2A58 - JenaLib

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Title :   STRUCTURE OF 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE FROM SCHIZOSACCHAROMYCES POMBE MUTANT W27Y WITH BOUND RIBOFLAVIN

Authors :   M. Koch, C. Breithaupt, S. Gerhardt, I. Haase, S. Weber, M. Cushman, R. H A. Bacher, M. Fischer

Date :   30 Jun 05 (Deposition) - 19 Jul 05 (Release) - 16 Jan 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   6, 7-Dimethyl-8-Ribityllumazine Synthase, Riboflavin, Riboflavin Biosynthesis, Lusy, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Koch, C. Breithaupt, S. Gerhardt, I. Haase, S. Weber, M. Cushman, R. Huber, A. Bacher, M. Fischer
Structural Basis Of Charge Transfer Complex Formation By Riboflavin Bound To 6, 7-Dimethyl-8-Ribityllumazine Synthase
Eur. J. Biochem. V. 271 3208 2004
PubMed-ID: 15265040 | Reference-DOI: 10.1111/J.1432-1033.2004.04253.X

Molecule 1 - 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE
	Chains	:	A, B, C, D, E
	EC Number	:	2.5.1.78
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	RIB4
	Mutation	:	YES
	Organism Common	:	FISSION YEAST
	Organism Scientific	:	SCHIZOSACCHAROMYCES POMBE
	Organism Taxid	:	4896
	Synonym	:	DMRL SYNTHASE, LUMAZINE SYNTHASE, RIBOFLAVIN SYNTHASE BETA CHAIN

		1	2	3	4	5
Asymmetric Unit	:	A	B	C	D	E
Biological Unit 1 (1x)	:	A	B	C	D	E
Biological Unit 2 (2x)	:	A	B	C	D	E

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 10)

No.	Name	Count	Type	Full Name
1	PO4	5	Ligand/Ion	PHOSPHATE ION
2	RBF	5	Ligand/Ion	RIBOFLAVIN

Biological Unit 1 (2, 10)

No.	Name	Count	Type	Full Name
1	PO4	5	Ligand/Ion	PHOSPHATE ION
2	RBF	5	Ligand/Ion	RIBOFLAVIN

Biological Unit 2 (2, 20)

No.	Name	Count	Type	Full Name
1	PO4	10	Ligand/Ion	PHOSPHATE ION
2	RBF	10	Ligand/Ion	RIBOFLAVIN

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:133 , GLY B:90 , SER B:91 , THR B:92 , RBF B:301 , HOH B:501	BINDING SITE FOR RESIDUE PO4 B 500
02	AC2	SOFTWARE	ARG B:133 , GLY C:90 , SER C:91 , THR C:92 , RBF C:302 , HOH C:502	BINDING SITE FOR RESIDUE PO4 C 501
03	AC3	SOFTWARE	ARG C:133 , GLY D:90 , SER D:91 , THR D:92 , RBF D:303	BINDING SITE FOR RESIDUE PO4 D 502
04	AC4	SOFTWARE	ARG D:133 , GLY E:90 , SER E:91 , THR E:92 , RBF E:304 , HOH E:504	BINDING SITE FOR RESIDUE PO4 E 503
05	AC5	SOFTWARE	GLY A:90 , SER A:91 , THR A:92 , RBF A:300 , HOH A:505 , HOH A:510 , ARG E:133	BINDING SITE FOR RESIDUE PO4 A 504
06	AC6	SOFTWARE	GLY A:61 , SER A:62 , TRP A:63 , GLU A:64 , VAL A:86 , LEU A:87 , ILE A:88 , HIS A:94 , PO4 A:504 , HOH A:506 , HOH A:507 , HOH A:509 , LEU E:119 , HIS E:142 , ALA E:149	BINDING SITE FOR RESIDUE RBF A 300
07	AC7	SOFTWARE	LEU A:119 , HIS A:142 , TRP A:146 , ALA A:149 , GLY B:61 , SER B:62 , TRP B:63 , GLU B:64 , VAL B:86 , LEU B:87 , ILE B:88 , HIS B:94 , PO4 B:500	BINDING SITE FOR RESIDUE RBF B 301
08	AC8	SOFTWARE	LEU B:119 , HIS B:142 , ALA B:149 , GLY C:61 , SER C:62 , TRP C:63 , GLU C:64 , VAL C:86 , LEU C:87 , ILE C:88 , HIS C:94 , PO4 C:501 , HOH C:505	BINDING SITE FOR RESIDUE RBF C 302
09	AC9	SOFTWARE	LEU C:119 , HIS C:142 , ALA C:149 , GLY D:61 , SER D:62 , TRP D:63 , GLU D:64 , VAL D:86 , LEU D:87 , ILE D:88 , HIS D:94 , PO4 D:502	BINDING SITE FOR RESIDUE RBF D 303
10	BC1	SOFTWARE	LEU D:119 , HIS D:142 , TRP D:146 , ALA D:149 , GLY E:61 , SER E:62 , TRP E:63 , GLU E:64 , VAL E:86 , LEU E:87 , ILE E:88 , HIS E:94 , PO4 E:503	BINDING SITE FOR RESIDUE RBF E 304

(no "SS Bond" information available for 2A58)

(no "Cis Peptide Bond" information available for 2A58)

(no "SAP(SNP)/Variant" information available for 2A58)

(no "PROSITE Motif" information available for 2A58)

(no "Exon" information available for 2A58)

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:146
 aligned with RIB4_SCHPO | Q9UUB1 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:146
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152      
           RIB4_SCHPO    13 LKGPELRILIVHARWNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASIARNTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMRVGLDSGVPVILGLLTVLNEEQALYRAGLNGGHNHGNDWGSAAVEMGLKAL 158
               SCOP domains d2a58a_ A: automated matches                                                                                                                       SCOP domains
               CATH domains 2a58A00 A:13-158  [code=3.40.50.960, no name defined]                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee...hhhhhhhhhhhhhhhhhhhhh.hhh.eeeee..hhhhhhhhhhhhhhhh...eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhh.......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a58 A  13 LKGPELRILIVHARYNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASIARNTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMRVGLDSGVPVILGLLTVLNEEQALYRAGLNGGHNHGNDWGSAAVEMGLKAL 158
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152

Chain B from PDB  Type:PROTEIN  Length:146
 aligned with RIB4_SCHPO | Q9UUB1 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:146
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152      
           RIB4_SCHPO    13 LKGPELRILIVHARWNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASIARNTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMRVGLDSGVPVILGLLTVLNEEQALYRAGLNGGHNHGNDWGSAAVEMGLKAL 158
               SCOP domains d2a58b_ B: automated matches                                                                                                                       SCOP domains
               CATH domains 2a58B00 B:13-158  [code=3.40.50.960, no name defined]                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee...hhhhhhhhhhhhhhhhhhhhh.hhh.eeeee..hhhhhhhhhhhhhhhh...eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhh.......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a58 B  13 LKGPELRILIVHARYNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASIARNTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMRVGLDSGVPVILGLLTVLNEEQALYRAGLNGGHNHGNDWGSAAVEMGLKAL 158
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152

Chain C from PDB  Type:PROTEIN  Length:146
 aligned with RIB4_SCHPO | Q9UUB1 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:146
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152      
           RIB4_SCHPO    13 LKGPELRILIVHARWNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASIARNTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMRVGLDSGVPVILGLLTVLNEEQALYRAGLNGGHNHGNDWGSAAVEMGLKAL 158
               SCOP domains d2a58c_ C: automated matches                                                                                                                       SCOP domains
               CATH domains 2a58C00 C:13-158  [code=3.40.50.960, no name defined]                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee..hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeee.hhhhhhhhhhhhhhhh...eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhh......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a58 C  13 LKGPELRILIVHARYNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASIARNTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMRVGLDSGVPVILGLLTVLNEEQALYRAGLNGGHNHGNDWGSAAVEMGLKAL 158
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152

Chain D from PDB  Type:PROTEIN  Length:146
 aligned with RIB4_SCHPO | Q9UUB1 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:146
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152      
           RIB4_SCHPO    13 LKGPELRILIVHARWNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASIARNTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMRVGLDSGVPVILGLLTVLNEEQALYRAGLNGGHNHGNDWGSAAVEMGLKAL 158
               SCOP domains d2a58d_ D: automated matches                                                                                                                       SCOP domains
               CATH domains 2a58D00 D:13-158  [code=3.40.50.960, no name defined]                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee..hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeee.hhhhhhhhhhhhhhhh...eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhh......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a58 D  13 LKGPELRILIVHARYNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASIARNTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMRVGLDSGVPVILGLLTVLNEEQALYRAGLNGGHNHGNDWGSAAVEMGLKAL 158
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152

Chain E from PDB  Type:PROTEIN  Length:146
 aligned with RIB4_SCHPO | Q9UUB1 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:146
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152      
           RIB4_SCHPO    13 LKGPELRILIVHARWNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASIARNTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMRVGLDSGVPVILGLLTVLNEEQALYRAGLNGGHNHGNDWGSAAVEMGLKAL 158
               SCOP domains d2a58e_ E: automated matches                                                                                                                       SCOP domains
               CATH domains 2a58E00 E:13-158  [code=3.40.50.960, no name defined]                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee..hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeee.hhhhhhhhhhhhhhhh...eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhh.......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a58 E  13 LKGPELRILIVHARYNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASIARNTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMRVGLDSGVPVILGLLTVLNEEQALYRAGLNGGHNHGNDWGSAAVEMGLKAL 158
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152

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(

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Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Lumazine synthase (27)

Superfamily: Lumazine synthase (27)

Family: Lumazine synthase (26)

Protein domain: automated matches (7)

Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] (3)

1a	d2a58a_	A:
1b	d2a58b_	B:
1c	d2a58c_	C:
1d	d2a58d_	D:
1e	d2a58e_	E:

Asymmetric Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.960, no name defined] (36)

Fission yeast (Schizosaccharomyces pombe) (10)

1a	2a58A00	A:13-158
1b	2a58B00	B:13-158
1c	2a58C00	C:13-158
1d	2a58D00	D:13-158
1e	2a58E00	E:13-158

(no "Pfam Domain" information available for 2A58)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E (RIB4_SCHPO | Q9UUB1)

molecular function
	GO:0000906	6,7-dimethyl-8-ribityllumazine synthase activity	Catalysis of the reaction: 3,4-dihydroxy-2-butanone-4-phosphate + 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione = 6,7-dimethyl-8-ribityllumazine + phosphate.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:1902444	riboflavin binding	Interacting selectively and non-covalently with riboflavin.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0009231	riboflavin biosynthetic process	The chemical reactions and pathways resulting in the formation of riboflavin (vitamin B2), the precursor for the coenzymes flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD).
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005758	mitochondrial intermembrane space	The region between the inner and outer lipid bilayers of the mitochondrial envelope.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0009349	riboflavin synthase complex	An flavoprotein that catalyzes the reaction the breakdown of dimethyl(ribityl)lumazine to form riboflavin and ribitylamino-amino-dihydroxypyrimidine.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2a58)

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	2a58
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	2.5.1.78
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UniProtKB/Swiss-Prot
	RIB4_SCHPO \| Q9UUB1	:	1kyv 1kyx 1kyy 1kz1 1kz4 1kz6 1kz9 2a57 2a59

1kyv	STRUCTURE OF 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE FROM SCHIZOSACCHAROMYCES POMBE WITH BOUND RIBOFLAVIN
1kz1	STRUCTURE OF 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE FROM SCHIZOSACCHAROMYCES POMBE MUTANT W27G
2a57	STRUCTURE OF 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE FROM SCHIZOSACCHAROMYCES POMBE MUTANT W27Y WITH BOUND LIGAND 6- CARBOXYETHYL-7-OXO-8-RIBITYLLUMAZINE

Description

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Ligands, Modified Residues, Ions (2, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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SCOP Domains (1, 5)

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Gene Ontology (9, 9)

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