3W07 - JenaLib

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Title :   ATOMIC RESOLUTION STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM METHANOTHERMOBACTER THERMOAUTOTROPHICUS BOUND WITH UMP.

Authors :   M. Fujihashi, E. F. Pai, K. Miki

Date :   22 Oct 12 (Deposition) - 20 Feb 13 (Release) - 29 May 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.03

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

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

Reference :   M. Fujihashi, K. Mito, E. F. Pai, K. Miki
Atomic Resolution Structure Of The Orotidine 5'-Monophosphate Decarboxylase Product Complex Combined Wit Surface Plasmon Resonance Analysis: Implications For The Catalytic Mechanism.
J. Biol. Chem. V. 288 9011 2013
PubMed-ID: 23395822 | Reference-DOI: 10.1074/JBC.M112.427252

Molecule 1 - OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
	Chains	:	A
	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	:	ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / DELTA H
	Synonym	:	OMP DECARBOXYLASE, OMPDCASE, OMPDECASE, ODCASE

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	U5P	1	Ligand/Ion	URIDINE-5'-MONOPHOSPHATE

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	U5P	2	Ligand/Ion	URIDINE-5'-MONOPHOSPHATE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:20 , LYS A:42 , ASP A:70 , LYS A:72 , ASP A:75 , ILE A:76 , THR A:79 , MET A:126 , SER A:127 , PRO A:180 , GLN A:185 , GLY A:202 , ARG A:203 , HOH A:402 , HOH A:403 , HOH A:406 , HOH A:407 , HOH A:408 , HOH A:411 , HOH A:416	BINDING SITE FOR RESIDUE U5P A 301
2	AC2	SOFTWARE	THR A:159 , PRO A:161 , GLY A:186 , ASN A:210 , HOH A:429 , HOH A:431 , HOH A:529	BINDING SITE FOR RESIDUE GOL A 302

(no "SS Bond" information available for 3W07)

(no "Cis Peptide Bond" information available for 3W07)

(no "SAP(SNP)/Variant" information available for 3W07)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	OMPDECASE	PS00156	Orotidine 5'-phosphate decarboxylase active site.	PYRF_METTH	67-80	1	A:67-80

Biological Unit 1 (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

(no "Exon" information available for 3W07)

Asymmetric 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:215
 aligned with PYRF_METTH | O26232 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:215
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220     
           PYRF_METTH    11 VMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFRGADSVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTRPERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYLADNPAAAAAGIIESIKDL 225
               SCOP domains d3w07a_ A: automated matches                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhh.eeeee...hhhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhh...eeee........hhhhhh....eeeehhhhhh..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------OMPDECASE     ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w07 A  11 VMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFPGADSVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTRPERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYLADNPAAAAAGIIESIKDL 225
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

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 Unit

Classes(

)

Folds(

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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)

d3w07a_

(no "CATH Domain" information available for 3W07)

(no "Pfam Domain" information available for 3W07)

Asymmetric Unit(hide GO term definitions)

Chain A (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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1loq	THE SAME MOLECULE IN COMPLEX WITH THE SAME LIGAND AT 1.5 A RESOLUTION
3g1d	THE SAME MOLECULE IN COMPLEX WITH THE SAME LIGAND AT 1.5 A RESOLUTION

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