1NQX - JenaLib

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Title :   CRYSTAL STRUCTURE OF LUMAZINE SYNTHASE FROM AQUIFEX AEOLICUS IN COMPLEX WITH INHIBITOR: 3-(7-HYDROXY-8-RIBITYLLUMAZINE-6-YL)PROPIONIC ACID

Authors :   X. Zhang, W. Meining, M. Cushman, I. Haase, M. Fischer, A. Bacher, R. Lad

Date :   23 Jan 03 (Deposition) - 23 Jan 04 (Release) - 16 Jan 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.82

Chains :   Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,B,C,D,E  (12x)

Keywords :   Lumazine Synthase, Aquifex Aeolicus, Inhibitor Complex, Vitamin Biosynthesis, Catalytic Mechanism, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Zhang, W. Meining, M. Cushman, I. Haase, M. Fischer, A. Bacher, R. Ladenstein
A Structure-Based Model Of The Reaction Catalyzed By Lumazine Synthase From Aquifex Aeolicus.
J. Mol. Biol. V. 328 167 2003
PubMed-ID: 12684006 | Reference-DOI: 10.1016/S0022-2836(03)00186-4

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
	Organism Scientific	:	AQUIFEX AEOLICUS
	Organism Taxid	:	63363
	Synonym	:	DMRL SYNTHASE, LUMAZINE SYNTHASE, RIBOFLAVIN SYNTHASE BETA CHAIN

		1	2	3	4	5
Asymmetric Unit	:	A	B	C	D	E
Biological Unit 1 (12x)	:	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	RLP	5	Ligand/Ion	3-(7-HYDROXY-8-RIBITYLLUMAZINE-6-YL) PROPIONIC ACID

Biological Unit 1 (2, 120)

No.	Name	Count	Type	Full Name
1	PO4	60	Ligand/Ion	PHOSPHATE ION
2	RLP	60	Ligand/Ion	3-(7-HYDROXY-8-RIBITYLLUMAZINE-6-YL) PROPIONIC ACID

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY A:84 , ALA A:85 , THR A:86 , RLP A:1201 , HOH A:1313 , HOH A:1345 , HOH A:1394 , ARG E:127	BINDING SITE FOR RESIDUE PO4 A 1251
02	AC2	SOFTWARE	ARG A:127 , GLY B:84 , ALA B:85 , THR B:86 , RLP B:2201 , HOH B:2313 , HOH B:2345 , HOH B:2394	BINDING SITE FOR RESIDUE PO4 B 2251
03	AC3	SOFTWARE	ARG B:127 , GLY C:84 , ALA C:85 , THR C:86 , RLP C:3201 , HOH C:3313 , HOH C:3345 , HOH C:3394	BINDING SITE FOR RESIDUE PO4 C 3251
04	AC4	SOFTWARE	ARG C:127 , GLY D:84 , ALA D:85 , THR D:86 , RLP D:4201 , HOH D:4313 , HOH D:4345 , HOH D:4394	BINDING SITE FOR RESIDUE PO4 D 4251
05	AC5	SOFTWARE	ARG D:127 , GLY E:84 , ALA E:85 , THR E:86 , RLP E:5201 , HOH E:5313 , HOH E:5345 , HOH E:5394	BINDING SITE FOR RESIDUE PO4 E 5251
06	AC6	SOFTWARE	PHE A:22 , ASN A:23 , GLY A:55 , SER A:56 , TRP A:57 , GLU A:58 , VAL A:80 , LEU A:81 , ILE A:82 , PO4 A:1251 , HOH A:1301 , HOH A:1331 , HOH A:1345 , HOH A:1364 , THR E:112 , PHE E:113 , LYS E:135 , GLU E:138 , HOH E:1340	BINDING SITE FOR RESIDUE RLP A 1201
07	AC7	SOFTWARE	THR A:112 , PHE A:113 , LYS A:135 , GLU A:138 , PHE B:22 , ASN B:23 , GLY B:55 , SER B:56 , TRP B:57 , GLU B:58 , VAL B:80 , LEU B:81 , ILE B:82 , PO4 B:2251 , HOH B:2301 , HOH B:2331 , HOH B:2340 , HOH B:2345 , HOH B:2364	BINDING SITE FOR RESIDUE RLP B 2201
08	AC8	SOFTWARE	THR B:112 , PHE B:113 , LYS B:135 , GLU B:138 , HOH B:3340 , PHE C:22 , ASN C:23 , GLY C:55 , SER C:56 , TRP C:57 , GLU C:58 , VAL C:80 , LEU C:81 , ILE C:82 , PO4 C:3251 , HOH C:3301 , HOH C:3331 , HOH C:3345 , HOH C:3364	BINDING SITE FOR RESIDUE RLP C 3201
09	AC9	SOFTWARE	THR C:112 , PHE C:113 , LYS C:135 , GLU C:138 , PHE D:22 , ASN D:23 , GLY D:55 , SER D:56 , TRP D:57 , GLU D:58 , VAL D:80 , LEU D:81 , ILE D:82 , PO4 D:4251 , HOH D:4301 , HOH D:4331 , HOH D:4340 , HOH D:4345 , HOH D:4364	BINDING SITE FOR RESIDUE RLP D 4201
10	BC1	SOFTWARE	THR D:112 , PHE D:113 , LYS D:135 , GLU D:138 , PHE E:22 , ASN E:23 , GLY E:55 , SER E:56 , TRP E:57 , GLU E:58 , VAL E:80 , LEU E:81 , ILE E:82 , PO4 E:5251 , HOH E:5301 , HOH E:5331 , HOH E:5340 , HOH E:5345 , HOH E:5364	BINDING SITE FOR RESIDUE RLP E 5201

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

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

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

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

(no "Exon" information available for 1NQX)

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:154
 aligned with RISB_AQUAE | O66529 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150    
           RISB_AQUAE     1 MQIYEGKLTAEGLRFGIVASRFNHALVDRLVEGAIDCIVRHGGREEDITLVRVPGSWEIPVAAGELARKEDIDAVIAIGVLIRGATPHFDYIASEVSKGLANLSLELRKPITFGVITADTLEQAIERAGTKHGNKGWEAALSAIEMANLFKSLR 154
               SCOP domains d1nqxa_ A: Lumazine synthase                                                                                                                               SCOP domains
               CATH domains 1nqxA00 A:1-154  [code=3.40.50.960, no name defined]                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..........eeeeee..hhhhhhhhhhhhhhhhhhh..hhh.eeeeee.hhhhhhhhhhhhhh.....eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhheee..eehhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nqx A   1 MQIYEGKLTAEGLRFGIVASRFNHALVDRLVEGAIDCIVRHGGREEDITLVRVPGSWEIPVAAGELARKEDIDAVIAIGVLIRGATPHFDYIASEVSKGLANLSLELRKPITFGVITADTLEQAIERAGTKHGNKGWEAALSAIEMANLFKSLR 154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain B from PDB  Type:PROTEIN  Length:154
 aligned with RISB_AQUAE | O66529 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150    
           RISB_AQUAE     1 MQIYEGKLTAEGLRFGIVASRFNHALVDRLVEGAIDCIVRHGGREEDITLVRVPGSWEIPVAAGELARKEDIDAVIAIGVLIRGATPHFDYIASEVSKGLANLSLELRKPITFGVITADTLEQAIERAGTKHGNKGWEAALSAIEMANLFKSLR 154
               SCOP domains d1nqxb_ B: Lumazine synthase                                                                                                                               SCOP domains
               CATH domains 1nqxB00 B:1-154  [code=3.40.50.960, no name defined]                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..........eeeeee..hhhhhhhhhhhhhhhhhhh..hhh.eeeeee.hhhhhhhhhhhhhh.....eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhheee..eehhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nqx B   1 MQIYEGKLTAEGLRFGIVASRFNHALVDRLVEGAIDCIVRHGGREEDITLVRVPGSWEIPVAAGELARKEDIDAVIAIGVLIRGATPHFDYIASEVSKGLANLSLELRKPITFGVITADTLEQAIERAGTKHGNKGWEAALSAIEMANLFKSLR 154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain C from PDB  Type:PROTEIN  Length:154
 aligned with RISB_AQUAE | O66529 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150    
           RISB_AQUAE     1 MQIYEGKLTAEGLRFGIVASRFNHALVDRLVEGAIDCIVRHGGREEDITLVRVPGSWEIPVAAGELARKEDIDAVIAIGVLIRGATPHFDYIASEVSKGLANLSLELRKPITFGVITADTLEQAIERAGTKHGNKGWEAALSAIEMANLFKSLR 154
               SCOP domains d1nqxc_ C: Lumazine synthase                                                                                                                               SCOP domains
               CATH domains 1nqxC00 C:1-154  [code=3.40.50.960, no name defined]                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..........eeeeee..hhhhhhhhhhhhhhhhhhh..hhh.eeeeee.hhhhhhhhhhhhhh.....eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhheee..eehhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nqx C   1 MQIYEGKLTAEGLRFGIVASRFNHALVDRLVEGAIDCIVRHGGREEDITLVRVPGSWEIPVAAGELARKEDIDAVIAIGVLIRGATPHFDYIASEVSKGLANLSLELRKPITFGVITADTLEQAIERAGTKHGNKGWEAALSAIEMANLFKSLR 154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain D from PDB  Type:PROTEIN  Length:154
 aligned with RISB_AQUAE | O66529 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150    
           RISB_AQUAE     1 MQIYEGKLTAEGLRFGIVASRFNHALVDRLVEGAIDCIVRHGGREEDITLVRVPGSWEIPVAAGELARKEDIDAVIAIGVLIRGATPHFDYIASEVSKGLANLSLELRKPITFGVITADTLEQAIERAGTKHGNKGWEAALSAIEMANLFKSLR 154
               SCOP domains d1nqxd_ D: Lumazine synthase                                                                                                                               SCOP domains
               CATH domains 1nqxD00 D:1-154  [code=3.40.50.960, no name defined]                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..........eeeeee..hhhhhhhhhhhhhhhhhhh..hhh.eeeeee.hhhhhhhhhhhhhh.....eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhheee..eehhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nqx D   1 MQIYEGKLTAEGLRFGIVASRFNHALVDRLVEGAIDCIVRHGGREEDITLVRVPGSWEIPVAAGELARKEDIDAVIAIGVLIRGATPHFDYIASEVSKGLANLSLELRKPITFGVITADTLEQAIERAGTKHGNKGWEAALSAIEMANLFKSLR 154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain E from PDB  Type:PROTEIN  Length:154
 aligned with RISB_AQUAE | O66529 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150    
           RISB_AQUAE     1 MQIYEGKLTAEGLRFGIVASRFNHALVDRLVEGAIDCIVRHGGREEDITLVRVPGSWEIPVAAGELARKEDIDAVIAIGVLIRGATPHFDYIASEVSKGLANLSLELRKPITFGVITADTLEQAIERAGTKHGNKGWEAALSAIEMANLFKSLR 154
               SCOP domains d1nqxe_ E: Lumazine synthase                                                                                                                               SCOP domains
               CATH domains 1nqxE00 E:1-154  [code=3.40.50.960, no name defined]                                                                                                       CATH domains
           Pfam domains (1) ---------DMRL_synthase-1nqxE01 E:10-153                                                                                                                  - Pfam domains (1)
           Pfam domains (2) ---------DMRL_synthase-1nqxE02 E:10-153                                                                                                                  - Pfam domains (2)
           Pfam domains (3) ---------DMRL_synthase-1nqxE03 E:10-153                                                                                                                  - Pfam domains (3)
           Pfam domains (4) ---------DMRL_synthase-1nqxE04 E:10-153                                                                                                                  - Pfam domains (4)
           Pfam domains (5) ---------DMRL_synthase-1nqxE05 E:10-153                                                                                                                  - Pfam domains (5)
         Sec.struct. author .eee..........eeeeee..hhhhhhhhhhhhhhhhhhh..hhh.eeeeee.hhhhhhhhhhhhhh.....eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhheee..eehhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nqx E   1 MQIYEGKLTAEGLRFGIVASRFNHALVDRLVEGAIDCIVRHGGREEDITLVRVPGSWEIPVAAGELARKEDIDAVIAIGVLIRGATPHFDYIASEVSKGLANLSLELRKPITFGVITADTLEQAIERAGTKHGNKGWEAALSAIEMANLFKSLR 154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

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)

Aquifex aeolicus [TaxId: 63363] (5)

1a	d1nqxa_	A:
1b	d1nqxb_	B:
1c	d1nqxc_	C:
1d	d1nqxd_	D:
1e	d1nqxe_	E:

Asymmetric 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)

Aquifex aeolicus. Organism_taxid: 63363. (5)

1a	1nqxA00	A:1-154
1b	1nqxB00	B:1-154
1c	1nqxC00	C:1-154
1d	1nqxD00	D:1-154
1e	1nqxE00	E:1-154

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: DMRL_synthase] (19)

Family: DMRL_synthase (19)

Aquifex aeolicus (4)

1a	DMRL_synthase-1nqxE01	E:10-153
1b	DMRL_synthase-1nqxE02	E:10-153
1c	DMRL_synthase-1nqxE03	E:10-153
1d	DMRL_synthase-1nqxE04	E:10-153
1e	DMRL_synthase-1nqxE05	E:10-153

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E (RISB_AQUAE | O66529)

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: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:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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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	RISB_AQUAE \| O66529	:	1hqk 1nqu 1nqv 1nqw 5mpp 5mq3 5mq7

1nqu	CRYSTAL STRUCTURE OF LUMAZINE SYNTHASE FROM AQUIFEX AEOLICUS IN COMPLEX WITH INHIBITOR: 6,7-DIOXO-5H-8- RIBITYLAMINOLUMAZINE
1nqv	CRYSTAL STRUCTURE OF LUMAZINE SYNTHASE FROM AQUIFEX AEOLICUS IN COMPLEX WITH INHIBITOR: 5-NITROSO-6-RIBITYL- AMINO-2,4(1H,3H)PYRIMIDINEDIONE
1nqw	CRYSTAL STRUCTURE OF LUMAZINE SYNTHASE FROM AQUIFEX AEOLICUS IN COMPLEX WITH INHIBITOR: 5-(6-D-RIBITYLAMINO-2, 4(1H,3H)PYRIMIDINEDIONE-5-YL)-1-PENTYL-PHOSPHONIC ACID

Description

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Ligands, Modified Residues, Ions (2, 10)

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SCOP Domains (1, 5)

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