2A59 - JenaLib

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Title :   STRUCTURE OF 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE FROM SCHIZOSACCHAROMYCES POMBE MUTANT W27Y WITH BOUND LIGAND 5-NITROSO-6-RIBITYLAMINO-2,4(1H,3H)-PYRIMIDINEDIONE

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 :   2.70

Chains :   Asym./Biol. Unit : A,B,C,D,E

Keywords :   6, 7-Dimethyl-8-Ribityllumazine Synthase, Schizosaccharomyces Pombe, Mutant W27Y, Lusy, 5-Nitroso-6-Ribitylamino-2, 4(1H, 3H)- Pyrimidinedione, 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/Biological Unit	:	A	B	C	D	E

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 10)

No.	Name	Count	Type	Full Name
1	LMZ	5	Ligand/Ion	5-NITROSO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE
2	PO4	5	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:133 , GLY B:90 , SER B:91 , THR B:92 , HOH B:501 , HOH B:510	BINDING SITE FOR RESIDUE PO4 B 500
02	AC2	SOFTWARE	ARG B:133 , GLY C:90 , SER C:91 , THR C:92 , HOH C:502 , HOH C:513	BINDING SITE FOR RESIDUE PO4 C 501
03	AC3	SOFTWARE	ARG C:133 , GLY D:90 , SER D:91 , THR D:92 , HOH D:504 , HOH D:507 , HOH D:510	BINDING SITE FOR RESIDUE PO4 D 502
04	AC4	SOFTWARE	ARG D:133 , GLY E:90 , SER E:91 , THR E:92 , HOH E:508 , HOH E:510	BINDING SITE FOR RESIDUE PO4 E 503
05	AC5	SOFTWARE	GLY A:90 , SER A:91 , THR A:92 , HOH A:505 , ARG E:133	BINDING SITE FOR RESIDUE PO4 A 504
06	AC6	SOFTWARE	TYR A:27 , ASN A:28 , GLY A:61 , SER A:62 , TRP A:63 , GLU A:64 , VAL A:86 , LEU A:87 , ILE A:88 , HIS A:94 , HOH A:506 , ILE E:118 , LEU E:119	BINDING SITE FOR RESIDUE LMZ A 300
07	AC7	SOFTWARE	ILE A:118 , LEU A:119 , TYR B:27 , ASN B:28 , GLY B:61 , SER B:62 , TRP B:63 , GLU B:64 , VAL B:86 , LEU B:87 , ILE B:88 , HIS B:94 , HOH B:503	BINDING SITE FOR RESIDUE LMZ B 301
08	AC8	SOFTWARE	ILE B:118 , LEU B:119 , TYR C:27 , ASN C:28 , GLY C:61 , SER C:62 , TRP C:63 , GLU C:64 , VAL C:86 , LEU C:87 , ILE C:88 , HIS C:94 , HOH C:504	BINDING SITE FOR RESIDUE LMZ C 302
09	AC9	SOFTWARE	ILE C:118 , LEU C:119 , TYR D:27 , ASN D:28 , GLY D:61 , SER D:62 , TRP D:63 , GLU D:64 , VAL D:86 , LEU D:87 , ILE D:88 , HIS D:94 , HOH D:506 , HOH D:508	BINDING SITE FOR RESIDUE LMZ D 303
10	BC1	SOFTWARE	ILE D:118 , LEU D:119 , TYR E:27 , ASN E:28 , GLY E:61 , SER E:62 , TRP E:63 , GLU E:64 , VAL E:86 , LEU E:87 , ILE E:88 , HIS E:94 , HOH E:506 , HOH E:509	BINDING SITE FOR RESIDUE LMZ E 304

(no "SS Bond" information available for 2A59)

(no "Cis Peptide Bond" information available for 2A59)

(no "SAP(SNP)/Variant" information available for 2A59)

(no "PROSITE Motif" information available for 2A59)

(no "Exon" information available for 2A59)

Asymmetric/Biological 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 d2a59a_ A: automated matches                                                                                                                       SCOP domains
               CATH domains 2a59A00 A:13-158  [code=3.40.50.960, no name defined]                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee..hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeee...hhhhhhhhhhhhhh...eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhh......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a59 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 d2a59b_ B: automated matches                                                                                                                       SCOP domains
               CATH domains 2a59B00 B:13-158  [code=3.40.50.960, no name defined]                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee..hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeee...hhhhhhhhhhhhhh...eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhh......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a59 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 d2a59c_ C: automated matches                                                                                                                       SCOP domains
               CATH domains 2a59C00 C:13-158  [code=3.40.50.960, no name defined]                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee..hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeee...hhhhhhhhhhhhhh...eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhh......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a59 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 d2a59d_ D: automated matches                                                                                                                       SCOP domains
               CATH domains 2a59D00 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......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a59 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 d2a59e_ E: automated matches                                                                                                                       SCOP domains
               CATH domains 2a59E00 E:13-158  [code=3.40.50.960, no name defined]                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee..hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeee...hhhhhhhhhhhhhh...eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhh......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a59 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/Biological Unit

Classes(

)

Folds(

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Superfamilies( (-)

)

Families(

)

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	d2a59a_	A:
1b	d2a59b_	B:
1c	d2a59c_	C:
1d	d2a59d_	D:
1e	d2a59e_	E:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

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	2a59A00	A:13-158
1b	2a59B00	B:13-158
1c	2a59C00	C:13-158
1d	2a59D00	D:13-158
1e	2a59E00	E:13-158

(no "Pfam Domain" information available for 2A59)

Asymmetric/Biological 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/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2a59)

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	2a59
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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 2a58

1kyv	STRUCTURE OF 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE FROM SCHIZOSACCHAROMYCES POMBE WITH BOUND RIBOFLAVIN
1kyy	STRUCTURE OF 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE FROM SCHIZOSACCHAROMYCES POMBE WITH BOUND LIGAND 5-NITRO-6-(D- RIBITYLAMINO)-2,4(1H,3H)-PYRIMIDINEDIONE
2a57	STRUCTURE OF 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE FROM SCHIZOSACCHAROMYCES POMBE MUTANT W27Y WITH BOUND LIGAND 6- CARBOXYETHYL-7-OXO-8-RIBITYLLUMAZINE
2a58	STRUCTURE OF 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE FROM SCHIZOSACCHAROMYCES POMBE MUTANT W27Y WITH BOUND LIGAND RIBOFLAVIN

Description

Compounds

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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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Exons (0, 0)

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SCOP Domains (1, 5)

CATH Domains (1, 5)

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Gene Ontology (9, 9)

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