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Title :   CRYSTAL STRUCTURE OF THE MUTANT R203A OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM COMPLEXED WITH INHIBITOR BMP

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

Date :   23 Jan 10 (Deposition) - 16 Jun 10 (Release) - 19 Jun 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

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

Keywords :   Mutant R203A, 6-Hydroxyuridine-5'-Phosphate, Decarboxylase, Pyrimidine Biosynthesis, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. J. Desai, B. M. Wood, A. A. Fedorov, E. V. Fedorov, B. Goryanova, T. L. Amyes, J. P. Richard, S. C. Almo, J. A. Gerlt
Conformational Changes In Orotidine 5'-Monophosphate Decarboxylase: A Structure-Based Explanation For How The 5'-Phosphate Group Activates The Enzyme.
Biochemistry V. 51 8665 2012
PubMed-ID: 23030629 | Reference-DOI: 10.1021/BI301188K

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	:	PYRF, MTH_129
	Mutation	:	YES
	Organism Scientific	:	METHANOTHERMOBACTER THERMAUTOTROPHICUS
	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 (1, 2)

No.	Name	Count	Type	Full Name
1	BMQ	2	Ligand/Ion	1-(5'-PHOSPHO-BETA-D-RIBOFURANOSYL)BARBITURIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:4 , ASP A:20 , LYS A:42 , ASP A:70 , LYS A:72 , MET A:126 , SER A:127 , PRO A:180 , VAL A:182 , GLN A:185 , GLY A:202 , ALA A:203 , HOH A:231 , HOH A:234 , HOH A:236 , HOH A:238 , HOH A:242 , HOH A:243 , HOH A:248 , HOH A:263 , ASP B:75 , ILE B:76 , THR B:79	BINDING SITE FOR RESIDUE BMQ A 229
2	AC2	SOFTWARE	ASP A:75 , ILE A:76 , THR A:79 , ARG B:4 , ASP B:20 , LYS B:42 , ASP B:70 , LYS B:72 , MET B:126 , SER B:127 , PRO B:180 , GLN B:185 , GLY B:202 , ALA B:203 , HOH B:236 , HOH B:238 , HOH B:239 , HOH B:241 , HOH B:244 , HOH B:250 , HOH B:257	BINDING SITE FOR RESIDUE BMQ B 229

(no "SS Bond" information available for 3LI0)

Asymmetric/Biological Unit

No.	Residues
1	Asn A:227	-	Pro A:228

(no "SAP(SNP)/Variant" information available for 3LI0)

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:67-80

(no "Exon" information available for 3LI0)

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:226
 aligned with PYRF_METTH | O26232 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:226
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222      
           PYRF_METTH     3 SRRVDVMDVMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFRGADSVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTRPERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYLADNPAAAAAGIIESIKDLLNP 228
               SCOP domains d3li0a_ A: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhh.eeeee...hhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhh...eeee........hhhhhh....eeeehhhhhh..hhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------OMPDECASE     ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3li0 A   3 SRRVDVMDVMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFPGADSVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTRPERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGASIYLADNPAAAAAGIIESIKDLLNP 228
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222

Chain B from PDB  Type:PROTEIN  Length:224
 aligned with PYRF_METTH | O26232 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:224
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222    
           PYRF_METTH     3 SRRVDVMDVMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFRGADSVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTRPERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYLADNPAAAAAGIIESIKDLL 226
               SCOP domains d3li0b_ B: automated matches                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------OMPdecase-3li0B01 B:13-218                                                                                                                                                                                    -------- Pfam domains (1)
           Pfam domains (2) ----------OMPdecase-3li0B02 B:13-218                                                                                                                                                                                    -------- Pfam domains (2)
         Sec.struct. author ........hhh.eeeee...hhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhh...eeee........hhhhhh....eeeehhhhhh..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------OMPDECASE     -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3li0 B   3 SRRVDVMDVMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFPGADSVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTRPERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGASIYLADNPAAAAAGIIESIKDLL 226
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222

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: automated matches (117)

Methanothermobacter thermautotrophicus [TaxId: 187420] (66)

1a	d3li0a_	A:
1b	d3li0b_	B:

(no "CATH Domain" information available for 3LI0)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: OMPdecase (84)

Methanobacterium thermoautotrophicum (strain Delta H) (55)

1a	OMPdecase-3li0B01	B:13-218
1b	OMPdecase-3li0B02	B:13-218

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
		Asn A:227 - Pro A:228	[ RasMol ]

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	4.1.1.23
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3lht	CRYSTAL STRUCTURE OF THE MUTANT V201F OF OROTIDINE 5'- MONOPHOSPHATE DECARBOXYLASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM COMPLEXED WITH INHIBITOR BMP
3lhu	CRYSTAL STRUCTURE OF THE MUTANT I199F OF OROTIDINE 5'- MONOPHOSPHATE DECARBOXYLASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM COMPLEXED WITH INHIBITOR BMP
3lhv	CRYSTAL STRUCTURE OF THE MUTANT V182A.I199A.V201A OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM COMPLEXED WITH INHIBITOR BMP
3lhw	CRYSTAL STRUCTURE OF THE MUTANT V182A OF OROTIDINE 5'- MONOPHOSPHATE DECARBOXYLASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM COMPLEXED WITH INHIBITOR BMP
3lhy	CRYSTAL STRUCTURE OF THE MUTANT I199A OF OROTIDINE 5'- MONOPHOSPHATE DECARBOXYLASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM COMPLEXED WITH INHIBITOR BMP
3lhz	CRYSTAL STRUCTURE OF THE MUTANT V201A OF OROTIDINE 5'- MONOPHOSPHATE DECARBOXYLASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM COMPLEXED WITH INHIBITOR BMP
3li1	CRYSTAL STRUCTURE OF THE MUTANT I218A OF OROTIDINE 5'- MONOPHOSPHATE DECARBOXYLASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM COMPLEXED WITH INHIBITOR BMP

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (8, 8)

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