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Title :   CRYSTAL STRUCTURE OF URACIL PHOSPHORIBOSYLTRANSFERASE (TM0721) FROM THERMOTOGA MARITIMA AT 2.30 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   03 Oct 03 (Deposition) - 14 Oct 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Tm0721, Uracil Phosphoribosyltransferase, Structural Genomics, Jcsg, Psi, Protein Structure Initiative, Joint Center For Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Uracil Phosphoribosyltransferase (Tm0721) From Thermotoga Maritima At 2. 30 A Resolution
To Be Published
PubMed: search

Molecule 1 - URACIL PHOSPHORIBOSYLTRANSFERASE
	Chains	:	A, B, C, D
	EC Number	:	2.4.2.9
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TM0721
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336
	Synonym	:	UMP PYROPHOSPHORYLASE, UPRTASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 13)

No.	Name	Count	Type	Full Name
1	SO4	9	Ligand/Ion	SULFATE ION
2	U5P	4	Ligand/Ion	URIDINE-5'-MONOPHOSPHATE

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LEU A:78 , ARG A:79 , ALA A:80 , ILE A:102 , U5P A:600 , HOH A:753 , HOH A:754 , HOH A:756 , HOH A:757 , TYR D:115	BINDING SITE FOR RESIDUE SO4 A 701
02	AC2	SOFTWARE	LEU B:78 , ARG B:79 , ALA B:80 , U5P B:601 , HOH B:768 , TYR C:115	BINDING SITE FOR RESIDUE SO4 B 702
03	AC3	SOFTWARE	TYR B:115 , LEU C:78 , ARG C:79 , ALA C:80 , U5P C:602 , HOH C:772 , HOH C:773 , HOH C:788	BINDING SITE FOR RESIDUE SO4 C 703
04	AC4	SOFTWARE	TYR A:115 , ARG D:79 , ALA D:80 , U5P D:603 , HOH D:794	BINDING SITE FOR RESIDUE SO4 D 704
05	AC5	SOFTWARE	ARG A:187 , ASN A:189 , ASP A:190 , HOH A:710	BINDING SITE FOR RESIDUE SO4 A 705
06	AC6	SOFTWARE	ARG B:187 , ASN B:189 , ASP B:190	BINDING SITE FOR RESIDUE SO4 B 706
07	AC7	SOFTWARE	ARG D:187 , ASN D:189 , ASP D:190	BINDING SITE FOR RESIDUE SO4 D 708
08	AC8	SOFTWARE	GLY A:25 , PRO A:26 , ARG A:207 , HOH A:748 , HOH A:759 , LYS D:70	BINDING SITE FOR RESIDUE SO4 A 709
09	AC9	SOFTWARE	LYS A:70 , GLY D:25 , PRO D:26 , ARG D:207 , HOH D:729	BINDING SITE FOR RESIDUE SO4 D 710
10	BC1	SOFTWARE	ARG A:104 , MET A:133 , ALA A:135 , THR A:136 , GLY A:137 , VAL A:138 , SER A:139 , GLY A:192 , TYR A:193 , ILE A:194 , GLY A:199 , ASP A:200 , ALA A:201 , SO4 A:701 , HOH A:712 , HOH A:737 , HOH A:754 , HOH A:755 , HOH A:756	BINDING SITE FOR RESIDUE U5P A 600
11	BC2	SOFTWARE	ARG B:104 , ASP B:131 , MET B:133 , ALA B:135 , THR B:136 , GLY B:137 , VAL B:138 , SER B:139 , GLY B:192 , TYR B:193 , ILE B:194 , GLY B:199 , ALA B:201 , SO4 B:702 , HOH B:707 , HOH B:724 , HOH B:768 , HOH B:774	BINDING SITE FOR RESIDUE U5P B 601
12	BC3	SOFTWARE	ARG C:104 , MET C:133 , ALA C:135 , THR C:136 , GLY C:137 , VAL C:138 , SER C:139 , GLY C:192 , TYR C:193 , ILE C:194 , GLY C:199 , ASP C:200 , ALA C:201 , SO4 C:703 , HOH C:705 , HOH C:707 , HOH C:710 , HOH C:774 , HOH C:788	BINDING SITE FOR RESIDUE U5P C 602
13	BC4	SOFTWARE	ARG D:104 , MET D:133 , ALA D:135 , THR D:136 , GLY D:137 , VAL D:138 , SER D:139 , GLY D:192 , TYR D:193 , ILE D:194 , GLY D:199 , ASP D:200 , ALA D:201 , SO4 D:704 , HOH D:719 , HOH D:733 , HOH D:794	BINDING SITE FOR RESIDUE U5P D 603

(no "SS Bond" information available for 1O5O)

Asymmetric/Biological Unit

No.	Residues
1	Leu A:78	-	Arg A:79
2	Ile A:195	-	Pro A:196
3	Leu B:78	-	Arg B:79
4	Ile B:195	-	Pro B:196
5	Leu C:78	-	Arg C:79
6	Ile C:195	-	Pro C:196
7	Leu D:78	-	Arg D:79
8	Ile D:195	-	Pro D:196

(no "SAP(SNP)/Variant" information available for 1O5O)

(no "PROSITE Motif" information available for 1O5O)

(no "Exon" information available for 1O5O)

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
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Chain A from PDB  Type:PROTEIN  Length:210
 aligned with UPP_THEMA | Q9WZI0 from UniProtKB/Swiss-Prot  Length:209

    Alignment length:210
                             1                                                                                                                                                                                                                
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209
            UPP_THEMA     - -MKNLVVVDHPLIKHKLTIMRDKNTGPKEFRELLREITLLLAYEATRHLKCEEVEVETPITKTIGYRINDKDIVVVPILRAGLVMADGILELLPNASVGHIGIYRDPETLQAVEYYAKLPPLNDDKEVFLLDPMLATGVSSIKAIEILKENGAKKITLVALIAAPEGVEAVEKKYEDVKIYVAALDERLNDHGYIIPGLGDAGDRLFRTK 209
               SCOP domains d1o5oa_ A: Uracil PRTase, Upp                                                                                                                                                                                      SCOP domains
               CATH domains 1o5oA00 A:0-209  [code=3.40.50.2020, no name defined]                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eee..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.....eeeeee....eeeeee.....eeeeeee.hhhhhhhhhhhhh...ee.eeeeee......eeeeeee........eeeee..ee..hhhhhhhhhhhhhh...eeeee..eehhhhhhhhhhhh...eeee.ee..ee.....ee....hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1o5o A   0 HMKNLVVVDHPLIKHKLTIMRDKNTGPKEFRELLREITLLLAYEATRHLKCEEVEVETPITKTIGYRINDKDIVVVPILRAGLVMADGILELLPNASVGHIGIYRDPETLQAVEYYAKLPPLNDDKEVFLLDPMLATGVSSIKAIEILKENGAKKITLVALIAAPEGVEAVEKKYEDVKIYVAALDERLNDHGYIIPGLGDAGDRLFRTK 209
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209

Chain B from PDB  Type:PROTEIN  Length:209
 aligned with UPP_THEMA | Q9WZI0 from UniProtKB/Swiss-Prot  Length:209

    Alignment length:209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200         
            UPP_THEMA     1 MKNLVVVDHPLIKHKLTIMRDKNTGPKEFRELLREITLLLAYEATRHLKCEEVEVETPITKTIGYRINDKDIVVVPILRAGLVMADGILELLPNASVGHIGIYRDPETLQAVEYYAKLPPLNDDKEVFLLDPMLATGVSSIKAIEILKENGAKKITLVALIAAPEGVEAVEKKYEDVKIYVAALDERLNDHGYIIPGLGDAGDRLFRTK 209
               SCOP domains d1o5ob_ B: Uracil PRTase, Upp                                                                                                                                                                                     SCOP domains
               CATH domains 1o5oB00 B:1-209  [code=3.40.50.2020, no name defined]                                                                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.....eeeeee....eeeeee.....eeeee...hhhhhhhhhhhhh...ee.eeeeee......eeeeeee........eeeee..ee..hhhhhhhhhhhhhh...eeeee..eehhhhhhhhhhhh...eeee.ee..ee.....ee....hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o5o B   1 MKNLVVVDHPLIKHKLTIMRDKNTGPKEFRELLREITLLLAYEATRHLKCEEVEVETPITKTIGYRINDKDIVVVPILRAGLVMADGILELLPNASVGHIGIYRDPETLQAVEYYAKLPPLNDDKEVFLLDPMLATGVSSIKAIEILKENGAKKITLVALIAAPEGVEAVEKKYEDVKIYVAALDERLNDHGYIIPGLGDAGDRLFRTK 209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

Chain C from PDB  Type:PROTEIN  Length:210
 aligned with UPP_THEMA | Q9WZI0 from UniProtKB/Swiss-Prot  Length:209

    Alignment length:210
                             1                                                                                                                                                                                                                
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209
            UPP_THEMA     - -MKNLVVVDHPLIKHKLTIMRDKNTGPKEFRELLREITLLLAYEATRHLKCEEVEVETPITKTIGYRINDKDIVVVPILRAGLVMADGILELLPNASVGHIGIYRDPETLQAVEYYAKLPPLNDDKEVFLLDPMLATGVSSIKAIEILKENGAKKITLVALIAAPEGVEAVEKKYEDVKIYVAALDERLNDHGYIIPGLGDAGDRLFRTK 209
               SCOP domains d1o5oc_ C: Uracil PRTase, Upp                                                                                                                                                                                      SCOP domains
               CATH domains 1o5oC00 C:0-209  [code=3.40.50.2020, no name defined]                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eee..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh....eeeeee....eeeeee.....eeeeeee.hhhhhhhhhhhhh...ee.eeeeee......eeeeeee........eeeee..ee..hhhhhhhhhhhhhh...eeeee..eehhhhhhhhhhhh...eeee.ee..ee.....ee....hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1o5o C   0 HMKNLVVVDHPLIKHKLTIMRDKNTGPKEFRELLREITLLLAYEATRHLKCEEVEVETPITKTIGYRINDKDIVVVPILRAGLVMADGILELLPNASVGHIGIYRDPETLQAVEYYAKLPPLNDDKEVFLLDPMLATGVSSIKAIEILKENGAKKITLVALIAAPEGVEAVEKKYEDVKIYVAALDERLNDHGYIIPGLGDAGDRLFRTK 209
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209

Chain D from PDB  Type:PROTEIN  Length:210
 aligned with UPP_THEMA | Q9WZI0 from UniProtKB/Swiss-Prot  Length:209

    Alignment length:210
                             1                                                                                                                                                                                                                
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209
            UPP_THEMA     - -MKNLVVVDHPLIKHKLTIMRDKNTGPKEFRELLREITLLLAYEATRHLKCEEVEVETPITKTIGYRINDKDIVVVPILRAGLVMADGILELLPNASVGHIGIYRDPETLQAVEYYAKLPPLNDDKEVFLLDPMLATGVSSIKAIEILKENGAKKITLVALIAAPEGVEAVEKKYEDVKIYVAALDERLNDHGYIIPGLGDAGDRLFRTK 209
               SCOP domains d1o5od_ D: Uracil PRTase, Upp                                                                                                                                                                                      SCOP domains
               CATH domains 1o5oD00 D:0-209  [code=3.40.50.2020, no name defined]                                                                                                                                                              CATH domains
           Pfam domains (1) ---------------------------------------------------------Pribosyltran-1o5oD01 D:57-161                                                                            ------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------Pribosyltran-1o5oD02 D:57-161                                                                            ------------------------------------------------ Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------Pribosyltran-1o5oD03 D:57-161                                                                            ------------------------------------------------ Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------------Pribosyltran-1o5oD04 D:57-161                                                                            ------------------------------------------------ Pfam domains (4)
         Sec.struct. author ....eee..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.....eeeeee....eeeeee.....eeeee...hhhhhhhhhhhhh...ee.eeeeee......eeeeeee........eeeee..ee..hhhhhhhhhhhhhh...eeeee..eehhhhhhhhhhhh...eeee.ee..ee.....ee....hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1o5o D   0 HMKNLVVVDHPLIKHKLTIMRDKNTGPKEFRELLREITLLLAYEATRHLKCEEVEVETPITKTIGYRINDKDIVVVPILRAGLVMADGILELLPNASVGHIGIYRDPETLQAVEYYAKLPPLNDDKEVFLLDPMLATGVSSIKAIEILKENGAKKITLVALIAAPEGVEAVEKKYEDVKIYVAALDERLNDHGYIIPGLGDAGDRLFRTK 209
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209

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: PRTase-like (145)

Superfamily: PRTase-like (145)

Family: Phosphoribosyltransferases (PRTases) (100)

Protein domain: Uracil PRTase, Upp (14)

Thermotoga maritima [TaxId: 2336] (1)

1a	d1o5oa_	A:
1b	d1o5ob_	B:
1c	d1o5oc_	C:
1d	d1o5od_	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)

Thermotoga maritima. Organism_taxid: 2336. (1)

1a	1o5oB00	B:1-209
1b	1o5oA00	A:0-209
1c	1o5oC00	C:0-209
1d	1o5oD00	D:0-209

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PRTase-like (59)

Family: Pribosyltran (59)

Thermotoga maritima (1)

1a	Pribosyltran-1o5oD01	D:57-161
1b	Pribosyltran-1o5oD02	D:57-161
1c	Pribosyltran-1o5oD03	D:57-161
1d	Pribosyltran-1o5oD04	D:57-161

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (UPP_THEMA | Q9WZI0)

molecular function
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	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:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	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:0004845	uracil phosphoribosyltransferase activity	Catalysis of the reaction: diphosphate + UMP = 5-phospho-alpha-D-ribose 1-diphosphate + uracil.
	GO:0004849	uridine kinase activity	Catalysis of the reaction: ATP + uridine = ADP + UMP.
biological process
	GO:0044206	UMP salvage	Any process which produces UMP, uridine monophosphate, from derivatives of it (e.g. cytidine, uridine, cytosine) without de novo synthesis.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0006206	pyrimidine nucleobase metabolic process	The chemical reactions and pathways involving pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases.
	GO:0043097	pyrimidine nucleoside salvage	Any process that generates a pyrimidine nucleoside, one of a family of organic molecules consisting of a pyrimidine base covalently bonded to a sugar ribose, from derivatives of it, without de novo synthesis.
	GO:0008655	pyrimidine-containing compound salvage	Any process that generates a pyrimidine-containing compound, any nucleobase, nucleoside, nucleotide or nucleic acid that contains a pyrimidine base, from derivatives of them without de novo synthesis.
	GO:0006223	uracil salvage	Any process that generates uracil, 2,4-dioxopyrimidine, 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.

Asymmetric/Biological Unit
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	1o5o
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Description

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Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 13)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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