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Title :   CRYSTAL STRUCTURE OF THE MUTANT D70N OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM COMPLEXED WITH SULFATE

Authors :   A. A. Fedorov, E. V. Fedorov, K. K. Chan, J. A. Gerlt, S. C. Almo

Date :   30 Jan 09 (Deposition) - 23 Jun 09 (Release) - 23 Jun 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

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

Keywords :   Orotidine 5'-Monophosphate Decarboxylase, D70N, Crystal Structure, Decarboxylase, Pyrimidine Biosynthesis, Lyase (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
	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 STR. DELTA H
	Organism Taxid	:	187420
	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	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:42 , ASN A:70 , LYS A:72 , HOH A:290 , HOH A:326 , HOH A:335 , ASP B:75 , ILE B:76 , HOH B:232	BINDING SITE FOR RESIDUE SO4 A 229
2	AC2	SOFTWARE	ASP A:75 , ILE A:76 , HOH A:233 , LYS B:42 , ASN B:70 , LYS B:72 , HOH B:233 , HOH B:292 , HOH B:327 , HOH B:337	BINDING SITE FOR RESIDUE SO4 B 229

(no "SS Bond" information available for 3G1Y)

(no "Cis Peptide Bond" information available for 3G1Y)

(no "SAP(SNP)/Variant" information available for 3G1Y)

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 3G1Y)

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:218
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214        
           PYRF_METTH     5 RVDVMDVMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFRGADSVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTRPERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYLADNPAAAAAGIIESI 222
               SCOP domains d3g1ya_ A: automated matches                                                                                                                                                                                               SCOP domains
               CATH domains 3g1yA00 A:5-222 Aldolase class I                                                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhh.eeeee...hhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhhhhhhh...eee..--hhhhhhhhhhhhh...eeee.---------.hhhhh..eeeehhhhhh---hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------OMPDECASE     ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g1y A   5 RVDVMDVMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFRKRFGCRIIANFKVADIPETNEKICRATFKAGADAIIVHGFPGADSVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGP--RPERLSRLREIIGQDSFLISP---------GETLRFADAIIVGRSIYL---PAAAAAGIIESI 222
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154  |  | 164       174     |   -     | 194       204  |   |214        
                                                                                                                                                                                  157  |                 180       190              207 211           
                                                                                                                                                                                     160

Chain B from PDB  Type:PROTEIN  Length:204
 aligned with PYRF_METTH | O26232 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:218
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214        
           PYRF_METTH     5 RVDVMDVMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFRGADSVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTRPERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYLADNPAAAAAGIIESI 222
               SCOP domains d3g1yb_ B: automated matches                                                                                                                                                                                               SCOP domains
               CATH domains 3g1yB00 B:5-222 Aldolase class I                                                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhh.eeeee...hhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhhhhhhh...eee..--hhhhhhhhhhhhh...eeee.---------.hhhhh..eeeehhhhhh---hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------OMPDECASE     ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g1y B   5 RVDVMDVMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFRKRFGCRIIANFKVADIPETNEKICRATFKAGADAIIVHGFPGADSVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGP--RPERLSRLREIIGQDSFLISP---------GETLRFADAIIVGRSIYL---PAAAAAGIIESI 222
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154  |  | 164       174     |   -     | 194       204  |   |214        
                                                                                                                                                                                  157  |                 180       190              207 211           
                                                                                                                                                                                     160

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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/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

)

Protein Domains( (-)

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Organisms( (-)

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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	d3g1ya_	A:
1b	d3g1yb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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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	3g1yA00	A:5-222
1b	3g1yB00	B:5-222

(no "Pfam Domain" information available for 3G1Y)

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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