3GDR - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE D91N MUTANT OF THE OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM SACCHAROMYCES CEREVISIAE

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 :   1.90

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

Keywords :   Orotidine 5'-Monophosphate Decarboxylase, Saccharomyces Cerevisiae, D91N Mutant, 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, C, D
	EC Number	:	4.1.1.23
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	URA3, YEL021W
	Mutation	:	YES
	Organism Common	:	YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	OMP DECARBOXYLASE, OMPDECASE, OMPDCASE, URIDINE 5'-MONOPHOSPHATE SYNTHASE, UMP SYNTHASE

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A			D
Biological Unit 2 (1x)	:		B	C

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3GDR)

(no "Site" information available for 3GDR)

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

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

Asymmetric Unit (1, 4)

								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/C/D	A	160	S
	* ID not provided by source

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

Biological Unit 1 (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/D	A	160	S
	* ID not provided by source

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

Biological Unit 2 (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	---	---	B/C	A	160	S
	* ID not provided by source

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	OMPDECASE	PS00156	Orotidine 5'-phosphate decarboxylase active site.	PYRF_YEAST	88-101	4	A:88-101 B:88-101 C:88-101 D:88-101

Biological Unit 1 (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 - - D:88-101

Biological Unit 2 (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	- B:88-101 C:88-101 -

Asymmetric Unit (1, 4)

	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	4	A:3-262 B:3-262 C:3-266 (gaps) D:3-266 (gaps)	260 260 264 264

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:260
 aligned with PYRF_YEAST | P03962 from UniProtKB/Swiss-Prot  Length:267

    Alignment length:260
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262
           PYRF_YEAST     3 KATYKERAATHPSPVAAKLFNIMHEKQTNLCASLDVRTTKELLELVEALGPKICLLKTHVDILTDFSMEGTVKPLKALSAKYNFLLFEDRKFADIGNTVKLQYSAGVYRIAEWADITNAHGVVGPGIVSGLKQAAEEVTKEPRGLLMLAELSCKGSLATGEYTKGTVDIAKSDKDFVIGFIAQRDMGGRDEGYDWLIMTPGVGLDDKGDALGQQYRTVDDVVSTGSDIIIVGRGLFAKGRDAKVEGERYRKAGWEAYLRR 262
               SCOP domains d3gdra_ A: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains 3gdrA00 A:3-262 Aldolase class I                                                                                                                                                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh.hhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhh.eeeehhhhh.......hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhh...hhhhh..eeee.....hhhhhhhhhhhhhhh....eeeee..........hhhhhhhhhhhhhh....eeeee......hhhhh...eeee..ee.......hhhhheehhhhhhhh..eeeehhhhh....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------S------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------OMPDECASE     ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:3-262 UniProt: 1-267 [INCOMPLETE]                                                                                                                                                                                                                   Transcript 1
                 3gdr A   3 KATYKERAATHPSPVAAKLFNIMHEKQTNLCASLDVRTTKELLELVEALGPKICLLKTHVDILTDFSMEGTVKPLKALSAKYNFLLFENRKFADIGNTVKLQYSAGVYRIAEWADITNAHGVVGPGIVSGLKQAAEEVTKEPRGLLMLAELSCKGSLATGEYTKGTVDIAKSDKDFVIGFIAQRDMGGRDEGYDWLIMTPGVGLDDKGDALGQQYRTVDDVVSTGSDIIIVGRGLFAKGRDAKVEGERYRKAGWEAYLRR 262
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262

Chain B from PDB  Type:PROTEIN  Length:260
 aligned with PYRF_YEAST | P03962 from UniProtKB/Swiss-Prot  Length:267

    Alignment length:260
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262
           PYRF_YEAST     3 KATYKERAATHPSPVAAKLFNIMHEKQTNLCASLDVRTTKELLELVEALGPKICLLKTHVDILTDFSMEGTVKPLKALSAKYNFLLFEDRKFADIGNTVKLQYSAGVYRIAEWADITNAHGVVGPGIVSGLKQAAEEVTKEPRGLLMLAELSCKGSLATGEYTKGTVDIAKSDKDFVIGFIAQRDMGGRDEGYDWLIMTPGVGLDDKGDALGQQYRTVDDVVSTGSDIIIVGRGLFAKGRDAKVEGERYRKAGWEAYLRR 262
               SCOP domains d3gdrb_ B: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains 3gdrB00 B:3-262 Aldolase class I                                                                                                                                                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh.hhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhh.eeeehhhhh.......hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhh...hhhhh..eeee.hhhhhhhhhhhhhhhhhhh....eeeee..........hhhhhhhhhhhhhh....eeeee......hhhhh...eeee..ee.......hhhhheehhhhhhh...eeeehhhhh....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------S------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------OMPDECASE     ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:3-262 UniProt: 1-267 [INCOMPLETE]                                                                                                                                                                                                                   Transcript 1
                 3gdr B   3 KATYKERAATHPSPVAAKLFNIMHEKQTNLCASLDVRTTKELLELVEALGPKICLLKTHVDILTDFSMEGTVKPLKALSAKYNFLLFENRKFADIGNTVKLQYSAGVYRIAEWADITNAHGVVGPGIVSGLKQAAEEVTKEPRGLLMLAELSCKGSLATGEYTKGTVDIAKSDKDFVIGFIAQRDMGGRDEGYDWLIMTPGVGLDDKGDALGQQYRTVDDVVSTGSDIIIVGRGLFAKGRDAKVEGERYRKAGWEAYLRR 262
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262

Chain C from PDB  Type:PROTEIN  Length:252
 aligned with PYRF_YEAST | P03962 from UniProtKB/Swiss-Prot  Length:267

    Alignment length:264
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262    
           PYRF_YEAST     3 KATYKERAATHPSPVAAKLFNIMHEKQTNLCASLDVRTTKELLELVEALGPKICLLKTHVDILTDFSMEGTVKPLKALSAKYNFLLFEDRKFADIGNTVKLQYSAGVYRIAEWADITNAHGVVGPGIVSGLKQAAEEVTKEPRGLLMLAELSCKGSLATGEYTKGTVDIAKSDKDFVIGFIAQRDMGGRDEGYDWLIMTPGVGLDDKGDALGQQYRTVDDVVSTGSDIIIVGRGLFAKGRDAKVEGERYRKAGWEAYLRRCGQQ 266
               SCOP domains d3gdrc_ C: automated matches                                                                                                                                                                                                                                             SCOP domains
               CATH domains 3gdrC00 C:3-266 Aldolase class I                                                                                                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhh.hhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhh.eeeehhhhh.......hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhh...hhhhh..eeee.hhhhhhhhhhhhhhhhhhh....eeeee...........hhhhhhhhhhhh.....eeeee......hhhhh...eeee....------------.hhhhhhhhh..eeee.........hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------S---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------OMPDECASE     --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: C:3-266 (gaps) UniProt: 1-267 [INCOMPLETE]                                                                                                                                                                                                                Transcript 1
                 3gdr C   3 KATYKERAATHPSPVAAKLFNIMHEKQTNLCASLDVRTTKELLELVEALGPKICLLKTHVDILTDFSMEGTVKPLKALSAKYNFLLFENRKFADIGNTVKLQYSAGVYRIAEWADITNAHGVVGPGIVSGLKQAAEEVTKEPRGLLMLAELSCKGSLATGEYTKGTVDIAKSDKDFVIGFIAQRDMGGRDEGYDWLIMTPGVG------------RTVDDVVSTGSDIIIVGRGLFAKGRDAKVEGERYRKAGWEAYLRRCGQQ 266
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202  |      -     | 222       232       242       252       262    
                                                                                                                                                                                                                                    205          218

Chain D from PDB  Type:PROTEIN  Length:252
 aligned with PYRF_YEAST | P03962 from UniProtKB/Swiss-Prot  Length:267

    Alignment length:264
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262    
           PYRF_YEAST     3 KATYKERAATHPSPVAAKLFNIMHEKQTNLCASLDVRTTKELLELVEALGPKICLLKTHVDILTDFSMEGTVKPLKALSAKYNFLLFEDRKFADIGNTVKLQYSAGVYRIAEWADITNAHGVVGPGIVSGLKQAAEEVTKEPRGLLMLAELSCKGSLATGEYTKGTVDIAKSDKDFVIGFIAQRDMGGRDEGYDWLIMTPGVGLDDKGDALGQQYRTVDDVVSTGSDIIIVGRGLFAKGRDAKVEGERYRKAGWEAYLRRCGQQ 266
               SCOP domains d3gdrd_ D: automated matches                                                                                                                                                                                                                                             SCOP domains
               CATH domains 3gdrD00 D:3-266 Aldolase class I                                                                                                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhh.hhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhh.eeeehhhhh.......hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhh...hhhhh..eeee.hhhhhhhhhhhhhhhhhhh....eeeee..........hhhhhhhhhhhhh.....eeeee......hhhhh...eeee....------------.hhhhhhhh...eeeehhhhh....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------S---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------OMPDECASE     --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: D:3-266 (gaps) UniProt: 1-267 [INCOMPLETE]                                                                                                                                                                                                                Transcript 1
                 3gdr D   3 KATYKERAATHPSPVAAKLFNIMHEKQTNLCASLDVRTTKELLELVEALGPKICLLKTHVDILTDFSMEGTVKPLKALSAKYNFLLFENRKFADIGNTVKLQYSAGVYRIAEWADITNAHGVVGPGIVSGLKQAAEEVTKEPRGLLMLAELSCKGSLATGEYTKGTVDIAKSDKDFVIGFIAQRDMGGRDEGYDWLIMTPGVG------------RTVDDVVSTGSDIIIVGRGLFAKGRDAKVEGERYRKAGWEAYLRRCGQQ 266
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202  |      -     | 222       232       242       252       262    
                                                                                                                                                                                                                                    205          218

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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	d3gdra_	A:
1b	d3gdrc_	C:
1c	d3gdrd_	D:
1d	d3gdrb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Aldolase class I (887)

Yeast (Saccharomyces cerevisiae) (5)

1a	3gdrA00	A:3-262
1b	3gdrB00	B:3-262
1c	3gdrC00	C:3-266
1d	3gdrD00	D:3-266

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (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 Unit
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	3gdr
		Family and Domain Information	:	ProDom \| SYSTERS
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	PYRF_YEAST \| P03962
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	4.1.1.23
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	PYRF_YEAST \| P03962
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UniProtKB/Swiss-Prot
	PYRF_YEAST \| P03962	:	1dqw 1dqx 3gdk 3gdl 3gdm 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 WT FORM)
3gdl	CRYSTAL STRUCTURE OF THE OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM SACCHAROMYCES CEREVISIAE COMPLEXED WITH 6-AZAURIDINE 5'-MONOPHOSPHATE
3gdm	CRYSTAL STRUCTURE OF THE K93R 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

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