVTDYDVFADIPVTAEEVTKVMAENTAKVKKLLYEVIRRLPEKPDERKCSCCQALKTALV-   -
               SCOP domains d1v4na_ A: 5'-deoxy-5'-methylthioadenosine phosphorylase                                                                                                                                                                                                                   SCOP domains
               CATH domains 1v4nA00 A:7-272  [code=3.40.50.1580, no name defined]                                                                                                                                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.............eee............eeeeee..eeeeeee........hhhhhhhhhhhhhhhhh...eeeeeeeeee.........ee...eeeee.......................hhhhhhhhhhhhhhhh..ee...eeeee......hhhhhhhhhhh....eee.hhhhhhhhhhhh..eeeeeeeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh...hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v4n A   7 EKASIGIIGGSGLYDPQILTNVKEIKVYTPYGEPSDNIILGELEGRKVAFLPRHGRGHRIPPHKINYRANIWALKSLGVKWVIAVSAVGSLRLDYKPGDFVVPNQFIDMTKGRTYTFFDGPTVAHVSMADPFCEHLRSIILDSAKDLGITTHDKGTYICIEGPRFSTRAESIVWKEVFKADIIGMTLVPEVNLACEAEMCYSVIGMVTDYDVFADIPVTAEEVTKVMAENTAKVKKLLYEVIRRLPEKPDERKCSCCQALKTALVL 272
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266

Chain B from PDB  Type:PROTEIN  Length:269
 aligned with F9VN03_SULTO | F9VN03 from UniProtKB/TrEMBL  Length:270

    Alignment length:269
                                                                                                                                                                                                                                                                                                     270 
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       | 
         F9VN03_SULTO     3 EPKEKASIGIIGGSGLYDPQILTNVKEIKVYTPYGEPSDNIILGELEGRKVAFLPRHGRGHRIPPHKINYRANIWALKSLGVKWVIAVSAVGSLRLDYKPGDFVVPNQFIDMTKGRTYTFFDGPTVAHVSMADPFCEHLRSIILDSAKDLGITTHDKGTYICIEGPRFSTRAESIVWKEVFKADIIGMTLVPEVNLACEAEMCYSVIGMVTDYDVFADIPVTAEEVTKVMAENTAKVKKLLYEVIRRLPEKPDERKCSCCQALKTALV-   -
               SCOP domains d1v4nb_ B: 5'-deoxy-5'-methylthioadenosine phosphorylase                                                                                                                                                                                                                      SCOP domains
               CATH domains 1v4nB00 B:4-272  [code=3.40.50.1580, no name defined]                                                                                                                                                                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee.............eee............eeeeee..eeeeeee........hhhhhhhhhhhhhhhhh...eeeeeeeeee.........ee...eeeee.......................hhhhhhhhhhhhhhhh..ee...eeeee......hhhhhhhhhhh....eee.hhhhhhhhhhhh..eeeeeeeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh...hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v4n B   4 EPKEKASIGIIGGSGLYDPQILTNVKEIKVYTPYGEPSDNIILGELEGRKVAFLPRHGRGHRIPPHKINYRANIWALKSLGVKWVIAVSAVGSLRLDYKPGDFVVPNQFIDMTKGRTYTFFDGPTVAHVSMADPFCEHLRSIILDSAKDLGITTHDKGTYICIEGPRFSTRAESIVWKEVFKADIIGMTLVPEVNLACEAEMCYSVIGMVTDYDVFADIPVTAEEVTKVMAENTAKVKKLLYEVIRRLPEKPDERKCSCCQALKTALVL 272
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263

Chain C from PDB  Type:PROTEIN  Length:267
 aligned with F9VN03_SULTO | F9VN03 from UniProtKB/TrEMBL  Length:270

    Alignment length:267
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       
         F9VN03_SULTO     4 PKEKASIGIIGGSGLYDPQILTNVKEIKVYTPYGEPSDNIILGELEGRKVAFLPRHGRGHRIPPHKINYRANIWALKSLGVKWVIAVSAVGSLRLDYKPGDFVVPNQFIDMTKGRTYTFFDGPTVAHVSMADPFCEHLRSIILDSAKDLGITTHDKGTYICIEGPRFSTRAESIVWKEVFKADIIGMTLVPEVNLACEAEMCYSVIGMVTDYDVFADIPVTAEEVTKVMAENTAKVKKLLYEVIRRLPEKPDERKCSCCQALKTALV 270
               SCOP domains d1v4nc_ C: 5'-deoxy-5'-methylthioadenosine phosphorylase                                                                                                                                                                                                                    SCOP domains
               CATH domains 1v4nC00 C:5-271  [code=3.40.50.1580, no name defined]                                                                                                                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee......hhhhh...eee............eeeeee..eeeee..........hhhhhhhhhhhhhhhhh...eeeeeeeeee.........ee...eeeee.......................hhhhhhhhhhhhhhhh..ee...eeeee......hhhhhhhhhhh....eee.hhhhhhhhhhhh..eeeeeeeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh...hhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v4n C   5 PKEKASIGIIGGSGLYDPQILTNVKEIKVYTPYGEPSDNIILGELEGRKVAFLPRHGRGHRIPPHKINYRANIWALKSLGVKWVIAVSAVGSLRLDYKPGDFVVPNQFIDMTKGRTYTFFDGPTVAHVSMADPFCEHLRSIILDSAKDLGITTHDKGTYICIEGPRFSTRAESIVWKEVFKADIIGMTLVPEVNLACEAEMCYSVIGMVTDYDVFADIPVTAEEVTKVMAENTAKVKKLLYEVIRRLPEKPDERKCSCCQALKTALV 271
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264

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) (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 tokodaii [TaxId: 111955] (1)

1a	d1v4na_	A:
1b	d1v4nb_	B:
1c	d1v4nc_	C:

Asymmetric/Biological 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 tokodaii. Organism_taxid: 111955. (1)

1a	1v4nA00	A:7-272
1b	1v4nC00	C:5-271
1c	1v4nB00	B:4-272

(no "Pfam Domain" information available for 1V4N)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C (F9VN03_SULTO | F9VN03)

molecular function
	GO:0017061	S-methyl-5-thioadenosine phosphorylase activity	Catalysis of the reaction: 5'-methylthioadenosine + phosphate = adenine + 5-methylthio-D-ribose 1-phosphate.
	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: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:0019509	L-methionine salvage from methylthioadenosine	The generation of L-methionine (2-amino-4-(methylthio)butanoic acid) from methylthioadenosine.
	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/Biological Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1v4n)

	Sites
(no "Sites" information available for 1v4n)

	Cis Peptide Bonds
		Gly A:126 - Pro A:127	[ RasMol ]
		Gly A:168 - Pro A:169	[ RasMol ]
		Gly B:126 - Pro B:127	[ RasMol ]
		Gly B:168 - Pro B:169	[ RasMol ]
		Gly C:126 - Pro C:127	[ RasMol ]
		Gly C:168 - Pro C:169	[ RasMol ]
		Val A:194 - Pro A:195	[ RasMol ]
		Val B:194 - Pro B:195	[ RasMol ]
		Val C:194 - Pro C:195	[ RasMol ]

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	1v4n
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Description

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Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (9, 9)

Cis Peptide Bonds (9, 9)

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