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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE MUTANT L123S OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM COMPLEXED WITH 6-AZAURIDINE 5'-MONOPHOSPHATE

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

Date :   21 Oct 10 (Deposition) - 21 Sep 11 (Release) - 19 Oct 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.30

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

Keywords :   Tim Barrel, Orotidine 5'-Monophosphate Decarboxylase, 6-Azauridine 5'-Monophosphate, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. Iiams, B. J. Desai, A. A. Fedorov, E. V. Fedorov, S. C. Almo, J. A. Gerl
Mechanism Of The Orotidine 5'-Monophosphate Decarboxylase-Catalyzed Reaction: Importance Of Residues In The Orotate Binding Site.
Biochemistry V. 50 8497 2011
PubMed-ID: 21870810 | Reference-DOI: 10.1021/BI2012355

Molecule 1 - OROTIDINE 5'-MONOPHOSPHATE 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	:	METHANOBACTERIUM THERMOAUTOTROPHICUM
	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, 3)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	UP6	2	Ligand/Ion	6-AZA URIDINE 5'-MONOPHOSPHATE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:20 , LYS A:42 , ASP A:70 , LYS A:72 , MET A:126 , SER A:127 , PRO A:180 , GLN A:185 , GLY A:202 , ARG A:203 , HOH A:240 , HOH A:249 , HOH A:250 , HOH A:253 , HOH A:258 , HOH A:259 , HOH A:265 , HOH A:273 , ASP B:75 , ILE B:76 , THR B:79	BINDING SITE FOR RESIDUE UP6 A 229
2	AC2	SOFTWARE	GLU A:33 , ASN A:210 , HOH A:283 , HOH A:292 , HOH A:369 , THR B:159 , PRO B:161 , GLY B:186 , HOH B:449	BINDING SITE FOR RESIDUE GOL A 230
3	AC3	SOFTWARE	ASP A:75 , ILE A:76 , THR A:79 , 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 , ARG B:203 , HOH B:242 , HOH B:247 , HOH B:255 , HOH B:256 , HOH B:261 , HOH B:275 , HOH B:293 , HOH B:439	BINDING SITE FOR RESIDUE UP6 B 229

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

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

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

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 3PBY)

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:219
 aligned with PYRF_METTH | O26232 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:219
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217         
           PYRF_METTH     8 VMDVMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFRGADSVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTRPERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYLADNPAAAAAGIIESIKDLL 226
               SCOP domains d3pbya_ 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..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------OMPDECASE     -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pby A   8 VMDVMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFPGADSVRACLNVAEEMGREVFLSTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTRPERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYLADNPAAAAAGIIESIKDLL 226
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217

Chain B from PDB  Type:PROTEIN  Length:218
 aligned with PYRF_METTH | O26232 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:218
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218        
           PYRF_METTH     9 MDVMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFRGADSVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTRPERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYLADNPAAAAAGIIESIKDLL 226
               SCOP domains d3pbyb_ B: automated matches                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhh.eeeee...hhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhh...eeee........hhhhhh....eeeehhhhhh..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------OMPDECASE     -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pby B   9 MDVMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFPGADSVRACLNVAEEMGREVFLSTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTRPERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYLADNPAAAAAGIIESIKDLL 226
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218

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)

Methanobacterium thermoautotrophicum [TaxId: 187420] (5)

1a	d3pbya_	A:
1b	d3pbyb_	B:

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

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

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

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	4.1.1.23
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3g18	THE SAME PROTEIN WT APO
3lhw
3ltp
3lts
3lty
3lv5
3lv6
3nq6
3nq7
3nqa
3nqc
3nqd
3nqe
3nqf
3nqg
3nqm
3p5y
3p5z
3p60
3p61
3pbu
3pbv
3pbw
3pc0
3siz
3sy5

Description

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Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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Gene Ontology (8, 8)

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