1KM0 - JenaLib

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Title :   CRYSTAL STRUCTURE OF OROTIDINE MONOPHOSPHATE DECARBOXYLASE MUTANT D70N COMPLEXED WITH 6-AZAUMP

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

Date :   13 Dec 01 (Deposition) - 28 Jun 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

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
(for further references see the PDB file header)

Molecule 1 - OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
	Chains	:	A, B, C, D
	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

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	UP6	4	Ligand/Ion	6-AZA URIDINE 5'-MONOPHOSPHATE

Biological Unit 1 (1, 2)

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

Biological Unit 2 (1, 2)

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

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:20 , LYS A:42 , ASN 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:4002 , HOH A:4007 , HOH A:4019 , HOH A:4020 , HOH A:4033 , HOH A:4115 , ASP B:75 , ILE B:76 , THR B:79	BINDING SITE FOR RESIDUE UP6 A 5001
2	AC2	SOFTWARE	ASP A:75 , ILE A:76 , THR A:79 , ASP B:20 , LYS B:42 , ASN 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:4009 , HOH B:4016 , HOH B:4021 , HOH B:4034 , HOH B:4047 , HOH B:4095	BINDING SITE FOR RESIDUE UP6 B 5002
3	AC3	SOFTWARE	ASP C:20 , LYS C:42 , ASN C:70 , LYS C:72 , MET C:126 , SER C:127 , PRO C:180 , GLN C:185 , GLY C:202 , ARG C:203 , HOH C:4004 , HOH C:4010 , HOH C:4029 , HOH C:4051 , HOH C:4057 , HOH C:4061 , ASP D:75 , ILE D:76 , THR D:79	BINDING SITE FOR RESIDUE UP6 C 5003
4	AC4	SOFTWARE	ASP C:75 , ILE C:76 , THR C:79 , ASP D:20 , LYS D:42 , ASN D:70 , LYS D:72 , MET D:126 , SER D:127 , PRO D:180 , GLN D:185 , VAL D:201 , GLY D:202 , ARG D:203 , HOH D:4003 , HOH D:4012 , HOH D:4031 , HOH D:4038 , HOH D:4039 , HOH D:4105	BINDING SITE FOR RESIDUE UP6 D 5004

(no "SS Bond" information available for 1KM0)

(no "Cis Peptide Bond" information available for 1KM0)

(no "SAP(SNP)/Variant" information available for 1KM0)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	OMPDECASE	PS00156	Orotidine 5'-phosphate decarboxylase active site.	PYRF_METTH	67-80	4	A:67-80 B:67-80 C:67-80 D: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 B: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	- - C:67-80 D:67-80

(no "Exon" information available for 1KM0)

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:237
 aligned with PYRF_METTH | O26232 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:237
                                                                                                                                                                                                                                                     228                 
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228         -       
           PYRF_METTH     9 MDVMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFRGADSVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTRPERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYLADNPAAAAAGIIESIKDLLNP-----------------   -
               SCOP domains d1km0a_ A: Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase)                                                                                                                                                                       SCOP domains
               CATH domains 1km0A00 A:9-245 Aldolase class I                                                                                                                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhh.eeeee...hhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhh...eeee........hhhhhh....eeeehhhhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------OMPDECASE     --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1km0 A   9 MDVMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFRKRFGCRIIANFKVADIPETNEKICRATFKAGADAIIVHGFPGADSVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTRPERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYLADNPAAAAAGIIESIKDLLIPEDPAANKARKEAELAAA 245
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238

Chain B from PDB  Type:PROTEIN  Length:212
 aligned with PYRF_METTH | O26232 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:212
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220  
           PYRF_METTH    11 VMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFRGADSVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTRPERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYLADNPAAAAAGIIESI 222
               SCOP domains d1km0b_ B: Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase)                                                                                                                                              SCOP domains
               CATH domains 1km0B00 B:11-222 Aldolase class I                                                                                                                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...hhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhh...eeee........hhhhhh....eeeehhhhhh..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------OMPDECASE     ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1km0 B  11 VMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFRKRFGCRIIANFKVADIPETNEKICRATFKAGADAIIVHGFPGADSVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTRPERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYLADNPAAAAAGIIESI 222
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain C from PDB  Type:PROTEIN  Length:235
 aligned with PYRF_METTH | O26232 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:235
                                                                                                                                                                                                                                                     228               
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228         -     
           PYRF_METTH     9 MDVMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFRGADSVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTRPERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYLADNPAAAAAGIIESIKDLLNP---------------   -
               SCOP domains d1km0c_ C: Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase)                                                                                                                                                                     SCOP domains
               CATH domains 1km0C00 C:9-243 Aldolase class I                                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhh.eeeee...hhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhh...eeee........hhhhhhhhh.eeeehhhhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------OMPDECASE     ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1km0 C   9 MDVMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFRKRFGCRIIANFKVADIPETNEKICRATFKAGADAIIVHGFPGADSVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTRPERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYLADNPAAAAAGIIESIKDLLIPEDPAANKARKEAELA 243
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238

Chain D from PDB  Type:PROTEIN  Length:214
 aligned with PYRF_METTH | O26232 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:214
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218    
           PYRF_METTH     9 MDVMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFRGADSVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTRPERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYLADNPAAAAAGIIESI 222
               SCOP domains d1km0d_ D: Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase)                                                                                                                                                SCOP domains
               CATH domains 1km0D00 D:9-222 Aldolase class I                                                                                                                                                                                       CATH domains
           Pfam domains (1) ----OMPdecase-1km0D01 D:13-218                                                                                                                                                                                    ---- Pfam domains (1)
           Pfam domains (2) ----OMPdecase-1km0D02 D:13-218                                                                                                                                                                                    ---- Pfam domains (2)
           Pfam domains (3) ----OMPdecase-1km0D03 D:13-218                                                                                                                                                                                    ---- Pfam domains (3)
           Pfam domains (4) ----OMPdecase-1km0D04 D:13-218                                                                                                                                                                                    ---- Pfam domains (4)
         Sec.struct. author ..hhh.eeeee...hhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhh...eeee........hhhhhh....eeeehhhhhh..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------OMPDECASE     ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1km0 D   9 MDVMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFRKRFGCRIIANFKVADIPETNEKICRATFKAGADAIIVHGFPGADSVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTRPERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYLADNPAAAAAGIIESI 222
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218

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	-	→ Gap	(green background, '-', border residues have a numbering label)
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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 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)

1a	d1km0a_	A:
1b	d1km0b_	B:
1c	d1km0c_	C:
1d	d1km0d_	D:

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)

1a	1km0A00	A:9-245
1b	1km0C00	C:9-243
1c	1km0D00	D:9-222
1d	1km0B00	B:11-222

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: OMPdecase (84)

Methanobacterium thermoautotrophicum (strain Delta H) (55)

1a	OMPdecase-1km0D01	D:13-218
1b	OMPdecase-1km0D02	D:13-218
1c	OMPdecase-1km0D03	D:13-218
1d	OMPdecase-1km0D04	D:13-218

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (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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