1KZL - JenaLib

Title :   RIBOFLAVIN SYNTHASE FROM S.POMBE BOUND TO CARBOXYETHYLLUMAZINE

Authors :   S. Gerhardt, A. K. Schott, N. Kairies, M. Cushman, B. Illarionov, W. Eisenreich, A. Bacher, R. Huber, S. Steinbacher, M. Fischer

Date :   07 Feb 02 (Deposition) - 06 Nov 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym./Biol. Unit : A

Keywords :   Biosynthesis Of Riboflavin, Riboflavin Synthase, X-Ray Structure, Schizosaccharomyces Pombe, Ligand Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Gerhardt, A. K. Schott, N. Kairies, M. Cushman, B. Illarionov, W. Eisenreich, A. Bacher, R. Huber, S. Steinbacher, M. Fischer
Studies On The Reaction Mechanism Of Riboflavin Synthase; X-Ray Crystal Structure Of A Complex With 6-Carboxyethyl-7-Oxo-8-Ribityllumazine
Structure V. 10 1371 2002
PubMed-ID: 12377123 | Reference-DOI: 10.1016/S0969-2126(02)00864-X
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:48 , GLN A:100 , CRM A:502 , HOH A:1019	BINDING SITE FOR RESIDUE HG A 1001
2	AC2	SOFTWARE	GLY A:4 , LEU A:5 , VAL A:6 , TYR A:139 , THR A:145 , SER A:146 , LEU A:147 , THR A:148 , MET A:160 , MET A:161 , ILE A:162 , TYR A:164 , THR A:165 , HOH A:1053 , HOH A:1084 , HOH A:1098	BINDING SITE FOR RESIDUE CRM A 501
3	AC3	SOFTWARE	THR A:47 , CYS A:48 , LEU A:49 , THR A:50 , GLY A:62 , ILE A:63 , ALA A:64 , SER A:67 , GLY A:101 , HIS A:102 , VAL A:103 , LYS A:137 , HG A:1001 , HOH A:1004 , HOH A:1019 , HOH A:1086	BINDING SITE FOR RESIDUE CRM A 502

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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
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Chain A from PDB  Type:PROTEIN  Length:202
 aligned with RISA_SCHPO | Q9Y7P0 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:202
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200  
           RISA_SCHPO     1 MFTGLVEAIGVVKDVQGTIDNGFAMKIEAPQILDDCHTGDSIAVNGTCLTVTDFDRYHFTVGIAPESLRLTNLGQCKAGDPVNLERAVLSSTRMGGHFVQGHVDTVAEIVEKKQDGEAIDFTFRPRDPFVLKYIVYKGYIALDGTSLTITHVDDSTFSIMMISYTQSKVIMAKKNVGDLVNVEVDQIGKYTEKLVEAHIADW 202
               SCOP domains d1kzla1 A:1-92 Riboflavin synthase                                                          d1kzla2 A:93-202 Riboflavin synthase                                                                           SCOP domains
               CATH domains 1kzlA01 A:1-89  [code=2.40.30.20, no name defined]                                       ------------1kzlA02 A:102-202  [code=2.40.30.20, no name defined]                                                 CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------Lum_binding-1kzlA01 A:100-185                                                         ----------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------Lum_binding-1kzlA02 A:100-185                                                         ----------------- Pfam domains (2)
         Sec.struct. author .......eeeeeeeeeee...eeeeeee.hhhh.......eeee..eeeeeeee...eeeeeehhhhhhhhhhhhh....eeeeee..................eeeeeeeeeee..eeeeeeee.hhhhhhhh....eeee..eeeeeeee....eeeeehhhhhh.hhhhhh....eeeeee.hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE LUMAZINE_BIND  PDB: A:1-97 UniProt: 1-97                                                         LUMAZINE_BIND  PDB: A:98-195 UniProt: 98-195                                                      ------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kzl A   1 MFTGLVEAIGVVKDVQGTIDNGFAMKIEAPQILDDCHTGDSIAVNGTCLTVTDFDRYHFTVGIAPESLRLTNLGQCKAGDPVNLERAVLSSTRMGGHFVQGHVDTVAEIVEKKQDGEAIDFTFRPRDPFVLKYIVYKGYIALDGTSLTITHVDDSTFSIMMISYTQSKVIMAKKNVGDLVNVEVDQIGKYTEKLVEAHIADW 202
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (RISA_SCHPO | Q9Y7P0)

molecular function
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0004746	riboflavin synthase activity	Catalysis of the reaction: 2 6,7-dimethyl-8-(1-D-ribityl)lumazine + H(+) = 5-amino-6-(D-ribitylamino)uracil + 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:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	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:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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.

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