3M41 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF THE MUTANT V182A OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM

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

Date :   10 Mar 10 (Deposition) - 16 Jun 10 (Release) - 16 Jun 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

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

Keywords :   Orotidine 5'-Monophosphate Decarboxylase, Mutant V182A, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. M. Wood, T. L. Amyes, A. A. Fedorov, E. V. Fedorov, A. Shabila, S. C. Almo, J. P. Richard, J. A. Gerlt
Conformational Changes In Orotidine 5'-Monophosphate Decarboxylase: "Remote" Residues That Stabilize The Active Conformation.
Biochemistry V. 49 3514 2010
PubMed-ID: 20369850 | Reference-DOI: 10.1021/BI100443A

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, 5)

No.	Name	Count	Type	Full Name
1	GOL	5	Ligand/Ion	GLYCEROL

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	MET A:12 , ILE A:38 , ASP A:39 , PHE A:63 , GLY A:64 , CYS A:65 , ARG A:107 , ASN A:111 , HOH A:270 , HOH A:338	BINDING SITE FOR RESIDUE GOL A 229
2	AC2	SOFTWARE	ARG A:5 , ARG A:168 , GLN A:173 , PHE A:195 , ASP A:197 , HOH A:380 , HOH A:392	BINDING SITE FOR RESIDUE GOL A 230
3	AC3	SOFTWARE	VAL A:48 , LEU A:49 , GLY A:52 , MET A:53 , VAL B:48 , LEU B:49 , GLY B:52 , MET B:53 , HOH B:268 , HOH B:276	BINDING SITE FOR RESIDUE GOL B 229
4	AC4	SOFTWARE	ARG B:5 , ARG B:168 , GLN B:173 , PHE B:195 , ASP B:197 , HOH B:232 , HOH B:234	BINDING SITE FOR RESIDUE GOL B 230
5	AC5	SOFTWARE	MET B:12 , ARG B:35 , ILE B:38 , ASP B:39 , PHE B:63 , GLY B:64 , CYS B:65 , ARG B:107 , ASN B:111 , HOH B:261 , HOH B:314	BINDING SITE FOR RESIDUE GOL B 231

(no "SS Bond" information available for 3M41)

(no "Cis Peptide Bond" information available for 3M41)

(no "SAP(SNP)/Variant" information available for 3M41)

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 3M41)

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:207
 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 d3m41a_ A: automated matches                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhh.eeee....hhhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhhhhhhh...eee....hhhhhhhhhhhhh...eeee.-----------......eeeehhhhhh..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------OMPDECASE     ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m41 A   5 RVDVMDVMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFPGADSVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTRPERLSRLREIIGQDSFLISP-----------TLRFADAIIVGRSIYLADNPAAAAAGIIESI 222
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174     |   -       194       204       214        
                                                                                                                                                                                                         180         192

Chain B from PDB  Type:PROTEIN  Length:208
 aligned with PYRF_METTH | O26232 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:219
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214         
           PYRF_METTH     5 RVDVMDVMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFRGADSVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTRPERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYLADNPAAAAAGIIESIK 223
               SCOP domains d3m41b_ B: automated matches                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------OMPdecase-3m41B01 B:13-218                                                                                                                                                                                    ----- Pfam domains (1)
           Pfam domains (2) --------OMPdecase-3m41B02 B:13-218                                                                                                                                                                                    ----- Pfam domains (2)
         Sec.struct. author ......hhh.eeeee...hhhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhhhhhhh...eee....hhhhhhhhhhhhh...eeee.-----------......eeeehhhhhh..hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------OMPDECASE     ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m41 B   5 RVDVMDVMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFPGADSVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTRPERLSRLREIIGQDSFLISP-----------TLRFADAIIVGRSIYLADNPAAAAAGIIESIK 223
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174     |   -       194       204       214         
                                                                                                                                                                                                         180         192

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	d3m41a_	A:
1b	d3m41b_	B:

(no "CATH Domain" information available for 3M41)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: OMPdecase (84)

Methanobacterium thermoautotrophicum (strain Delta H) (55)

1a	OMPdecase-3m41B01	B:13-218
1b	OMPdecase-3m41B02	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.

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(no "Cis Peptide Bonds" information available for 3m41)

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3g18	CRYSTAL STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM
3m1z	CRYSTAL STRUCTURE OF THE MUTANT V182A,V201A OF OROTIDINE 5' -MONOPHOSPHATE' DECARBOXYLASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM COMPLEXED WITH INHIBITOR BMP
3m43	CRYSTAL STRUCTURE OF THE MUTANT I199A OF OROTIDINE 5'- MONOPHOSPHATE DECARBOXYLASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM
3m44	CRYSTAL STRUCTURE OF THE MUTANT V201A OF OROTIDINE 5'- MONOPHOSPHATE DECARBOXYLASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM
3m47	CRYSTAL STRUCTURE OF THE MUTANT I218A OF OROTIDINE 5'- MONOPHOSPHATE DECARBOXYLASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM
3m5x	CRYSTAL STRUCTURE OF THE MUTANT V182A,I199A OF OROTIDINE 5' -MONOPHOSPHATE DECARBOXYLASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM
3m5y	CRYSTAL STRUCTURE OF THE MUTANT V182A,V201A OF OROTIDINE 5' -MONOPHOSPHATE DECARBOXYLASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM
3m5z	CRYSTAL STRUCTURE OF THE MUTANT V182A,I218A OF OROTIDINE 5' -MONOPHOSPHATE DECARBOXYLASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM

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Ligands, Modified Residues, Ions (1, 5)

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