1Y0B - JenaLib

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Title :   CRYSTAL STRUCTURE OF XANTHINE PHOSPHORIBOSYLTRANSFERASE FROM BACILLUS SUBTILIS.

Authors :   M. E. Cuff, R. Wu, A. Joachimiak, Midwest Center For Structural Gen (Mcsg)

Date :   15 Nov 04 (Deposition) - 22 Feb 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Xanthine, Purine Metabolism, Phosphoribosyltransferase, Structural Genomics, Psi, Protein Structure Initative, Midwest Center For Structural Genomics, Mcsg, Protein Structure Initiative, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. E. Cuff, R. Wu, A. Joachimiak, Mcsg
Crystal Structure Of Xanthine Phosphoribosyltransferase Fro Bacillus Subtilis
To Be Published
PubMed: search

Molecule 1 - XANTHINE PHOSPHORIBOSYLTRANSFERASE
	Chains	:	A, B, C, D
	EC Number	:	2.4.2.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PMCSG7
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	XPT
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 24)

No.	Name	Count	Type	Full Name
1	G4P	4	Ligand/Ion	GUANOSINE-5',3'-TETRAPHOSPHATE
2	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
3	NA	8	Ligand/Ion	SODIUM ION

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	G4P	2	Ligand/Ion	GUANOSINE-5',3'-TETRAPHOSPHATE
2	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
3	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (2, 8)

No.	Name	Count	Type	Full Name
1	G4P	2	Ligand/Ion	GUANOSINE-5',3'-TETRAPHOSPHATE
2	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
3	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:125 , NA A:887 , G4P A:888 , HOH A:906	BINDING SITE FOR RESIDUE NA A 886
02	AC2	SOFTWARE	ASP A:124 , ASP A:125 , NA A:886 , G4P A:888 , HOH A:892 , HOH A:895	BINDING SITE FOR RESIDUE NA A 887
03	AC3	SOFTWARE	ASP B:125 , NA B:887 , G4P B:888 , HOH B:922	BINDING SITE FOR RESIDUE NA B 886
04	AC4	SOFTWARE	ASP B:124 , ASP B:125 , NA B:886 , G4P B:888 , HOH B:894 , HOH B:903	BINDING SITE FOR RESIDUE NA B 887
05	AC5	SOFTWARE	ASP C:125 , NA C:887 , G4P C:888 , HOH C:913	BINDING SITE FOR RESIDUE NA C 886
06	AC6	SOFTWARE	ASP C:124 , ASP C:125 , NA C:886 , G4P C:888 , HOH C:890 , HOH C:895	BINDING SITE FOR RESIDUE NA C 887
07	AC7	SOFTWARE	ASP D:125 , NA D:887 , G4P D:888 , HOH D:943	BINDING SITE FOR RESIDUE NA D 886
08	AC8	SOFTWARE	ASP D:124 , ASP D:125 , NA D:886 , G4P D:888 , HOH D:896 , HOH D:902	BINDING SITE FOR RESIDUE NA D 887
09	AC9	SOFTWARE	LEU A:20 , ASN A:27 , GLU A:58 , SER A:59 , SER A:60 , LYS A:81 , ASP A:125 , PHE A:126 , LYS A:156 , NA A:886 , NA A:887 , HOH A:895 , HOH A:898 , HOH A:900 , HOH A:901 , HOH A:905 , HOH A:906 , HOH A:907 , HOH A:920 , HOH A:923 , HOH A:1012 , ARG B:80 , LEU B:85 , HOH B:915	BINDING SITE FOR RESIDUE G4P A 888
10	BC1	SOFTWARE	ARG A:80 , LEU A:85 , GLN B:18 , VAL B:19 , LEU B:20 , ASN B:27 , GLU B:58 , SER B:59 , SER B:60 , LYS B:81 , ASP B:125 , PHE B:126 , LYS B:156 , NA B:886 , NA B:887 , HOH B:891 , HOH B:897 , HOH B:899 , HOH B:903 , HOH B:921 , HOH B:922 , HOH B:935 , HOH B:936 , HOH B:937 , HOH B:949	BINDING SITE FOR RESIDUE G4P B 888
11	BC2	SOFTWARE	VAL C:19 , LEU C:20 , ASN C:27 , GLU C:58 , SER C:59 , SER C:60 , LYS C:81 , ASP C:125 , PHE C:126 , LYS C:156 , NA C:886 , NA C:887 , HOH C:889 , HOH C:890 , HOH C:891 , HOH C:900 , HOH C:913 , HOH C:923 , HOH C:963 , HOH C:969 , HOH C:1032 , ARG D:80 , LEU D:85	BINDING SITE FOR RESIDUE G4P C 888
12	BC3	SOFTWARE	ARG C:80 , LEU C:85 , THR C:86 , HOH C:960 , GLN D:18 , VAL D:19 , LEU D:20 , ASN D:27 , GLU D:58 , SER D:59 , SER D:60 , LYS D:81 , ASP D:125 , PHE D:126 , LYS D:156 , NA D:886 , NA D:887 , HOH D:890 , HOH D:891 , HOH D:896 , HOH D:903 , HOH D:916 , HOH D:943 , HOH D:961 , HOH D:980 , HOH D:997 , HOH D:1047 , HOH D:1095	BINDING SITE FOR RESIDUE G4P D 888

(no "SS Bond" information available for 1Y0B)

Asymmetric Unit

No.	Residues
1	Glu A:58	-	Ser A:59
2	Glu B:58	-	Ser B:59
3	Glu C:58	-	Ser C:59
4	Glu D:58	-	Ser D:59

(no "SAP(SNP)/Variant" information available for 1Y0B)

(no "PROSITE Motif" information available for 1Y0B)

(no "Exon" information available for 1Y0B)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:193
 aligned with XPT_BACSU | P42085 from UniProtKB/Swiss-Prot  Length:194

    Alignment length:193
                              1                                                                                                                                                                                              
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188   
            XPT_BACSU     - --MEALKRKIEEEGVVLSDQVLKVDSFLNHQIDPLLMQRIGDEFASRFAKDGITKIVTIESSGIAPAVMTGLKLGVPVVFARKHKSLTLTDNLLTASVYSFTKQTESQIAVSGTHLSDQDHVLIIDDFLANGQAAHGLVSIVKQAGASIAGIGIVIEKSFQPGRDELVKLGYRVESLARIQSLEEGKVSFVQE 191
               SCOP domains --d1y0ba1 A:1-191 Xanthine phosphoribosyltransferase                                                                                                                                              SCOP domains
               CATH domains 1y0bA00 A:-1-191  [code=3.40.50.2020, no name defined]                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhheee...eee.......eehhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhh..eeee...........eeeeeeee....eeeeeeee.hhh....eeeeeeeee..hhhhhhhhhhhhhh..eeeeeeeeeee...hhhhhhhhh...eeeeeeeee......ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y0b A  -1 NAmEALKRKIEEEGVVLSDQVLKVDSFLNHQIDPLLmQRIGDEFASRFAKDGITKIVTIESSGIAPAVmTGLKLGVPVVFARKHKSLTLTDNLLTASVYSFTKQTESQIAVSGTHLSDQDHVLIIDDFLANGQAAHGLVSIVKQAGASIAGIGIVIEKSFQPGRDELVKLGYRVESLARIQSLEEGKVSFVQE 191
                              |      8        18        28      | 38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188   
                              |                                35-MSE                          67-MSE                                                                                                                        
                              1-MSE

Chain B from PDB  Type:PROTEIN  Length:192
 aligned with XPT_BACSU | P42085 from UniProtKB/Swiss-Prot  Length:194

    Alignment length:195
                               1                                                                                                                                                                                               
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187     
            XPT_BACSU     - ---MEALKRKIEEEGVVLSDQVLKVDSFLNHQIDPLLMQRIGDEFASRFAKDGITKIVTIESSGIAPAVMTGLKLGVPVVFARKHKSLTLTDNLLTASVYSFTKQTESQIAVSGTHLSDQDHVLIIDDFLANGQAAHGLVSIVKQAGASIAGIGIVIEKSFQPGRDELVKLGYRVESLARIQSLEEGKVSFVQEV 192
               SCOP domains d1y0bb_ B: Xanthine phosphoribosyltransferase                                                                                                                                                       SCOP domains
               CATH domains -----1y0bB01 B:3-188  [code=3.40.50.2020, no name defined]                                                                                                                                     ---- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhee.....ee.......eehhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhh..eeee...........eeeeeee..---.eeeeeee.hhh....eeeeeeeee..hhhhhhhhhhhhhh..eeeeeeeeeee...hhhhhhhhh...eeeeeeeeehhhhh.ee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y0b B  -2 SNAmEALKRKIEEEGVVLSDQVLKVDSFLNHQIDPLLmQRIGDEFASRFAKDGITKIVTIESSGIAPAVmTGLKLGVPVVFARKHKSLTLTDNLLTASVYSF---TESQIAVSGTHLSDQDHVLIIDDFLANGQAAHGLVSIVKQAGASIAGIGIVIEKSFQPGRDELVKLGYRVESLARIQSLEEGKVSFVQEV 192
                               |     7        17        27       |37        47        57        67        77        87        97 |   | 107       117       127       137       147       157       167       177       187     
                               1-MSE                            35-MSE                          67-MSE                          99 103

Chain C from PDB  Type:PROTEIN  Length:189
 aligned with XPT_BACSU | P42085 from UniProtKB/Swiss-Prot  Length:194

    Alignment length:192
                               1                                                                                                                                                                                            
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187  
            XPT_BACSU     - ---MEALKRKIEEEGVVLSDQVLKVDSFLNHQIDPLLMQRIGDEFASRFAKDGITKIVTIESSGIAPAVMTGLKLGVPVVFARKHKSLTLTDNLLTASVYSFTKQTESQIAVSGTHLSDQDHVLIIDDFLANGQAAHGLVSIVKQAGASIAGIGIVIEKSFQPGRDELVKLGYRVESLARIQSLEEGKVSFV 189
               SCOP domains d1y0bc_ C: Xanthine phosphoribosyltransferase                                                                                                                                                    SCOP domains
               CATH domains 1y0bC00 C:-2-189  [code=3.40.50.2020, no name defined]                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhheee...eee.......eehhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhh..eeee...........eeeeeee..---.eeeeeee.hhh....eeeeeeeee..hhhhhhhhhhhhhh..eeeeeeeeeee...hhhhhhhhh...eeeeeeeeehhhhh.ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1y0b C  -2 SNAmEALKRKIEEEGVVLSDQVLKVDSFLNHQIDPLLmQRIGDEFASRFAKDGITKIVTIESSGIAPAVmTGLKLGVPVVFARKHKSLTLTDNLLTASVYSF---TESQIAVSGTHLSDQDHVLIIDDFLANGQAAHGLVSIVKQAGASIAGIGIVIEKSFQPGRDELVKLGYRVESLARIQSLEEGKVSFV 189
                               |     7        17        27       |37        47        57        67        77        87        97 |   | 107       117       127       137       147       157       167       177       187  
                               1-MSE                            35-MSE                          67-MSE                          99 103

Chain D from PDB  Type:PROTEIN  Length:194
 aligned with XPT_BACSU | P42085 from UniProtKB/Swiss-Prot  Length:194

    Alignment length:194
                               1                                                                                                                                                                                              
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187    
            XPT_BACSU     - ---MEALKRKIEEEGVVLSDQVLKVDSFLNHQIDPLLMQRIGDEFASRFAKDGITKIVTIESSGIAPAVMTGLKLGVPVVFARKHKSLTLTDNLLTASVYSFTKQTESQIAVSGTHLSDQDHVLIIDDFLANGQAAHGLVSIVKQAGASIAGIGIVIEKSFQPGRDELVKLGYRVESLARIQSLEEGKVSFVQE 191
               SCOP domains d1y0bd_ D: Xanthine phosphoribosyltransferase                                                                                                                                                      SCOP domains
               CATH domains 1y0bD00 D:-2-191  [code=3.40.50.2020, no name defined]                                                                                                                                             CATH domains
           Pfam domains (1) ----------------------------Pribosyltran-1y0bD01 D:26-154                                                                                                    ------------------------------------- Pfam domains (1)
           Pfam domains (2) ----------------------------Pribosyltran-1y0bD02 D:26-154                                                                                                    ------------------------------------- Pfam domains (2)
           Pfam domains (3) ----------------------------Pribosyltran-1y0bD03 D:26-154                                                                                                    ------------------------------------- Pfam domains (3)
           Pfam domains (4) ----------------------------Pribosyltran-1y0bD04 D:26-154                                                                                                    ------------------------------------- Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhhhhhee.....ee.......eehhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhh..eeee...........eeeeeeee....eeeeeeee.hhh....eeeeeeeee..hhhhhhhhhhhhhh..eeeeeeeeeee...hhhhhhhhh...eeeeeeeeehhhhh.ee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y0b D  -2 SNAmEALKRKIEEEGVVLSDQVLKVDSFLNHQIDPLLmQRIGDEFASRFAKDGITKIVTIESSGIAPAVmTGLKLGVPVVFARKHKSLTLTDNLLTASVYSFTKQTESQIAVSGTHLSDQDHVLIIDDFLANGQAAHGLVSIVKQAGASIAGIGIVIEKSFQPGRDELVKLGYRVESLARIQSLEEGKVSFVQE 191
                               |     7        17        27       |37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187    
                               1-MSE                            35-MSE                          67-MSE

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: PRTase-like (145)

Superfamily: PRTase-like (145)

Family: Phosphoribosyltransferases (PRTases) (100)

Protein domain: Xanthine phosphoribosyltransferase (2)

Bacillus subtilis [TaxId: 1423] (2)

1a	d1y0ba1	A:1-191
1b	d1y0bb_	B:
1c	d1y0bc_	C:
1d	d1y0bd_	D:

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=3.40.50.2020, no name defined] (117)

Bacillus subtilis. Organism_taxid: 1423. (8)

1a	1y0bC00	C:-2-189
1b	1y0bA00	A:-1-191
1c	1y0bD00	D:-2-191
1d	1y0bB01	B:3-188

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PRTase-like (59)

Family: Pribosyltran (59)

Bacillus subtilis (2)

1a	Pribosyltran-1y0bD01	D:26-154
1b	Pribosyltran-1y0bD02	D:26-154
1c	Pribosyltran-1y0bD03	D:26-154
1d	Pribosyltran-1y0bD04	D:26-154

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (XPT_BACSU | P42085)

molecular function
	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).
	GO:0000310	xanthine phosphoribosyltransferase activity	Catalysis of the reaction: 5-phospho-alpha-D-ribose 1-diphosphate + xanthine = (9-D-ribosylxanthine)-5'-phosphate + diphosphate.
biological process
	GO:0032265	XMP salvage	Any process which produces xanthosine monophosphate from derivatives of it, without de novo synthesis.
	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:0006166	purine ribonucleoside salvage	Any process which produces a purine nucleoside from derivatives of it, without de novo synthesis.
	GO:0043101	purine-containing compound salvage	Any process that generates a purine-containing compound, any nucleobase, nucleoside, nucleotide or nucleic acid that contains a purine base, from derivatives of them without de novo synthesis.
	GO:0046110	xanthine metabolic process	The chemical reactions and pathways involving xanthine, 2,6-dihydroxypurine, a purine formed in the metabolic breakdown of guanine but not present in nucleic acids.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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	Cis Peptide Bonds
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		Glu D:58 - Ser D:59	[ RasMol ]

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	1y0b
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Description

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Ligands, Modified Residues, Ions (3, 24)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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