1A97 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   XPRTASE FROM E. COLI COMPLEXED WITH GMP

Authors :   S. Vos, R. J. Parry, M. R. Burns, J. De Jersey, J. L. Martin

Date :   16 Apr 98 (Deposition) - 11 Nov 98 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Phosphoribosyltransferase, Transferase, Purine Salvage Enzyme, Glycosyltransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Vos, R. J. Parry, M. R. Burns, J. De Jersey, J. L. Martin
Structures Of Free And Complexed Forms Of Escherichia Coli Xanthine-Guanine Phosphoribosyltransferase.
J. Mol. Biol. V. 282 875 1998
PubMed-ID: 9743633 | Reference-DOI: 10.1006/JMBI.1998.2051
(for further references see the PDB file header)

Molecule 1 - XANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
	Atcc	:	ATCC 37145
	Cellular Location	:	CYTOPLASM
	Chains	:	A, B, C, D
	Collection	:	ATCC 37145
	EC Number	:	2.4.2.22
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cellular Location	:	CYTOPLASM
	Expression System Collection	:	ATCC 87050
	Expression System Gene	:	GPT
	Expression System Plasmid	:	PT7-7
	Expression System Strain	:	SPHI606
	Expression System Taxid	:	562
	Gene	:	GPT
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Strain	:	HB101
	Synonym	:	XPRT

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 6)

No.	Name	Count	Type	Full Name
1	5GP	2	Ligand/Ion	GUANOSINE-5'-MONOPHOSPHATE
2	BO3	4	Ligand/Ion	BORIC ACID

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP B:66 , ASN B:67 , VAL D:35 , ARG D:37 , GLY D:38 , ASP D:88	BINDING SITE FOR RESIDUE BO3 D 301
2	AC2	SOFTWARE	VAL A:35 , SER A:36 , GLY A:38 , ASP A:88 , ASN C:67	BINDING SITE FOR RESIDUE BO3 A 302
3	AC3	SOFTWARE	VAL C:35 , SER C:36 , GLY C:38 , ASP C:88 , 5GP C:306	BINDING SITE FOR RESIDUE BO3 C 303
4	AC4	SOFTWARE	SER B:36 , ARG B:37 , GLY B:38 , ASP B:88 , 5GP B:305	BINDING SITE FOR RESIDUE BO3 B 304
5	AC5	SOFTWARE	ARG B:69 , LEU B:90 , ASP B:92 , THR B:93 , GLY B:94 , THR B:96 , TRP B:134 , ILE B:135 , BO3 B:304 , HOH B:401	BINDING SITE FOR RESIDUE 5GP B 305
6	AC6	SOFTWARE	ARG C:69 , ASP C:88 , LEU C:90 , ASP C:92 , THR C:93 , GLY C:94 , GLY C:95 , THR C:96 , LYS C:115 , TRP C:134 , ILE C:135 , BO3 C:303 , HOH C:417	BINDING SITE FOR RESIDUE 5GP C 306

(no "SS Bond" information available for 1A97)

Asymmetric/Biological Unit

No.	Residues
1	Met A:24	-	Pro A:25
2	Ser A:36	-	Arg A:37
3	Met B:24	-	Pro B:25
4	Ser B:36	-	Arg B:37
5	Met C:24	-	Pro C:25
6	Ser C:36	-	Arg C:37
7	Met D:24	-	Pro D:25
8	Ser D:36	-	Arg D:37

(no "SAP(SNP)/Variant" information available for 1A97)

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PUR_PYR_PR_TRANSFER	PS00103	Purine/pyrimidine phosphoribosyl transferases signature.	XGPT_ECOLI	84-96	4	A:84-96 B:84-96 C:84-96 D:84-96

(no "Exon" information available for 1A97)

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:144
 aligned with XGPT_ECOLI | P0A9M5 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:148
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142        
           XGPT_ECOLI     3 EKYIVTWDMLQIHARKLASRLMPSEQWKGIIAVSRGGLVPGALLARELGIRHVDTVCISSYDHDNQRELKVLKRAEGDGEGFIVIDDLVDTGGTAVAIREMYPKAHFVTIFAKPAGRPLVDDYVVDIPQDTWIEQPWDMGVVFVPPIS 150
               SCOP domains d1a97a_ A: Xanthine-guanine PRTase (XPRTase)                                                                                                         SCOP domains
               CATH domains 1a97A00 A:3-150  [code=3.40.50.2020, no name defined]                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..hhhhhhhhhhhhhh...hhh..eeeeee.hhhhhhhhhhhhh....eeeeeeeee.----.eeeeee........eeeee........hhhhhhh....eeee.eee...hhh.....eee....eee.hhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------PUR_PYR_PR_TR------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a97 A   3 EKYIVTWDMLQIHARKLASRLMPSEQWKGIIAVSRGGLVPGALLARELGIRHVDTVAISSYD----RELKVLKRAEGDGEGFIVIDDLVDTGGTAVAIREMYPKAHFVTIFAKPAGRPLVDDYVVDIPQDTWIEQPWDMGVVFVPPIS 150
                                    12        22        32        42        52        62 |    | 72        82        92       102       112       122       132       142        
                                                                                        64   69

Chain B from PDB  Type:PROTEIN  Length:148
 aligned with XGPT_ECOLI | P0A9M5 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:148
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142        
           XGPT_ECOLI     3 EKYIVTWDMLQIHARKLASRLMPSEQWKGIIAVSRGGLVPGALLARELGIRHVDTVCISSYDHDNQRELKVLKRAEGDGEGFIVIDDLVDTGGTAVAIREMYPKAHFVTIFAKPAGRPLVDDYVVDIPQDTWIEQPWDMGVVFVPPIS 150
               SCOP domains d1a97b_ B: Xanthine-guanine PRTase (XPRTase)                                                                                                         SCOP domains
               CATH domains 1a97B00 B:3-150  [code=3.40.50.2020, no name defined]                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..hhhhhhhhhhhhhh...hhh..eeeeee.hhhhhhhhhhhh.....eeeeeeeeeee..eeeeeeee........eeeee......hhhhhhhhh....eeee.eeehhhhhh.....eee....eee.hhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------PUR_PYR_PR_TR------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a97 B   3 EKYIVTWDMLQIHARKLASRLMPSEQWKGIIAVSRGGLVPGALLARELGIRHVDTVAISSYDHDNQRELKVLKRAEGDGEGFIVIDDLVDTGGTAVAIREMYPKAHFVTIFAKPAGRPLVDDYVVDIPQDTWIEQPWDMGVVFVPPIS 150
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142

Chain C from PDB  Type:PROTEIN  Length:148
 aligned with XGPT_ECOLI | P0A9M5 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:148
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142        
           XGPT_ECOLI     3 EKYIVTWDMLQIHARKLASRLMPSEQWKGIIAVSRGGLVPGALLARELGIRHVDTVCISSYDHDNQRELKVLKRAEGDGEGFIVIDDLVDTGGTAVAIREMYPKAHFVTIFAKPAGRPLVDDYVVDIPQDTWIEQPWDMGVVFVPPIS 150
               SCOP domains d1a97c_ C: Xanthine-guanine PRTase (XPRTase)                                                                                                         SCOP domains
               CATH domains 1a97C00 C:3-150  [code=3.40.50.2020, no name defined]                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..hhhhhhhhhhhhhh........eeeeee..hhhhhhhhhhhh....eeeeeeeeeee..eeeeeeee........eeeee......hhhhhhhhh....eeee.eeehhhhhh.....eee....eee.hhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------PUR_PYR_PR_TR------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a97 C   3 EKYIVTWDMLQIHARKLASRLMPSEQWKGIIAVSRGGLVPGALLARELGIRHVDTVAISSYDHDNQRELKVLKRAEGDGEGFIVIDDLVDTGGTAVAIREMYPKAHFVTIFAKPAGRPLVDDYVVDIPQDTWIEQPWDMGVVFVPPIS 150
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142

Chain D from PDB  Type:PROTEIN  Length:141
 aligned with XGPT_ECOLI | P0A9M5 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:148
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142        
           XGPT_ECOLI     3 EKYIVTWDMLQIHARKLASRLMPSEQWKGIIAVSRGGLVPGALLARELGIRHVDTVCISSYDHDNQRELKVLKRAEGDGEGFIVIDDLVDTGGTAVAIREMYPKAHFVTIFAKPAGRPLVDDYVVDIPQDTWIEQPWDMGVVFVPPIS 150
               SCOP domains d1a97d_ D: Xanthine-guanine PRTase (XPRTase)                                                                                                         SCOP domains
               CATH domains 1a97D00 D:3-150  [code=3.40.50.2020, no name defined]                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..hhhhhhhhhhhhhhh..hhh..eeeee..hhhhhhhhhhhh.....eeee.....-------.............eeeee......hhhhhhhhh....eeee.eee...hhh.....eee....eee.hhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------PUR_PYR_PR_TR------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a97 D   3 EKYIVTWDMLQIHARKLASRLMPSEQWKGIIAVSRGGLVPGALLARELGIRHVDTVAISSY-------LKVLKRAEGDGEGFIVIDDLVDTGGTAVAIREMYPKAHFVTIFAKPAGRPLVDDYVVDIPQDTWIEQPWDMGVVFVPPIS 150
                                    12        22        32        42        52        62|       72        82        92       102       112       122       132       142        
                                                                                       63      71

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( (-)

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Class: Alpha and beta proteins (a/b) (23833)

Fold: PRTase-like (145)

Superfamily: PRTase-like (145)

Family: Phosphoribosyltransferases (PRTases) (100)

Protein domain: Xanthine-guanine PRTase (XPRTase) (6)

Escherichia coli [TaxId: 562] (5)

1a	d1a97a_	A:
1b	d1a97b_	B:
1c	d1a97c_	C:
1d	d1a97d_	D:

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=3.40.50.2020, no name defined] (117)

Escherichia coli. Organism_taxid: 562. Strain: hb101. (2)

1a	1a97B00	B:3-150
1b	1a97C00	C:3-150
1c	1a97A00	A:3-150
1d	1a97D00	D:3-150

(no "Pfam Domain" information available for 1A97)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (XGPT_ECOLI | P0A9M5)

molecular function
	GO:0004422	hypoxanthine phosphoribosyltransferase activity	Catalysis of the reaction: IMP + diphosphate = hypoxanthine + 5-phospho-alpha-D-ribose 1-diphosphate.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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: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:0032263	GMP salvage	Any process which produces guanosine monophosphate from derivatives of it, without de novo synthesis.
	GO:0032264	IMP salvage	Any process which produces inosine monophosphate from derivatives of it, without de novo synthesis.
	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.
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.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
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		Met D:24 - Pro D:25	[ RasMol ]
		Ser A:36 - Arg A:37	[ RasMol ]
		Ser B:36 - Arg B:37	[ RasMol ]
		Ser C:36 - Arg C:37	[ RasMol ]
		Ser D:36 - Arg D:37	[ RasMol ]

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	1a97
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(no "Related Entries Specified in the PDB File" available for 1A97)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

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