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Title :   CRYSTAL STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM BACILLUS SUBTILIS COMPLEXED WITH UMP

Authors :   T. C. Appleby, C. L. Kinsland, T. P. Begley, S. E. Ealick

Date :   03 Nov 99 (Deposition) - 06 Mar 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Decarboxylase, Ump, Tim Barrel, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. C. Appleby, C. Kinsland, T. P. Begley, S. E. Ealick
The Crystal Structure And Mechanism Of Orotidine 5'-Monophosphate Decarboxylase.
Proc. Natl. Acad. Sci. Usa V. 97 2005 2000
PubMed-ID: 10681442 | Reference-DOI: 10.1073/PNAS.259441296
(for further references see the PDB file header)

Molecule 1 - OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
	Chains	:	A, B, C
	EC Number	:	4.1.1.23
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-16B
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	U5P	3	Ligand/Ion	URIDINE-5'-MONOPHOSPHATE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	U5P	2	Ligand/Ion	URIDINE-5'-MONOPHOSPHATE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	U5P	2	Ligand/Ion	URIDINE-5'-MONOPHOSPHATE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:11 , LYS A:33 , LYS A:62 , LEU A:122 , THR A:123 , VAL A:160 , PRO A:182 , ARG A:185 , GLN A:194 , VAL A:212 , GLY A:214 , ARG A:215 , HOH A:254 , HOH A:255 , HOH A:268 , HOH A:273 , ASP B:65 , ILE B:66 , THR B:69	BINDING SITE FOR RESIDUE U5P A 250
2	AC2	SOFTWARE	ASP A:65 , ILE A:66 , THR A:69 , ASP B:11 , LYS B:33 , LYS B:62 , LEU B:122 , THR B:123 , VAL B:160 , PRO B:182 , ARG B:185 , GLN B:194 , VAL B:212 , GLY B:214 , ARG B:215 , HOH B:264 , HOH B:271 , HOH B:278 , HOH B:284	BINDING SITE FOR RESIDUE U5P B 251
3	AC3	SOFTWARE	ASP C:11 , LYS C:33 , LYS C:62 , ASP C:65 , ILE C:66 , THR C:69 , LEU C:122 , THR C:123 , VAL C:160 , PRO C:182 , ARG C:185 , GLN C:194 , VAL C:212 , GLY C:214 , ARG C:215 , HOH C:256 , HOH C:261 , HOH C:264 , HOH C:275	BINDING SITE FOR RESIDUE U5P C 252

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

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

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

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	OMPDECASE	PS00156	Orotidine 5'-phosphate decarboxylase active site.	PYRF_BACSU	57-70	3	A:57-70 B:57-70 C:57-70

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_BACSU	57-70	2	A:57-70 B:57-70 -

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_BACSU	57-70	2	- - C:57-70

(no "Exon" information available for 1DBT)

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:237
 aligned with PYRF_BACSU | P25971 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:237
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       
           PYRF_BACSU     1 MKNNLPIIALDFASAEETLAFLAPFQQEPLFVKVGMELFYQEGPSIVKQLKERNCELFLDLKLHDIPTTVNKAMKRLASLGVDLVNVHAAGGKKMMQAALEGLEEGTPAGKKRPSLIAVTQLTSTSEQIMKDELLIEKSLIDTVVHYSKQAEESGLDGVVCSVHEAKAIYQAVSPSFLTVTPGIRMSEDAANDQVRVATPAIAREKGSSAIVVGRSITKAEDPVKAYKAVRLEWEGI 237
               SCOP domains d1dbta_ A: Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase)                                                                                                                                                                       SCOP domains
               CATH domains 1dbtA00 A:1-237 Aldolase class I                                                                                                                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee....hhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhh.......eeeee......hhhhhhhh.....hhhhhhhhhhhhhhhh...eee.hhhhhhhhh.......eeee.................hhhhhhhh...eeeehhhhhh..hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------OMPDECASE     ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dbt A   1 MKNNLPIIALDFASAEETLAFLAPFQQEPLFVKVGMELFYQEGPSIVKQLKERNCELFLDLKLHDIPTTVNKAMKRLASLGVDLVNVHAAGGKKMMQAALEGLEEGTPAGKKRPSLIAVTQLTSTSEQIMKDELLIEKSLIDTVVHYSKQAEESGLDGVVCSVHEAKAIYQAVSPSFLTVTPGIRMSEDAANDQVRVATPAIAREKGSSAIVVGRSITKAEDPVKAYKAVRLEWEGI 237
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

Chain B from PDB  Type:PROTEIN  Length:234
 aligned with PYRF_BACSU | P25971 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:234
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232    
           PYRF_BACSU     3 NNLPIIALDFASAEETLAFLAPFQQEPLFVKVGMELFYQEGPSIVKQLKERNCELFLDLKLHDIPTTVNKAMKRLASLGVDLVNVHAAGGKKMMQAALEGLEEGTPAGKKRPSLIAVTQLTSTSEQIMKDELLIEKSLIDTVVHYSKQAEESGLDGVVCSVHEAKAIYQAVSPSFLTVTPGIRMSEDAANDQVRVATPAIAREKGSSAIVVGRSITKAEDPVKAYKAVRLEWEG 236
               SCOP domains d1dbtb_ B: Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase)                                                                                                                                                                    SCOP domains
               CATH domains 1dbtB00 B:3-236 Aldolase class I                                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee...hhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhhh.......eeeee......hhhhhhhh.....hhhhhhhhhhhhhhhh...eee.hhhhhhhhhh......eeee.................hhhhhhhh...eeeehhhhhh..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------OMPDECASE     ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1dbt B   3 NNLPIIALDFASAEETLAFLAPFQQEPLFVKVGMELFYQEGPSIVKQLKERNCELFLDLKLHDIPTTVNKAMKRLASLGVDLVNVHAAGGKKMMQAALEGLEEGTPAGKKRPSLIAVTQLTSTSEQIMKDELLIEKSLIDTVVHYSKQAEESGLDGVVCSVHEAKAIYQAVSPSFLTVTPGIRMSEDAANDQVRVATPAIAREKGSSAIVVGRSITKAEDPVKAYKAVRLEWEG 236
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232

Chain C from PDB  Type:PROTEIN  Length:234
 aligned with PYRF_BACSU | P25971 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:234
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232    
           PYRF_BACSU     3 NNLPIIALDFASAEETLAFLAPFQQEPLFVKVGMELFYQEGPSIVKQLKERNCELFLDLKLHDIPTTVNKAMKRLASLGVDLVNVHAAGGKKMMQAALEGLEEGTPAGKKRPSLIAVTQLTSTSEQIMKDELLIEKSLIDTVVHYSKQAEESGLDGVVCSVHEAKAIYQAVSPSFLTVTPGIRMSEDAANDQVRVATPAIAREKGSSAIVVGRSITKAEDPVKAYKAVRLEWEG 236
               SCOP domains d1dbtc_ C: Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase)                                                                                                                                                                    SCOP domains
               CATH domains 1dbtC00 C:3-236 Aldolase class I                                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eee....hhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhhh.......eeeee......hhhhhhhh.....hhhhhhhhhhhhhhhh...eee.hhhhhhhhh.......eeee.................hhhhhhhh...eeeehhhhhh..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------OMPDECASE     ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1dbt C   3 NNLPIIALDFASAEETLAFLAPFQQEPLFVKVGMELFYQEGPSIVKQLKERNCELFLDLKLHDIPTTVNKAMKRLASLGVDLVNVHAAGGKKMMQAALEGLEEGTPAGKKRPSLIAVTQLTSTSEQIMKDELLIEKSLIDTVVHYSKQAEESGLDGVVCSVHEAKAIYQAVSPSFLTVTPGIRMSEDAANDQVRVATPAIAREKGSSAIVVGRSITKAEDPVKAYKAVRLEWEG 236
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232

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(

)

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

Bacillus subtilis [TaxId: 1423] (1)

1a	d1dbta_	A:
1b	d1dbtb_	B:
1c	d1dbtc_	C:

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)

Bacillus subtilis. Organism_taxid: 1423. (4)

1a	1dbtA00	A:1-237
1b	1dbtB00	B:3-236
1c	1dbtC00	C:3-236

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (PYRF_BACSU | P25971)

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: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.

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