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Title :   CRYSTAL STRUCTURE OF THE OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM SACCHAROMYCES CEREVISIAE COMPLEXED WITH 6-AZAURIDINE 5'-MONOPHOSPHATE

Authors :   A. A. Fedorov, E. V. Fedorov, B. M. Wood, J. A. Gerlt, S. C. Almo

Date :   24 Feb 09 (Deposition) - 23 Jun 09 (Release) - 23 Jun 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

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

Keywords :   Orotidine 5'-Monophosphate Decarboxylase, Saccharomyces Cerevisiae, 6-Azauridine 5'-Monophosphate, Crystal Structure, Decarboxylase, Lyase, Phosphoprotein, Pyrimidine Biosynthesis, Ubl Conjugation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. K. Chan, B. M. Wood, A. A. Fedorov, E. V. Fedorov, H. J. Imker, T. L. Amyes, J. P. Richard, S. C. Almo, J. A. Gerlt
Mechanism Of The Orotidine 5'-Monophosphate Decarboxylase-Catalyzed Reaction: Evidence For Substrate Destabilization.
Biochemistry V. 48 5518 2009
PubMed-ID: 19435314 | Reference-DOI: 10.1021/BI900623R
(for further references see the PDB file header)

Molecule 1 - OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
	Chains	:	A, B
	EC Number	:	4.1.1.23
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	URA3, YEL021W
	Organism Common	:	YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	OMP DECARBOXYLASE, OMPDECASE, OMPDCASE, URIDINE 5'-MONOPHOSPHATE SYNTHASE, UMP SYNTHASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	UP6	2	Ligand/Ion	6-AZA URIDINE 5'-MONOPHOSPHATE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:35 , ASP A:37 , LYS A:59 , HIS A:61 , ASP A:91 , LYS A:93 , LEU A:153 , SER A:154 , PRO A:202 , GLN A:215 , TYR A:217 , GLY A:234 , ARG A:235 , HOH A:274 , HOH A:278 , HOH A:283 , HOH A:306 , HOH A:358 , ASP B:96 , ILE B:97 , THR B:100	BINDING SITE FOR RESIDUE UP6 A 301
2	AC2	SOFTWARE	ASP A:96 , ILE A:97 , THR A:100 , SER B:35 , ASP B:37 , LYS B:59 , HIS B:61 , ASP B:91 , LYS B:93 , LEU B:153 , SER B:154 , PRO B:202 , GLN B:215 , TYR B:217 , GLY B:234 , ARG B:235 , HOH B:282 , HOH B:287 , HOH B:294 , HOH B:314 , HOH B:387	BINDING SITE FOR RESIDUE UP6 B 301

(no "SS Bond" information available for 3GDL)

(no "Cis Peptide Bond" information available for 3GDL)

Asymmetric/Biological Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_PYRF_YEAST_001 *	A	160	S	PYRF_YEAST	---	---	A/B	A	160	S
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	OMPDECASE	PS00156	Orotidine 5'-phosphate decarboxylase active site.	PYRF_YEAST	88-101	2	A:88-101 B:88-101

Asymmetric/Biological Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YEL021W	1	YEL021W.1	V:116167-116970	804	PYRF_YEAST	1-267	267	2	A:5-261 B:5-261	257 257

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:257
 aligned with PYRF_YEAST | P03962 from UniProtKB/Swiss-Prot  Length:267

    Alignment length:257
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       
           PYRF_YEAST     5 TYKERAATHPSPVAAKLFNIMHEKQTNLCASLDVRTTKELLELVEALGPKICLLKTHVDILTDFSMEGTVKPLKALSAKYNFLLFEDRKFADIGNTVKLQYSAGVYRIAEWADITNAHGVVGPGIVSGLKQAAEEVTKEPRGLLMLAELSCKGSLATGEYTKGTVDIAKSDKDFVIGFIAQRDMGGRDEGYDWLIMTPGVGLDDKGDALGQQYRTVDDVVSTGSDIIIVGRGLFAKGRDAKVEGERYRKAGWEAYLR 261
               SCOP domains d3gdla_ A: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains 3gdlA00 A:5-261 Aldolase class I                                                                                                                                                                                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh.hhhhhhhhhhhhhhh..eee.....hhhhhhhhhhhhhhhh.eeeehhhhh.......hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhh...hhhhhh.eeeee.hhhhhhhhhhhhhhhhhh....eeeee..........hhhhhhhhhhhhh.....eeeee......hhhhh...eeee.................hhhhhhhh...eeeehhhhhh...hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------S----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------OMPDECASE     ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:5-261 UniProt: 1-267 [INCOMPLETE]                                                                                                                                                                                                                Transcript 1
                 3gdl A   5 TYKERAATHPSPVAAKLFNIMHEKQTNLCASLDVRTTKELLELVEALGPKICLLKTHVDILTDFSMEGTVKPLKALSAKYNFLLFEDRKFADIGNTVKLQYSAGVYRIAEWADITNAHGVVGPGIVSGLKQAAEEVTKEPRGLLMLAELSCKGSLATGEYTKGTVDIAKSDKDFVIGFIAQRDMGGRDEGYDWLIMTPGVGLDDKGDALGQQYRTVDDVVSTGSDIIIVGRGLFAKGRDAKVEGERYRKAGWEAYLR 261
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254

Chain B from PDB  Type:PROTEIN  Length:257
 aligned with PYRF_YEAST | P03962 from UniProtKB/Swiss-Prot  Length:267

    Alignment length:257
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       
           PYRF_YEAST     5 TYKERAATHPSPVAAKLFNIMHEKQTNLCASLDVRTTKELLELVEALGPKICLLKTHVDILTDFSMEGTVKPLKALSAKYNFLLFEDRKFADIGNTVKLQYSAGVYRIAEWADITNAHGVVGPGIVSGLKQAAEEVTKEPRGLLMLAELSCKGSLATGEYTKGTVDIAKSDKDFVIGFIAQRDMGGRDEGYDWLIMTPGVGLDDKGDALGQQYRTVDDVVSTGSDIIIVGRGLFAKGRDAKVEGERYRKAGWEAYLR 261
               SCOP domains d3gdlb_ B: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains 3gdlB00 B:5-261 Aldolase class I                                                                                                                                                                                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh.hhhhhhhhhhhhhhh..eee.....hhhhhhhhhhhhhhhh.eeeehhhhh.......hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhh...hhhhhh.eeeee.hhhhhhhhhhhhhhhhhh....eeeee..........hhhhhhhhhhhhh.....eeeee......hhhhh...eeee.................hhhhhhhh...eeeehhhhhh...hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------S----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------OMPDECASE     ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:5-261 UniProt: 1-267 [INCOMPLETE]                                                                                                                                                                                                                Transcript 1
                 3gdl B   5 TYKERAATHPSPVAAKLFNIMHEKQTNLCASLDVRTTKELLELVEALGPKICLLKTHVDILTDFSMEGTVKPLKALSAKYNFLLFEDRKFADIGNTVKLQYSAGVYRIAEWADITNAHGVVGPGIVSGLKQAAEEVTKEPRGLLMLAELSCKGSLATGEYTKGTVDIAKSDKDFVIGFIAQRDMGGRDEGYDWLIMTPGVGLDDKGDALGQQYRTVDDVVSTGSDIIIVGRGLFAKGRDAKVEGERYRKAGWEAYLR 261
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254

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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Ribulose-phoshate binding barrel (356)

Family: Decarboxylase (172)

Protein domain: automated matches (117)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (5)

1a	d3gdla_	A:
1b	d3gdlb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Aldolase class I (887)

Yeast (Saccharomyces cerevisiae) (5)

1a	3gdlA00	A:5-261
1b	3gdlB00	B:5-261

(no "Pfam Domain" information available for 3GDL)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PYRF_YEAST | P03962)

molecular function
	GO:0016831	carboxy-lyase activity	Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
	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:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0004590	orotidine-5'-phosphate decarboxylase activity	Catalysis of the reaction: H(+) + orotidine 5'-phosphate = CO(2) + UMP.
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:0006207	'de novo' pyrimidine nucleobase biosynthetic process	The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases, beginning with the synthesis of a pyrimidine ring from simpler precursors.
	GO:0006222	UMP biosynthetic process	The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate.
	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: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.
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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	PYRF_YEAST \| P03962	:	1dqw 1dqx 3gdk 3gdm 3gdr 3gdt

1dqw	CRYSTAL STRUCTURE OF OROTIDINE 5'-PHOSPHATE DECARBOXYLASE (THE SAME PROTEIN WITH DIFFERENT UNIT CELL PARAMETERS)
3gdk	CRYSTAL STRUCTURE OF THE OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM SACCHAROMYCES CEREVISIAE (THE SAME PROTEIN IN APO FORM)
3gdm	CRYSTAL STRUCTURE OF THE K93R MUTANT OF THE OROTIDINE 5'- MONOPHOSPHATE DECARBOXYLASE FROM SACCHAROMYCES CEREVISIAE
3gdr	CRYSTAL STRUCTURE OF THE D91N MUTANT OF THE OROTIDINE 5'- MONOPHOSPHATE DECARBOXYLASE FROM SACCHAROMYCES CEREVISIAE
3gdt	CRYSTAL STRUCTURE OF THE D91N MUTANT OF THE OROTIDINE 5'- MONOPHOSPHATE DECARBOXYLASE FROM SACCHAROMYCES CEREVISIAE COMPLEXED WITH 6-AZAURIDINE 5'-MONOPHOSPHATE

Description

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Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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