1DQW - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF OROTIDINE 5'-PHOSPHATE DECARBOXYLASE

Authors :   M. V. Milburn, B. G. Miller, A. M. Hassell, R. Wolfenden, S. A. Short

Date :   05 Jan 00 (Deposition) - 20 Mar 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Tim Barrel, Orotidine 5'-Phosphate, Uridine 5'-Phosphate, Decarboxylase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. G. Miller, A. M. Hassell, R. Wolfenden, M. V. Milburn, S. A. Short
Anatomy Of A Proficient Enzyme: The Structure Of Orotidine 5'-Monophosphate Decarboxylase In The Presence And Absence Of A Potential Transition State Analog.
Proc. Natl. Acad. Sci. Usa V. 97 2011 2000
PubMed-ID: 10681417 | Reference-DOI: 10.1073/PNAS.030409797
(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 Plasmid	:	PCDA6022
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1DQW)

(no "Site" information available for 1DQW)

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

(no "Cis Peptide Bond" information available for 1DQW)

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	S	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/B	S	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	---	---	C/D	S	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 B: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	- - C:88-101 D: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:1-267 B:1-267 C:1-267 D:1-267	267 267 267 267

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

    Alignment length:267
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       
           PYRF_YEAST     1 MSKATYKERAATHPSPVAAKLFNIMHEKQTNLCASLDVRTTKELLELVEALGPKICLLKTHVDILTDFSMEGTVKPLKALSAKYNFLLFEDRKFADIGNTVKLQYSAGVYRIAEWADITNAHGVVGPGIVSGLKQAAEEVTKEPRGLLMLAELSCKGSLATGEYTKGTVDIAKSDKDFVIGFIAQRDMGGRDEGYDWLIMTPGVGLDDKGDALGQQYRTVDDVVSTGSDIIIVGRGLFAKGRDAKVEGERYRKAGWEAYLRRCGQQN 267
               SCOP domains d1dqwa_ A: Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase)                                                                                                                                                                                                     SCOP domains
               CATH domains 1dqwA00 A:1-267 Aldolase class I                                                                                                                                                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh.hhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhh.eeeehhhhh.......hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhh...hhhhhh.eeeee....hhhhhhhhhhhhhhh....eeeee..........hhhhhhhhhhhhh.....eeeee..............eeee.................hhhhhhhh...eeeehhhhh....hhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------S----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------OMPDECASE     ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-267 UniProt: 1-267                                                                                                                                                                                                                                       Transcript 1
                 1dqw A   1 MHKATYKERAATHPSPVAAKLFNIMHEKQTNLCASLDVRTTKELLELVEALGPKICLLKTHVDILTDFSMEGTVKPLKALSAKYNFLLFEDRKFADIGNTVKLQYSAGVYRIAEWADITNAHGVVGPGIVSGLKQAAEEVTKEPRGLLMLAELSCKGSLSTGEYTKGTVDIAKSDKDFVIGFIAQRDMGGRDEGYDWLIMTPGVGLDDKGDALGQQYRTVDDVVSTGSDIIIVGRGLFAKGRDAKVEGERYRKAGWEAYLRRCGQQD 267
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260

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

    Alignment length:267
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       
           PYRF_YEAST     1 MSKATYKERAATHPSPVAAKLFNIMHEKQTNLCASLDVRTTKELLELVEALGPKICLLKTHVDILTDFSMEGTVKPLKALSAKYNFLLFEDRKFADIGNTVKLQYSAGVYRIAEWADITNAHGVVGPGIVSGLKQAAEEVTKEPRGLLMLAELSCKGSLATGEYTKGTVDIAKSDKDFVIGFIAQRDMGGRDEGYDWLIMTPGVGLDDKGDALGQQYRTVDDVVSTGSDIIIVGRGLFAKGRDAKVEGERYRKAGWEAYLRRCGQQN 267
               SCOP domains d1dqwb_ B: Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase)                                                                                                                                                                                                     SCOP domains
               CATH domains 1dqwB00 B:1-267 Aldolase class I                                                                                                                                                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh.hhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhh.eeeehhhhh.......hhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhh...hhhhh..eeeee....hhhhhhhhhhhhhhh....eeeee..........hhhhhhhhhhhhh.....eeeee......hhhhh...eeee.................hhhhhhhh...eeeehhhhh....hhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------S----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------OMPDECASE     ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:1-267 UniProt: 1-267                                                                                                                                                                                                                                       Transcript 1
                 1dqw B   1 MHKATYKERAATHPSPVAAKLFNIMHEKQTNLCASLDVRTTKELLELVEALGPKICLLKTHVDILTDFSMEGTVKPLKALSAKYNFLLFEDRKFADIGNTVKLQYSAGVYRIAEWADITNAHGVVGPGIVSGLKQAAEEVTKEPRGLLMLAELSCKGSLSTGEYTKGTVDIAKSDKDFVIGFIAQRDMGGRDEGYDWLIMTPGVGLDDKGDALGQQYRTVDDVVSTGSDIIIVGRGLFAKGRDAKVEGERYRKAGWEAYLRRCGQQD 267
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260

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

    Alignment length:267
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       
           PYRF_YEAST     1 MSKATYKERAATHPSPVAAKLFNIMHEKQTNLCASLDVRTTKELLELVEALGPKICLLKTHVDILTDFSMEGTVKPLKALSAKYNFLLFEDRKFADIGNTVKLQYSAGVYRIAEWADITNAHGVVGPGIVSGLKQAAEEVTKEPRGLLMLAELSCKGSLATGEYTKGTVDIAKSDKDFVIGFIAQRDMGGRDEGYDWLIMTPGVGLDDKGDALGQQYRTVDDVVSTGSDIIIVGRGLFAKGRDAKVEGERYRKAGWEAYLRRCGQQN 267
               SCOP domains d1dqwc_ C: Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase)                                                                                                                                                                                                     SCOP domains
               CATH domains 1dqwC00 C:1-267 Aldolase class I                                                                                                                                                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh.hhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhh.eeeehhhhh.......hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhh...hhhhhh.eeeee....hhhhhhhhhhhhhhh....eeeee..........hhhhhhhhhhhhh.....eeeee......hhhhh...eeeee................hhhhhhhh...eeeehhhhh....hhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------S----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------OMPDECASE     ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: C:1-267 UniProt: 1-267                                                                                                                                                                                                                                       Transcript 1
                 1dqw C   1 MHKATYKERAATHPSPVAAKLFNIMHEKQTNLCASLDVRTTKELLELVEALGPKICLLKTHVDILTDFSMEGTVKPLKALSAKYNFLLFEDRKFADIGNTVKLQYSAGVYRIAEWADITNAHGVVGPGIVSGLKQAAEEVTKEPRGLLMLAELSCKGSLSTGEYTKGTVDIAKSDKDFVIGFIAQRDMGGRDEGYDWLIMTPGVGLDDKGDALGQQYRTVDDVVSTGSDIIIVGRGLFAKGRDAKVEGERYRKAGWEAYLRRCGQQD 267
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260

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

    Alignment length:267
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       
           PYRF_YEAST     1 MSKATYKERAATHPSPVAAKLFNIMHEKQTNLCASLDVRTTKELLELVEALGPKICLLKTHVDILTDFSMEGTVKPLKALSAKYNFLLFEDRKFADIGNTVKLQYSAGVYRIAEWADITNAHGVVGPGIVSGLKQAAEEVTKEPRGLLMLAELSCKGSLATGEYTKGTVDIAKSDKDFVIGFIAQRDMGGRDEGYDWLIMTPGVGLDDKGDALGQQYRTVDDVVSTGSDIIIVGRGLFAKGRDAKVEGERYRKAGWEAYLRRCGQQN 267
               SCOP domains d1dqwd_ D: Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase)                                                                                                                                                                                                     SCOP domains
               CATH domains 1dqwD00 D:1-267 Aldolase class I                                                                                                                                                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh.hhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhh.eeeehhhhh.......hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhh...hhhhhh.eeeee....hhhhhhhhhhhhhhh....eeeee..........hhhhhhhhhhhhh.....eeeee..............eeee.................hhhhhhhh...eeeehhhhh....hhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------S----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------OMPDECASE     ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: D:1-267 UniProt: 1-267                                                                                                                                                                                                                                       Transcript 1
                 1dqw D   1 MHKATYKERAATHPSPVAAKLFNIMHEKQTNLCASLDVRTTKELLELVEALGPKICLLKTHVDILTDFSMEGTVKPLKALSAKYNFLLFEDRKFADIGNTVKLQYSAGVYRIAEWADITNAHGVVGPGIVSGLKQAAEEVTKEPRGLLMLAELSCKGSLSTGEYTKGTVDIAKSDKDFVIGFIAQRDMGGRDEGYDWLIMTPGVGLDDKGDALGQQYRTVDDVVSTGSDIIIVGRGLFAKGRDAKVEGERYRKAGWEAYLRRCGQQD 267
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260

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: TIM beta/alpha-barrel (3956)

Superfamily: Ribulose-phoshate binding barrel (356)

Family: Decarboxylase (172)

Protein domain: Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase) (28)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (2)

1a	d1dqwa_	A:
1b	d1dqwb_	B:
1c	d1dqwc_	C:
1d	d1dqwd_	D:

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)

Baker's yeast (Saccharomyces cerevisiae) (49)

1a	1dqwA00	A:1-267
1b	1dqwB00	B:1-267
1c	1dqwC00	C:1-267
1d	1dqwD00	D:1-267

(no "Pfam Domain" information available for 1DQW)

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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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
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Biological Units
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	1dqw
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	PYRF_YEAST \| P03962	:	1dqx 3gdk 3gdl 3gdm 3gdr 3gdt

1dqx	1DQX IS THE CRYSTAL STRUCTURE OF THE SAME PROTEIN COMPLEXED WITH 6-HYDROXYURIDINE 5'PHOSPHATE.

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Ligands, Modified Residues, Ions (0, 0)

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Exons (1, 4)

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