2YYT - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF UNCHARACTERIZED CONSERVED PROTEIN FROM GEOBACILLUS KAUSTOPHILUS

Authors :   M. Kanagawa, S. Baba, Y. Nakamura, Y. Bessho, S. Kuramitsu, S. Yokoyama G. Sampei, Riken Structural Genomics/Proteomics Initiative (R

Date :   02 May 07 (Deposition) - 06 Nov 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Tim Barrel, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Kanagawa, S. Baba, Y. Nakamura, Y. Bessho, S. Kuramitsu, S. Yokoyama, G. Kawai, G. Sampei
Crystal Structure Of Uncharacterized Conserved Protein From Geobacillus Kaustophilus
To Be Published
PubMed: search

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	:	PET-HISTEV
	Expression System Strain	:	BL21-CODONPLUS(DE3)-RIL-X
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	GEOBACILLUS KAUSTOPHILUS
	Organism Taxid	:	235909
	Strain	:	HTA426
	Synonym	:	OMP DECARBOXYLASE, OMPDCASE, OMPDECASE

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2YYT)

(no "Site" information available for 2YYT)

(no "SS Bond" information available for 2YYT)

(no "Cis Peptide Bond" information available for 2YYT)

(no "SAP(SNP)/Variant" information available for 2YYT)

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_GEOKA	56-69	4	A:58-71 B:58-71 C:58-71 D:58-71

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_GEOKA	56-69	2	A:58-71 - C:58-71 -

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_GEOKA	56-69	2	- B:58-71 - D:58-71

(no "Exon" information available for 2YYT)

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_GEOKA | Q5L0U0 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:231
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233 
           PYRF_GEOKA     4 PFIVALDFPSKQEVERFLRPFAGTPLFVKVGMELYYQEGPAIVAFLKEQGHAVFLDLKLHDIPNTVKQAMKGLARVGADLVNVHAAGGRRMMEAAIEGLDAGTPSGRMRPRCIAVTQLTSTDERMLHEELWISRPLVETVAHYAALAKESGLDGVVCSANEAAFIKERCGASFLAVTPGIRFADDAAHDQVRVVTPRKARALGSDYIVIGRSLTRAADPLRTYARLQHEWN 234
               SCOP domains d2yyta_ A: automated matches                                                                                                                                                                                                            SCOP domains
               CATH domains 2yytA00 A:6-236 Aldolase class I                                                                                                                                                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....hhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhh........eeeee......hhhhhhhh.....hhhhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhh...eeee----------------.hhhhhhhh...eeeehhhhhh..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------OMPDECASE     --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yyt A   6 PFIVALDFPSKQEVERFLRPFAGTPLFVKVGMELYYQEGPAIVAFLKEQGHAVFLDLKLHDIPNTVKQAMKGLARVGADLVNVHAAGGRRMMEAAIEGLDAGTPSGRMRPRCIAVTQLTSTDERMLHEELWISRPLVETVAHYAALAKESGLDGVVCSANEAAFIKERCGASFLAVT----------------VTPRKARALGSDYIVIGRSLTRAADPLRTYARLQHEWN 236
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175      |  -         -   |   205       215       225       235 
                                                                                                                                                                                                          182              199

Chain B from PDB  Type:PROTEIN  Length:215
 aligned with PYRF_GEOKA | Q5L0U0 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:231
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233 
           PYRF_GEOKA     4 PFIVALDFPSKQEVERFLRPFAGTPLFVKVGMELYYQEGPAIVAFLKEQGHAVFLDLKLHDIPNTVKQAMKGLARVGADLVNVHAAGGRRMMEAAIEGLDAGTPSGRMRPRCIAVTQLTSTDERMLHEELWISRPLVETVAHYAALAKESGLDGVVCSANEAAFIKERCGASFLAVTPGIRFADDAAHDQVRVVTPRKARALGSDYIVIGRSLTRAADPLRTYARLQHEWN 234
               SCOP domains d2yytb_ B: automated matches                                                                                                                                                                                                            SCOP domains
               CATH domains 2yytB00 B:6-236 Aldolase class I                                                                                                                                                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....hhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhh........eeeee......hhhhhhhh.....hhhhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhh...eeee----------------.hhhhhhhh...eeeehhhhhh..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------OMPDECASE     --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yyt B   6 PFIVALDFPSKQEVERFLRPFAGTPLFVKVGMELYYQEGPAIVAFLKEQGHAVFLDLKLHDIPNTVKQAMKGLARVGADLVNVHAAGGRRMMEAAIEGLDAGTPSGRMRPRCIAVTQLTSTDERMLHEELWISRPLVETVAHYAALAKESGLDGVVCSANEAAFIKERCGASFLAVT----------------VTPRKARALGSDYIVIGRSLTRAADPLRTYARLQHEWN 236
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175      |  -         -   |   205       215       225       235 
                                                                                                                                                                                                          182              199

Chain C from PDB  Type:PROTEIN  Length:215
 aligned with PYRF_GEOKA | Q5L0U0 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:231
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233 
           PYRF_GEOKA     4 PFIVALDFPSKQEVERFLRPFAGTPLFVKVGMELYYQEGPAIVAFLKEQGHAVFLDLKLHDIPNTVKQAMKGLARVGADLVNVHAAGGRRMMEAAIEGLDAGTPSGRMRPRCIAVTQLTSTDERMLHEELWISRPLVETVAHYAALAKESGLDGVVCSANEAAFIKERCGASFLAVTPGIRFADDAAHDQVRVVTPRKARALGSDYIVIGRSLTRAADPLRTYARLQHEWN 234
               SCOP domains d2yytc_ C: automated matches                                                                                                                                                                                                            SCOP domains
               CATH domains 2yytC00 C:6-236 Aldolase class I                                                                                                                                                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....hhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhh........eeeee......hhhhhhhh.....hhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhh...eeee----------------.hhhhhhhh...eeeehhhhhh..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------OMPDECASE     --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yyt C   6 PFIVALDFPSKQEVERFLRPFAGTPLFVKVGMELYYQEGPAIVAFLKEQGHAVFLDLKLHDIPNTVKQAMKGLARVGADLVNVHAAGGRRMMEAAIEGLDAGTPSGRMRPRCIAVTQLTSTDERMLHEELWISRPLVETVAHYAALAKESGLDGVVCSANEAAFIKERCGASFLAVT----------------VTPRKARALGSDYIVIGRSLTRAADPLRTYARLQHEWN 236
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175      |  -         -   |   205       215       225       235 
                                                                                                                                                                                                          182              199

Chain D from PDB  Type:PROTEIN  Length:215
 aligned with PYRF_GEOKA | Q5L0U0 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:231
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233 
           PYRF_GEOKA     4 PFIVALDFPSKQEVERFLRPFAGTPLFVKVGMELYYQEGPAIVAFLKEQGHAVFLDLKLHDIPNTVKQAMKGLARVGADLVNVHAAGGRRMMEAAIEGLDAGTPSGRMRPRCIAVTQLTSTDERMLHEELWISRPLVETVAHYAALAKESGLDGVVCSANEAAFIKERCGASFLAVTPGIRFADDAAHDQVRVVTPRKARALGSDYIVIGRSLTRAADPLRTYARLQHEWN 234
               SCOP domains d2yytd_ D: automated matches                                                                                                                                                                                                            SCOP domains
               CATH domains 2yytD00 D:6-236 Aldolase class I                                                                                                                                                                                                        CATH domains
           Pfam domains (1) OMPdecase-2yytD01 D:6-231                                                                                                                                                                                                         ----- Pfam domains (1)
           Pfam domains (2) OMPdecase-2yytD02 D:6-231                                                                                                                                                                                                         ----- Pfam domains (2)
           Pfam domains (3) OMPdecase-2yytD03 D:6-231                                                                                                                                                                                                         ----- Pfam domains (3)
           Pfam domains (4) OMPdecase-2yytD04 D:6-231                                                                                                                                                                                                         ----- Pfam domains (4)
         Sec.struct. author .eeee....hhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhh........eeeee......hhhhhhhh.....hhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhh...eeee----------------.hhhhhhhh...eeeehhhhhh..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------OMPDECASE     --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yyt D   6 PFIVALDFPSKQEVERFLRPFAGTPLFVKVGMELYYQEGPAIVAFLKEQGHAVFLDLKLHDIPNTVKQAMKGLARVGADLVNVHAAGGRRMMEAAIEGLDAGTPSGRMRPRCIAVTQLTSTDERMLHEELWISRPLVETVAHYAALAKESGLDGVVCSANEAAFIKERCGASFLAVT----------------VTPRKARALGSDYIVIGRSLTRAADPLRTYARLQHEWN 236
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175      |  -         -   |   205       215       225       235 
                                                                                                                                                                                                          182              199

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(

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Folds(

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Superfamilies( (-)

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Families(

)

Protein Domains( (-)

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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)

Geobacillus kaustophilus [TaxId: 235909] (2)

1a	d2yyta_	A:
1b	d2yytb_	B:
1c	d2yytc_	C:
1d	d2yytd_	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)

Geobacillus kaustophilus. Organism_taxid: 235909. Strain: hta426. (2)

1a	2yytA00	A:6-236
1b	2yytB00	B:6-236
1c	2yytC00	C:6-236
1d	2yytD00	D:6-236

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: OMPdecase (84)

Geobacillus kaustophilus (2)

1a	OMPdecase-2yytD01	D:6-231
1b	OMPdecase-2yytD02	D:6-231
1c	OMPdecase-2yytD03	D:6-231
1d	OMPdecase-2yytD04	D:6-231

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (PYRF_GEOKA | Q5L0U0)

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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	2yyt
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	4.1.1.23
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UniProtKB/Swiss-Prot
	PYRF_GEOKA \| Q5L0U0	:	2yyu

2yyu	THE SAME PROTEIN IN COMPLEX WITH CYTIDINE-5'-MONOPHOSPHATE RELATED ID: GKA001001155.1 RELATED DB: TARGETDB

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