1QK5 - JenaLib

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Title :   TOXOPLASMA GONDII HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE WITH XMP, PYROPHOSPHATE AND TWO MG2+ IONS

Authors :   A. Heroux, E. L. White, L. J. Ross, R. L. Davis, D. W. Borhani

Date :   09 Jul 99 (Deposition) - 17 Oct 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

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

Reference :   A. Heroux, E. L. White, L. J. Ross, R. L. Davis, D. W. Borhani
Crystal Structure Of Toxoplasma Gondii Hypoxanthine-Guanine Phosphoribosyltransferase With Xmp, Pyrophosphate And Two Mg2+ Ions Bound: Insights Into The Catalytic Mechanism
Biochemistry V. 38 14495 1999
PubMed-ID: 10545171 | Reference-DOI: 10.1021/BI990508I
(for further references see the PDB file header)

Molecule 1 - HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.4.2.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PETC1-D150A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET15B
	Mutation	:	YES
	Organism Scientific	:	TOXOPLASMA GONDII
	Organism Taxid	:	383379
	Strain	:	RH
	Synonym	:	HGPRTASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	MG	4	Ligand/Ion	MAGNESIUM ION
2	POP	2	Ligand/Ion	PYROPHOSPHATE 2-
3	XMP	2	Ligand/Ion	XANTHOSINE-5'-MONOPHOSPHATE

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	POP	4	Ligand/Ion	PYROPHOSPHATE 2-
3	XMP	4	Ligand/Ion	XANTHOSINE-5'-MONOPHOSPHATE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	XMP A:300 , POP A:301 , HOH A:2062 , HOH A:2065 , HOH A:2099	BINDING SITE FOR RESIDUE MG A 302
2	AC2	SOFTWARE	ASP A:206 , POP A:301 , HOH A:2083 , HOH A:2084 , HOH A:2102	BINDING SITE FOR RESIDUE MG A 303
3	AC3	SOFTWARE	POP B:301 , HOH B:2049 , HOH B:2053 , HOH B:2054 , HOH B:2077	BINDING SITE FOR RESIDUE MG B 302
4	AC4	SOFTWARE	ASP B:206 , POP B:301 , HOH B:2063 , HOH B:2064 , HOH B:2078	BINDING SITE FOR RESIDUE MG B 303
5	AC5	SOFTWARE	ASP A:147 , ILE A:148 , ALA A:150 , THR A:151 , GLY A:152 , PHE A:153 , THR A:154 , LYS A:178 , TRP A:199 , ILE A:200 , TYR A:205 , ASP A:206 , POP A:301 , MG A:302 , HOH A:2097 , HOH A:2098 , HOH A:2099 , HOH A:2100 , HOH A:2102	BINDING SITE FOR RESIDUE XMP A 300
6	AC6	SOFTWARE	LYS A:79 , GLY A:80 , ARG A:114 , LYS A:116 , ASP A:206 , ARG A:212 , XMP A:300 , MG A:302 , MG A:303 , HOH A:2062 , HOH A:2065 , HOH A:2084 , HOH A:2086 , HOH A:2098 , HOH A:2101 , HOH A:2102	BINDING SITE FOR RESIDUE POP A 301
7	AC7	SOFTWARE	ASP B:147 , ILE B:148 , ALA B:150 , THR B:151 , GLY B:152 , PHE B:153 , THR B:154 , LYS B:178 , VAL B:198 , TRP B:199 , ILE B:200 , TYR B:205 , ASP B:206 , POP B:301 , HOH B:2076 , HOH B:2077 , HOH B:2078	BINDING SITE FOR RESIDUE XMP B 300
8	AC8	SOFTWARE	LYS B:79 , GLY B:80 , ARG B:114 , LYS B:116 , ASP B:206 , ARG B:212 , XMP B:300 , MG B:302 , MG B:303 , HOH B:2049 , HOH B:2053 , HOH B:2054 , HOH B:2063 , HOH B:2077 , HOH B:2079 , HOH B:2080	BINDING SITE FOR RESIDUE POP B 301

(no "SS Bond" information available for 1QK5)

Asymmetric Unit

No.	Residues
1	Leu A:78	-	Lys A:79
2	Leu B:78	-	Lys B:79

(no "SAP(SNP)/Variant" information available for 1QK5)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PUR_PYR_PR_TRANSFER	PS00103	Purine/pyrimidine phosphoribosyl transferases signature.	HGXR_TOXGO	142-154	2	A:142-154 B:142-154

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PUR_PYR_PR_TRANSFER	PS00103	Purine/pyrimidine phosphoribosyl transferases signature.	HGXR_TOXGO	142-154	4	A:142-154 B:142-154

(no "Exon" information available for 1QK5)

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:215
 aligned with HGXR_TOXGO | Q26997 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:230
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230
           HGXR_TOXGO     1 MASKPIEDYGKGKGRIEPMYIPDNTFYNADDFLVPPHCKPYIDKILLPGGLVKDRVEKLAYDIHRTYFGEELHIICILKGSRGFFNLLIDYLATIQKYSGRESSVPPFFEHYVRLKSYQNDNSTGQLTVLSDDLSIFRDKHVLIVEDIVDTGFTLTEFGERLKAVGPKSMRIATLVEKRTDRSNSLKGDFVGFSIEDVWIVGCCYDFNEMFRDFDHVAVLSDAARKKFEK 230
               SCOP domains d1qk5a_ A: Hypoxanthine-guanine-xanthine PRTase                                                                                                                                                                                        SCOP domains
               CATH domains 1qk5A00 A:1-230  [code=3.40.50.2020, no name defined]                                                                                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh....................hhh...............hhhhhhhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhhhhhhh.........eeeeee..-----------.....hhhhhh..eeeeee.....hhhhhhhhhhhhh....eeeeee.eee..----........eee.........................hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------PUR_PYR_PR_TR---------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qk5 A   1 MASKPIEDYGKGKGRIEPMYIPDNTFYNADDFLVPPHCKPYIDKILLPGGLVKDRVEKLAYDIHRTYFGEELHIICILKGSRGFFNLLIDYLATIQKYSGRESSVPPFFEHYVRLK-----------TVLSDDLSIFRDKHVLIVEDIVATGFTLTEFGERLKAVGPKSMRIATLVEKRT----SLKGDFVGFSIEDVWIVGCCYDFNEMFRDFDHVAVLSDAARKKFEK 230
                                    10        20        30        40        50        60        70        80        90       100       110     |   -       130       140       150       160       170       180    |  190       200       210       220       230
                                                                                                                                             116         128                                                 180  185

Chain B from PDB  Type:PROTEIN  Length:217
 aligned with HGXR_TOXGO | Q26997 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:230
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230
           HGXR_TOXGO     1 MASKPIEDYGKGKGRIEPMYIPDNTFYNADDFLVPPHCKPYIDKILLPGGLVKDRVEKLAYDIHRTYFGEELHIICILKGSRGFFNLLIDYLATIQKYSGRESSVPPFFEHYVRLKSYQNDNSTGQLTVLSDDLSIFRDKHVLIVEDIVDTGFTLTEFGERLKAVGPKSMRIATLVEKRTDRSNSLKGDFVGFSIEDVWIVGCCYDFNEMFRDFDHVAVLSDAARKKFEK 230
               SCOP domains d1qk5b_ B: Hypoxanthine-guanine-xanthine PRTase                                                                                                                                                                                        SCOP domains
               CATH domains 1qk5B00 B:1-230  [code=3.40.50.2020, no name defined]                                                                                                                                                                                  CATH domains
           Pfam domains (1) ------------------------------------------Pribosyltran-1qk5B01 B:43-176                                                                                                         ----    ---------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------Pribosyltran-1qk5B02 B:43-176                                                                                                         ----    ---------------------------------------------- Pfam domains (2)
         Sec.struct. author ....hhhhh....................hhh.....hhhhh.....hhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh.........eeeeeeee---------..eeee.hhhhhh..eeeeee.....hhhhhhhhhhhhhhh..eeeeee.eee..----........eee.........................hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------PUR_PYR_PR_TR---------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qk5 B   1 MASKPIEDYGKGKGRIEPMYIPDNTFYNADDFLVPPHCKPYIDKILLPGGLVKDRVEKLAYDIHRTYFGEELHIICILKGSRGFFNLLIDYLATIQKYSGRESSVPPFFEHYVRLK---------QLTVLSDDLSIFRDKHVLIVEDIVATGFTLTEFGERLKAVGPKSMRIATLVEKRT----SLKGDFVGFSIEDVWIVGCCYDFNEMFRDFDHVAVLSDAARKKFEK 230
                                    10        20        30        40        50        60        70        80        90       100       110     |   -     | 130       140       150       160       170       180    |  190       200       210       220       230
                                                                                                                                             116       126                                                   180  185

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(

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Folds(

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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: Hypoxanthine-guanine-xanthine PRTase (7)

Toxoplasma gondii [TaxId: 5811] (5)

1a	d1qk5a_	A:
1b	d1qk5b_	B:

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)

Toxoplasma gondii. Organism_taxid: 383379. Strain: rh. (3)

1a	1qk5A00	A:1-230
1b	1qk5B00	B:1-230

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PRTase-like (59)

Family: Pribosyltran (59)

Toxoplasma gondii (2)

1a	Pribosyltran-1qk5B01	B:43-176
1b	Pribosyltran-1qk5B02	B:43-176

Asymmetric Unit(hide GO term definitions)

Chain A,B (HGXR_TOXGO | Q26997)

molecular function
	GO:0052657	guanine phosphoribosyltransferase activity	Catalysis of the reaction: GMP + diphosphate = guanine + 5-phospho-alpha-D-ribose 1-diphosphate.
	GO:0004422	hypoxanthine phosphoribosyltransferase activity	Catalysis of the reaction: IMP + diphosphate = hypoxanthine + 5-phospho-alpha-D-ribose 1-diphosphate.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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: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
		Leu A:78 - Lys A:79	[ RasMol ]
		Leu B:78 - Lys B:79	[ RasMol ]

Biological Unit
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	1qk5
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UniProtKB/Swiss-Prot
	HGXR_TOXGO \| Q26997	:	1dbr 1fsg 1qk3 1qk4

1dbr	HYPOXANTHINE GUANINE XANTHINE
1hmp	HYPOXANTHINE GUANINE PHOSPHORIBOSYLTRANSFERASE
1qk3	HYPOXANTHINE GUANINE PHOSPHORIBOSYLTRANSFERASE
1qk4	HYPOXANTHINE GUANINE PHOSPHORIBOSYLTRANSFERASE

Description

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Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (0, 0)

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