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Title :   CRYSTAL STRUCTURE OF OROTIDINE MONOPHOSPHATE DECARBOXYLASE COMPLEX WITH XMP

Authors :   N. Wu, E. F. Pai

Date :   06 May 02 (Deposition) - 07 Aug 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

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

Reference :   N. Wu, E. F. Pai
Crystal Structures Of Inhibitor Complexes Reveal An Alternate Binding Mode In Orotidine-5'-Monophosphate Decarboxylase.
J. Biol. Chem. V. 277 28080 2002
PubMed-ID: 12011084 | Reference-DOI: 10.1074/JBC.M202362200
(for further references see the PDB file header)

Molecule 1 - OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE
	Chains	:	A, B
	EC Number	:	4.1.1.23
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Taxid	:	562
	Organism Scientific	:	METHANOTHERMOBACTER THERMAUTOTROPHICUS STR. DELTA H
	Organism Taxid	:	187420
	Strain	:	DELTA H
	Synonym	:	OMP DECARBOXYLASE, OMPDCASE, OMPDECASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	BU2	2	Ligand/Ion	1,3-BUTANEDIOL
2	XMP	2	Ligand/Ion	XANTHOSINE-5'-MONOPHOSPHATE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:70 , LYS A:72 , LEU A:123 , VAL A:155 , XMP A:2001 , HOH A:3015	BINDING SITE FOR RESIDUE BU2 A 5001
2	AC2	SOFTWARE	LYS B:1042 , ASP B:1070 , LYS B:1072 , ILE B:1096 , VAL B:1155 , XMP B:2002	BINDING SITE FOR RESIDUE BU2 B 5002
3	AC3	SOFTWARE	ALA A:18 , ASP A:20 , LYS A:42 , ASP A:70 , MET A:126 , SER A:127 , SER A:158 , PRO A:180 , GLY A:202 , ARG A:203 , HOH A:3009 , HOH A:3011 , HOH A:3012 , HOH A:3015 , HOH A:3085 , BU2 A:5001 , ILE B:1076 , HOH B:3066	BINDING SITE FOR RESIDUE XMP A 2001
4	AC4	SOFTWARE	ILE A:76 , ALA B:1018 , ASP B:1020 , LYS B:1042 , ASP B:1070 , SER B:1127 , PRO B:1157 , SER B:1158 , PRO B:1180 , GLY B:1202 , ARG B:1203 , HOH B:3059 , HOH B:3112 , HOH B:3155 , HOH B:3159 , BU2 B:5002	BINDING SITE FOR RESIDUE XMP B 2002

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

Asymmetric/Biological Unit

No.	Residues
1	Asp B:1188	-	Pro B:1189

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

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_METTH	67-80	2	A:67-80 B:1067-1080

(no "Exon" information available for 1LOL)

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:204
 aligned with PYRF_METTH | O26232 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:212
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220  
          PYRF_METTH     11 VMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFRGADSVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTRPERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYLADNPAAAAAGIIESI  222
               SCOP domains d1lola_ A: Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase)                                                                                                                                              SCOP domains
               CATH domains 1lolA00 A:11-222 Aldolase class I                                                                                                                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhh.eeeee...hhhhhhhhhhhhh....eeeeehhhhhhhh.hhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhh.eeeee..........hhhhhhhhhhhhhhhh...eee....hhhhhhhhhhhhh...eeeee.--------.hhhhh..eeeehhhhhh..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------OMPDECASE     ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1lol A   11 VMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFPGADSVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTRPERLSRLREIIGQDSFLISPG--------GETLRFADAIIVGRSIYLADNPAAAAAGIIESI  222
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180|      190       200       210       220  
                                                                                                                                                                                                    181      190

Chain B from PDB  Type:PROTEIN  Length:214
 aligned with PYRF_METTH | O26232 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:219
                                                                                                                                                                                                                                                   228 
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       | 
          PYRF_METTH     11 VMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFRGADSVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTRPERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYLADNPAAAAAGIIESIKDLLNP-    -
               SCOP domains d1lolb_ B: Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase)                                                                                                                                                     SCOP domains
               CATH domains 1lolB00 B:1011-1229 Aldolase class I                                                                                                                                                                                        CATH domains
           Pfam domains (1) --OMPdecase-1lolB01 B:1013-1218                                                                                                                                                                                 ----------- Pfam domains (1)
           Pfam domains (2) --OMPdecase-1lolB02 B:1013-1218                                                                                                                                                                                 ----------- Pfam domains (2)
         Sec.struct. author hhh.eeee....hhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhh.eeeee......hhhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhh...eeeee.-----....hhhhh..eeeehhhhhh..hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------OMPDECASE     ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1lol B 1011 VMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFPGADSVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTRPERLSRLREIIGQDSFLISPG-----GDPGETLRFADAIIVGRSIYLADNPAAAAAGIIESIKDLLIPE 1229
                                  1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180|     1190      1200      1210      1220         
                                                                                                                                                                                                   1181  1187

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: TIM beta/alpha-barrel (3956)

Superfamily: Ribulose-phoshate binding barrel (356)

Family: Decarboxylase (172)

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

Methanobacterium thermoautotrophicum [TaxId: 145262] (16)

1a	d1lola_	A:
1b	d1lolb_	B:

Asymmetric/Biological 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)

Delta h (Methanothermobacter thermautotrophicus str) (13)

1a	1lolB00	B:1011-1229
1b	1lolA00	A:11-222

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: OMPdecase (84)

Methanobacterium thermoautotrophicum (strain Delta H) (55)

1a	OMPdecase-1lolB01	B:1013-1218
1b	OMPdecase-1lolB02	B:1013-1218

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PYRF_METTH | O26232)

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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Asp B:1188 - Pro B:1189	[ RasMol ]

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1loq	OROTIDINE MONOPHOSPHATE DECARBOXYLASE COMPLEXED WITH UMP
1lor	OROTIDINE MONOPHOSPHATE DECARBOXYLASE COMPLEXED WITH BMP
1los	OROTIDINE MONOPHOSPHATE DECARBOXYLASE MUTANT DELTA R203A COMPLEXED WITH 6-AZAUMP
1lp6	OROTIDINE MONOPHOSPHATE DECARBOXYLASE COMPLEXED WITH CMP

Description

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Ligands, Modified Residues, Ions (2, 4)

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