1KYY - JenaLib

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Title :   LUMAZINE SYNTHASE FROM S.POMBE BOUND TO NITROPYRIMIDINEDIONE

Authors :   S. Gerhardt, I. Haase, S. Steinbacher, J. T. Kaiser, M. Cushman, A. Bach R. Huber, M. Fischer

Date :   06 Feb 02 (Deposition) - 24 Jul 02 (Release) - 23 Jan 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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 :   Riboflavin Biosynthesis, Lumazine Synthase, Schizosaccharomyces Pombe, Ligand Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Gerhardt, I. Haase, S. Steinbacher, J. T. Kaiser, M. Cushman, A. Bacher, R. Huber, M. Fischer
The Structural Basis Of Riboflavin Binding To Schizosaccharomyces Pombe 6, 7-Dimethyl-8-Ribityllumazine Synthase.
J. Mol. Biol. V. 318 1317 2002
PubMed-ID: 12083520 | Reference-DOI: 10.1016/S0022-2836(02)00116-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 Plasmid	:	PNCO113
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	FISSION YEAST
	Organism Scientific	:	SCHIZOSACCHAROMYCES POMBE
	Organism Taxid	:	4896

		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	INI	5	Mod. Residue	5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE
2	PO4	5	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (2, 10)

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

Biological Unit 2 (2, 20)

No.	Name	Count	Type	Full Name
1	INI	10	Mod. Residue	5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE
2	PO4	10	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY A:90 , SER A:91 , THR A:92 , HOH A:1002 , HOH A:1010 , ARG E:133	BINDING SITE FOR RESIDUE PO4 A 1001
02	AC2	SOFTWARE	ARG A:133 , SER B:91 , THR B:92 , HOH B:1004 , HOH B:1010 , HOH B:1016 , HOH B:1026	BINDING SITE FOR RESIDUE PO4 B 1002
03	AC3	SOFTWARE	ARG D:133 , GLY E:90 , SER E:91 , THR E:92 , HIS E:94 , HOH E:1005 , HOH E:1007 , HOH E:1016	BINDING SITE FOR RESIDUE PO4 E 1003
04	AC4	SOFTWARE	ARG C:133 , SER D:91 , THR D:92 , HOH D:1005 , HOH D:1008 , HOH D:1016	BINDING SITE FOR RESIDUE PO4 D 1004
05	AC5	SOFTWARE	ARG B:133 , GLY C:90 , SER C:91 , THR C:92 , HOH C:1006 , HOH C:1009 , HOH C:1016 , HOH C:1035	BINDING SITE FOR RESIDUE PO4 C 1005
06	AC6	SOFTWARE	TRP A:27 , GLY A:61 , SER A:62 , TRP A:63 , GLU A:64 , VAL A:86 , LEU A:87 , ILE A:88 , HIS A:94 , ILE A:98 , HOH A:1003 , HOH A:1005 , HOH A:1024 , HOH A:1027 , ILE E:118 , LEU E:119	BINDING SITE FOR RESIDUE INI A 201
07	AC7	SOFTWARE	ILE A:118 , LEU A:119 , TRP B:27 , GLY B:61 , SER B:62 , TRP B:63 , GLU B:64 , VAL B:86 , LEU B:87 , ILE B:88 , HIS B:94 , ILE B:98 , HOH B:1003 , HOH B:1013 , HOH B:1025 , HOH B:1026	BINDING SITE FOR RESIDUE INI B 202
08	AC8	SOFTWARE	ILE B:118 , LEU B:119 , TRP C:27 , GLY C:61 , SER C:62 , TRP C:63 , GLU C:64 , VAL C:86 , LEU C:87 , ILE C:88 , HIS C:94 , ILE C:98 , HOH C:1008 , HOH C:1015 , HOH C:1039 , HOH C:1040	BINDING SITE FOR RESIDUE INI C 203
09	AC9	SOFTWARE	ILE C:118 , LEU C:119 , TRP D:27 , GLY D:61 , SER D:62 , TRP D:63 , GLU D:64 , VAL D:86 , LEU D:87 , ILE D:88 , HIS D:94 , ILE D:98 , HOH D:1006 , HOH D:1014 , HOH D:1015 , HOH D:1019	BINDING SITE FOR RESIDUE INI D 204
10	BC1	SOFTWARE	ILE D:118 , LEU D:119 , TRP E:27 , 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:1004	BINDING SITE FOR RESIDUE INI E 205

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

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

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

(no "PROSITE Motif" information available for 1KYY)

(no "Exon" information available for 1KYY)

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:149
 aligned with RIB4_SCHPO | Q9UUB1 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:149
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149         
           RIB4_SCHPO    10 PSDLKGPELRILIVHARWNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASIARNTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMRVGLDSGVPVILGLLTVLNEEQALYRAGLNGGHNHGNDWGSAAVEMGLKAL 158
               SCOP domains d1kyya_ A: Lumazine synthase                                                                                                                          SCOP domains
               CATH domains 1kyyA00 A:10-158  [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.......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kyy A  10 PSDLKGPELRILIVHARWNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASIARNTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMRVGLDSGVPVILGLLTVLNEEQALYRAGLNGGHNHGNDWGSAAVEMGLKAL 158
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149

Chain B from PDB  Type:PROTEIN  Length:147
 aligned with RIB4_SCHPO | Q9UUB1 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:147
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       
           RIB4_SCHPO    12 DLKGPELRILIVHARWNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASIARNTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMRVGLDSGVPVILGLLTVLNEEQALYRAGLNGGHNHGNDWGSAAVEMGLKAL 158
               SCOP domains d1kyyb_ B: Lumazine synthase                                                                                                                        SCOP domains
               CATH domains 1kyyB00 B:12-158  [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......hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kyy B  12 DLKGPELRILIVHARWNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASIARNTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMRVGLDSGVPVILGLLTVLNEEQALYRAGLNGGHNHGNDWGSAAVEMGLKAL 158
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151

Chain C from PDB  Type:PROTEIN  Length:149
 aligned with RIB4_SCHPO | Q9UUB1 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:149
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150         
           RIB4_SCHPO    11 SDLKGPELRILIVHARWNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASIARNTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMRVGLDSGVPVILGLLTVLNEEQALYRAGLNGGHNHGNDWGSAAVEMGLKALY 159
               SCOP domains d1kyyc_ C: Lumazine synthase                                                                                                                          SCOP domains
               CATH domains 1kyyC00 C:11-159  [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......hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kyy C  11 SDLKGPELRILIVHARWNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASIARNTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMRVGLDSGVPVILGLLTVLNEEQALYRAGLNGGHNHGNDWGSAAVEMGLKALY 159
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain D from PDB  Type:PROTEIN  Length:147
 aligned with RIB4_SCHPO | Q9UUB1 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:147
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       
           RIB4_SCHPO    12 DLKGPELRILIVHARWNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASIARNTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMRVGLDSGVPVILGLLTVLNEEQALYRAGLNGGHNHGNDWGSAAVEMGLKAL 158
               SCOP domains d1kyyd_ D: Lumazine synthase                                                                                                                        SCOP domains
               CATH domains 1kyyD00 D:12-158  [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.......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kyy D  12 DLKGPELRILIVHARWNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASIARNTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMRVGLDSGVPVILGLLTVLNEEQALYRAGLNGGHNHGNDWGSAAVEMGLKAL 158
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151

Chain E from PDB  Type:PROTEIN  Length:152
 aligned with RIB4_SCHPO | Q9UUB1 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:152
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156  
           RIB4_SCHPO     7 GPNPSDLKGPELRILIVHARWNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASIARNTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMRVGLDSGVPVILGLLTVLNEEQALYRAGLNGGHNHGNDWGSAAVEMGLKAL 158
               SCOP domains d1kyye_ E: Lumazine synthase                                                                                                                             SCOP domains
               CATH domains 1kyyE00 E:7-158  [code=3.40.50.960, no name defined]                                                                                                     CATH domains
           Pfam domains (1) --------DMRL_synthase-1kyyE01 E:15-157                                                                                                                 - Pfam domains (1)
           Pfam domains (2) --------DMRL_synthase-1kyyE02 E:15-157                                                                                                                 - Pfam domains (2)
           Pfam domains (3) --------DMRL_synthase-1kyyE03 E:15-157                                                                                                                 - Pfam domains (3)
           Pfam domains (4) --------DMRL_synthase-1kyyE04 E:15-157                                                                                                                 - Pfam domains (4)
           Pfam domains (5) --------DMRL_synthase-1kyyE05 E:15-157                                                                                                                 - Pfam domains (5)
         Sec.struct. author .............eeeeee..hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeee.hhhhhhhhhhhhhhhh...eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhh......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kyy E   7 GPNPSDLKGPELRILIVHARWNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASIARNTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMRVGLDSGVPVILGLLTVLNEEQALYRAGLNGGHNHGNDWGSAAVEMGLKAL 158
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156

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( (-)

)

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: Lumazine synthase (19)

Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] (7)

1a	d1kyya_	A:
1b	d1kyyb_	B:
1c	d1kyyc_	C:
1d	d1kyyd_	D:
1e	d1kyye_	E:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

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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	1kyyE00	E:7-158
1b	1kyyB00	B:12-158
1c	1kyyD00	D:12-158
1d	1kyyA00	A:10-158
1e	1kyyC00	C:11-159

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.

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

1kyv	1KYV CONTAINS THE SAME PROTEIN COMPLEXED WITH RIBOFLAVIN.
1kyx	1KYX CONTAINS THE SAME PROTEIN COMPLEXED WITH CARBOXYETHYLLUMAZINE.
1kz1	1KZ1 CONTAINS THE SAME PROTEIN, W27G MUTANT.
1kz4	1KZ4 CONTAINS THE SAME PROTEIN, W63Y MUTANT.
1kz6	1KZ6 CONTAINS THE SAME PROTEIN, W63Y/L119F MUTANT.
1kz9	1KZ9 CONTAINS THE SAME PROTEIN, L119F MUTANT.

Description

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Ligands, Modified Residues, Ions (2, 10)

Sites (10, 10)

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