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Description

Title :   CRYSTAL STRUCTURE OF OROTIDINE MONOPHOSPHATE DECARBOXYLASE MUTANT D70A COMPLEXED WITH UMP

Authors :   N. Wu, W. Gillon, E. F. Pai

Date :   13 Dec 01 (Deposition) - 28 Jun 02 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

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

Keywords :   Tim Barrel, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Wu, W. Gillon, E. F. Pai
Mapping The Active Site-Ligand Interactions Of Orotidine 5'-Monophosphate Decarboxylase By Crystallography.
Biochemistry V. 41 4002 2002
PubMed-ID: 11900543 | Reference-DOI: 10.1021/BI015758P

Compounds

Molecule 1 - OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
	Chains	:	A
	EC Number	:	4.1.1.23
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	METHANOTHERMOBACTER THERMAUTOTROPHICUS
	Organism Taxid	:	145262
	Synonym	:	OMP DECARBOXYLASE; OMPDCASE

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (2, 3)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	U	1	Ligand/Ion	URIDINE-5'-MONOPHOSPHATE

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	U	-1	Ligand/Ion	URIDINE-5'-MONOPHOSPHATE

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	U	-1	Ligand/Ion	URIDINE-5'-MONOPHOSPHATE

Sites (3, 3)

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:42 , ALA A:70 , LYS A:72 , ILE A:96 , U A:2001	BINDING SITE FOR RESIDUE CL A 5001
2	AC2	SOFTWARE	ALA A:74 , HOH A:3001 , HOH A:3003 , HOH A:3004	BINDING SITE FOR RESIDUE CL A 5002
3	AC3	SOFTWARE	ASP A:20 , LYS A:42 , 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:3006 , HOH A:3009 , HOH A:3011 , HOH A:3012 , HOH A:3013 , HOH A:3014 , CL A:5001	BINDING SITE FOR RESIDUE U A 2001

SS Bonds (0, 0)

(no "SS Bond" information available for 1KLZ)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 1KLZ)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 1KLZ)

PROSITE Motifs (1, 1)

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

Biological Unit 2 (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

Exons (0, 0)

(no "Exon" information available for 1KLZ)

Sequences/Alignments

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:209
 aligned with PYRF_METTH | O26232 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:209
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213         
           PYRF_METTH    14 RLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFRGADSVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTRPERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYLADNPAAAAAGIIESI 222
               SCOP domains d1klza_ A: Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase)                                                                                                                                           SCOP domains
               CATH domains 1klzA00 A:14-222 Aldolase class I                                                                                                                                                                                 CATH domains
               Pfam domains OMPdecase-1klzA01 A:14-218                                                                                                                                                                                   ---- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhh...eeee........hhhhhh....eeeehhhhhh..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------OMPDECASE     ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1klz A  14 RLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFRKRFGCRIIAAFKVADIPETNEKICRATFKAGADAIIVHGFPGADSVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTRPERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYLADNPAAAAAGIIESI 222
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

Asymmetric 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: Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase) (28)

Methanobacterium thermoautotrophicum [TaxId: 145262] (16)

d1klza_

CATH Domains (1, 1)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Aldolase class I (887)

Methanothermobacter thermautotrophicus. Organism_taxid: 145262. (20)

1klzA00

A:14-222

Pfam Domains (1, 1)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: OMPdecase (84)

Methanobacterium thermoautotrophicum (strain Delta H) (55)

OMPdecase-1klzA01

A:14-218

Gene Ontology (8, 8)

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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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	PYRF_METTH \| O26232	:	1dv7 1dvj 1kly 1km0 1km1 1km2 1km3 1km4 1km5 1km6 1lol 1loq 1lor 1los 1lp6 1x1z 2e6y 2zz1 2zz2 2zz3 2zz4 2zz5 2zz6 2zz7 3g18 3g1a 3g1d 3g1f 3g1h 3g1s 3g1v 3g1x 3g1y 3g22 3g24 3lht 3lhu 3lhv 3lhw 3lhy 3lhz 3li0 3li1 3lld 3llf 3ltp 3lts 3lty 3lv5 3lv6 3m1z 3m41 3m43 3m44 3m47 3m5x 3m5y 3m5z 3nq6 3nq7 3nqa 3nqc 3nqd 3nqe 3nqf 3nqg 3nqm 3p5y 3p5z 3p60 3p61 3pbu 3pbv 3pbw 3pby 3pc0 3qez 3qf0 3qmr 3qms 3qmt 3rlu 3rlv 3sec 3sgu 3siz 3sj3 3ssj 3sw6 3sy5 3thq 3v1p 3w07 3wjw 3wjx 3wjy 3wjz 3wk0 3wk1 3wk2 3wk3 4fx6 4fx8 4fxr 4gc4 4lc6 4lc8 4lw7 4nt0 4nuw 4nx5 4o11 4o8r

Related Entries Specified in the PDB File

1kly 1km0 1km1 1km2 1km3 1km4 1km5 1km6