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Title :   CRYSTAL STRUCTURE OF SALMONELLA TYPHIMURIUM OMP SYNTHASE IN COMPLEX WITH MGPRPP AND OROTATE

Authors :   A. A. Fedorov, K. Panneerselvam, W. Shi, C. Grubmeyer, S. C. Almo

Date :   16 Apr 02 (Deposition) - 08 May 02 (Release) - 17 Oct 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Loop Closure, Monomer Closure, Orotate Phosphoribosyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Grubmeyer, M. R. Hansen, A. A. Fedorov, S. C. Almo
Structure Of Salmonella Typhimurium Omp Synthase In A Complete Substrate Complex.
Biochemistry V. 51 4397 2012
PubMed-ID: 22531064 | Reference-DOI: 10.1021/BI300083P
(for further references see the PDB file header)

Molecule 1 - OMP SYNTHASE
	Chains	:	A, B
	EC Number	:	2.4.2.10
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PCG13
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	SALMONELLA TYPHIMURIUM
	Organism Taxid	:	602
	Synonym	:	OROTATE PHOSPHORIBOSYLTRANSFERASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 4)

No.	Name	Count	Type	Full Name
1	MG	1	Ligand/Ion	MAGNESIUM ION
2	ORO	2	Ligand/Ion	OROTIC ACID
3	PRP	1	Ligand/Ion	ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH B:3026 , HOH B:3053 , PRP B:5002	BINDING SITE FOR RESIDUE MG B 5003
2	AC2	SOFTWARE	LEU A:1025 , LYS A:1026 , PHE A:1034 , PHE A:1035 , THR A:1128 , ARG A:1156 , HOH A:3220	BINDING SITE FOR RESIDUE ORO A 4001
3	AC3	SOFTWARE	HOH A:3001 , LEU B:2025 , LYS B:2026 , PHE B:2034 , PHE B:2035 , ASP B:2125 , THR B:2128 , ARG B:2156 , HOH B:3002 , HOH B:3017 , HOH B:3020 , PRP B:5002	BINDING SITE FOR RESIDUE ORO B 5001
4	AC4	SOFTWARE	ARG A:1099 , LYS A:1103 , HIS A:1105 , HOH A:3001 , LYS B:2026 , TYR B:2072 , LYS B:2073 , LYS B:2100 , ASP B:2124 , ASP B:2125 , VAL B:2126 , THR B:2128 , ALA B:2129 , GLY B:2130 , THR B:2131 , ALA B:2132 , HOH B:3002 , HOH B:3015 , HOH B:3017 , HOH B:3053 , ORO B:5001 , MG B:5003	BINDING SITE FOR RESIDUE PRP B 5002

(no "SS Bond" information available for 1LH0)

Asymmetric/Biological Unit

No.	Residues
1	Ala A:1071	-	Tyr A:1072
2	Ala B:2071	-	Tyr B:2072

(no "SAP(SNP)/Variant" information available for 1LH0)

Asymmetric/Biological 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.	PYRE_SALTY	120-132	2	A:1120-1132 B:2120-2132

(no "Exon" information available for 1LH0)

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:213
 aligned with PYRE_SALTY | P08870 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   
          PYRE_SALTY      1 MKPYQRQFIEFALNKQVLKFGEFTLKSGRKSPYFFNAGLFNTGRDLALLGRFYAEALVDSGIEFDLLFGPAYKGIPIATTTAVALAEHHDKDLPYCFNRKEAKDHGEGGSLVGSALQGRVMLVDDVITAGTAIRESMEIIQAHGATLAGVLISLDRQERGRGEISAIQEVERDYGCKVISIITLKDLIAYLEEKPDMAEHLAAVRAYREEFGV  213
               SCOP domains d1lh0a_ A: Orotate PRTase                                                                                                                                                                                             SCOP domains
               CATH domains 1lh0A00 A:1001-1213  [code=3.40.50.2020, no name defined]                                                                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..eeeeeee.....eeeeee.hhhh.hhhhhhhhhhhhhhhhhhhh....eee....hhhhhhhhhhhhhhhhhh....eeee............eee.....eeeee.......hhhhhhhhhhhhh..eeeeeeeeee.........hhhhhhhhhhh.eeeeeeehhhhhhhhhhh..hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------PUR_PYR_PR_TR--------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1lh0 A 1001 MKPYQRQFIEFALNKQVLKFGEFTLKSGRKSPYFFNAGLFNTGRDLALLGRFYAEALVDSGIEFDLLFGPAYKGIPIATTTAVALAEHHDKDLPYCFNRKEAKDHGEGGSLVGSALQGRVMLVDDVITAGTAIRESMEIIQAHGATLAGVLISLDRQERGRGEISAIQEVERDYGCKVISIITLKDLIAYLEEKPDMAEHLAAVRAYREEFGV 1213
                                  1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210

Chain B from PDB  Type:PROTEIN  Length:206
 aligned with PYRE_SALTY | P08870 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   
          PYRE_SALTY      1 MKPYQRQFIEFALNKQVLKFGEFTLKSGRKSPYFFNAGLFNTGRDLALLGRFYAEALVDSGIEFDLLFGPAYKGIPIATTTAVALAEHHDKDLPYCFNRKEAKDHGEGGSLVGSALQGRVMLVDDVITAGTAIRESMEIIQAHGATLAGVLISLDRQERGRGEISAIQEVERDYGCKVISIITLKDLIAYLEEKPDMAEHLAAVRAYREEFGV  213
               SCOP domains d1lh0b_ B: Orotate PRTase                                                                                                                                                                                             SCOP domains
               CATH domains 1lh0B00 B:2001-2213  [code=3.40.50.2020, no name defined]                                                                                                                                                             CATH domains
           Pfam domains (1) ------------------------------------Pribosyltran-1lh0B01 B:2037-2154                                                                                      ----------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------Pribosyltran-1lh0B02 B:2037-2154                                                                                      ----------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhh..eeeeeee.....eeeeee.hhhh.hhhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhhhhhh....eeee...-------..eee.....eeeeeeeee..hhhhhhhhhhhhhh..eeeeeeeeee.........hhhhhhhhhhh.eeeeeeehhhhhhhhh....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------PUR_PYR_PR_TR--------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1lh0 B 2001 MKPYQRQFIEFALNKQVLKFGEFTLKSGRKSPYFFNAGLFNTGRDLALLGRFYAEALVDSGIEFDLLFGPAYKGIPIATTTAVALAEHHDKDLPYCFNRKE-------GSLVGSALQGRVMLVDDVITAGTAIRESMEIIQAHGATLAGVLISLDRQERGRGEISAIQEVERDYGCKVISIITLKDLIAYLEEKPDMAEHLAAVRAYREEFGV 2213
                                  2010      2020      2030      2040      2050      2060      2070      2080      2090      2100|     2110      2120      2130      2140      2150      2160      2170      2180      2190      2200      2210   
                                                                                                                             2101    2109

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: Orotate PRTase (5)

Salmonella typhimurium [TaxId: 90371] (3)

1a	d1lh0a_	A:
1b	d1lh0b_	B:

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)

Salmonella typhimurium. Organism_taxid: 602. (2)

1a	1lh0B00	B:2001-2213
1b	1lh0A00	A:1001-1213

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PRTase-like (59)

Family: Pribosyltran (59)

Salmonella typhimurium (3)

1a	Pribosyltran-1lh0B01	B:2037-2154
1b	Pribosyltran-1lh0B02	B:2037-2154

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PYRE_SALTY | P08870)

molecular function
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0004588	orotate phosphoribosyltransferase activity	Catalysis of the reaction: orotidine 5'-phosphate + diphosphate = orotate + 5-phospho-alpha-D-ribose 1-diphosphate.
	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).
biological process
	GO:0044205	'de novo' UMP biosynthetic process	The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate, starting with the synthesis of (S)-dihydroorotate from bicarbonate; UMP biosynthesis may either occur via reduction by quinone, NAD(+) or oxygen.
	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:0006221	pyrimidine nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala A:1071 - Tyr A:1072	[ RasMol ]
		Ala B:2071 - Tyr B:2072	[ RasMol ]

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1i2i	1I2I IS THE THE SAME PROTEIN COMPLEX NOT COMPLETELY REFINED

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