1I18 - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - model 1, sites (Jmol Viewer)

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Title :   SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF RIBOFLAVIN SYNTHASE FROM E. COLI

Authors :   V. Truffault, M. Coles, T. Diercks, K. Abelmann, S. Eberhardt, H. Luett A. Bacher, H. Kessler

Date :   31 Jan 01 (Deposition) - 05 Sep 01 (Release) - 13 Jul 11 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B  (21x)
NMR Structure *: A,B  (1x)

Keywords :   Greek-Key-Barrel, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. Truffault, M. Coles, T. Diercks, K. Abelmann, S. Eberhardt, H. Luttgen, A. Bacher, H. Kessler
The Solution Structure Of The N-Terminal Domain Of Riboflavin Synthase.
J. Mol. Biol. V. 309 949 2001
PubMed-ID: 11399071 | Reference-DOI: 10.1006/JMBI.2001.4683

Molecule 1 - RIBOFLAVIN SYNTHASE ALPHA CHAIN
	Chains	:	A, B
	EC Number	:	2.5.1.9
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	N-TERMINAL DOMAIN, RESIDUES 1-97
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2
NMR Structure (21x)	:	A	B
NMR Structure * (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

NMR Structure (1, 2)

No.	Name	Count	Type	Full Name
1	RBF	2	Ligand/Ion	RIBOFLAVIN

NMR Structure * (1, 2)

No.	Name	Count	Type	Full Name
1	RBF	2	Ligand/Ion	RIBOFLAVIN

NMR Structure (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:48 , LEU A:49 , THR A:50 , ASP A:62 , LEU A:63 , MET A:64 , THR A:67 , ILE A:70 , ILE B:5	BINDING SITE FOR RESIDUE RBF A 98
2	AC2	SOFTWARE	ILE A:5 , CYS B:48 , LEU B:49 , THR B:50 , ASP B:62 , LEU B:63 , MET B:64 , THR B:67 , ILE B:70	BINDING SITE FOR RESIDUE RBF B 99

(no "SS Bond" information available for 1I18)

(no "Cis Peptide Bond" information available for 1I18)

(no "SAP(SNP)/Variant" information available for 1I18)

NMR Structure (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LUMAZINE_BIND	PS51177	Riboflavin synthase alpha chain lumazine-binding repeat profile.	RISA_ECOLI	1-97 98-195	2	A:1-97 B:1-97 -
1	LUMAZINE_BIND	PS51177		RISA_SHIFL	1-97 98-195	2	A:1-97 B:1-97 -

NMR Structure * (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LUMAZINE_BIND	PS51177	Riboflavin synthase alpha chain lumazine-binding repeat profile.	RISA_ECOLI	1-97 98-195	2	A:1-97 B:1-97 -
1	LUMAZINE_BIND	PS51177		RISA_SHIFL	1-97 98-195	2	A:1-97 B:1-97 -

(no "Exon" information available for 1I18)

NMR Structure

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:97
 aligned with RISA_ECOLI | P0AFU8 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:97
                                    10        20        30        40        50        60        70        80        90       
            RISA_ECOLI    1 MFTGIVQGTAKLVSIDEKPNFRTHVVELPDHMLDGLETGASVAHNGCCLTVTEINGNHVSFDLMKETLRITNLGDLKVGDWVNVERAAKFSDEIGGH 97
               SCOP domains d1i18a_ A: Riboflavin synthase                                                                    SCOP domains
               CATH domains 1i18A00 A:1-97  [code=2.40.30.20, no name defined]                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeee..eeeeeee.............eeee..eeeeeeeee..eeeeeehhhhhhhhhhhhh....eeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) LUMAZINE_BIND  PDB: A:1-97 UniProt: 1-97                                                          PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                  1i18 A  1 MFTGIVQGTAKLVSIDEKPNFRTHVVELPDHMLDGLETGASVAHNGCCLTVTEINGNHVSFDLMKETLRITNLGDLKVGDWVNVERAAKFSDEIGGH 97
                                    10        20        30        40        50        60        70        80        90

Chain A from PDB  Type:PROTEIN  Length:97
 aligned with RISA_SHIFL | P0AFU9 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:97
                                    10        20        30        40        50        60        70        80        90       
            RISA_SHIFL    1 MFTGIVQGTAKLVSIDEKPNFRTHVVELPDHMLDGLETGASVAHNGCCLTVTEINGNHVSFDLMKETLRITNLGDLKVGDWVNVERAAKFSDEIGGH 97
               SCOP domains d1i18a_ A: Riboflavin synthase                                                                    SCOP domains
               CATH domains 1i18A00 A:1-97  [code=2.40.30.20, no name defined]                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeee..eeeeeee.............eeee..eeeeeeeee..eeeeeehhhhhhhhhhhhh....eeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE LUMAZINE_BIND  PDB: A:1-97 UniProt: 1-97                                                          PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                  1i18 A  1 MFTGIVQGTAKLVSIDEKPNFRTHVVELPDHMLDGLETGASVAHNGCCLTVTEINGNHVSFDLMKETLRITNLGDLKVGDWVNVERAAKFSDEIGGH 97
                                    10        20        30        40        50        60        70        80        90

Chain B from PDB  Type:PROTEIN  Length:97
 aligned with RISA_ECOLI | P0AFU8 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:97
                                    10        20        30        40        50        60        70        80        90       
            RISA_ECOLI    1 MFTGIVQGTAKLVSIDEKPNFRTHVVELPDHMLDGLETGASVAHNGCCLTVTEINGNHVSFDLMKETLRITNLGDLKVGDWVNVERAAKFSDEIGGH 97
               SCOP domains d1i18b_ B: Riboflavin synthase                                                                    SCOP domains
               CATH domains 1i18B00 B:1-97  [code=2.40.30.20, no name defined]                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeee..eeeeeee.............eeee..eeeeeeeee..eeeeeehhhhhhhhhhhhh....eeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) LUMAZINE_BIND  PDB: B:1-97 UniProt: 1-97                                                          PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                  1i18 B  1 MFTGIVQGTAKLVSIDEKPNFRTHVVELPDHMLDGLETGASVAHNGCCLTVTEINGNHVSFDLMKETLRITNLGDLKVGDWVNVERAAKFSDEIGGH 97
                                    10        20        30        40        50        60        70        80        90

Chain B from PDB  Type:PROTEIN  Length:97
 aligned with RISA_SHIFL | P0AFU9 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:97
                                    10        20        30        40        50        60        70        80        90       
            RISA_SHIFL    1 MFTGIVQGTAKLVSIDEKPNFRTHVVELPDHMLDGLETGASVAHNGCCLTVTEINGNHVSFDLMKETLRITNLGDLKVGDWVNVERAAKFSDEIGGH 97
               SCOP domains d1i18b_ B: Riboflavin synthase                                                                    SCOP domains
               CATH domains 1i18B00 B:1-97  [code=2.40.30.20, no name defined]                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeee..eeeeeee.............eeee..eeeeeeeee..eeeeeehhhhhhhhhhhhh....eeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE LUMAZINE_BIND  PDB: B:1-97 UniProt: 1-97                                                          PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                  1i18 B  1 MFTGIVQGTAKLVSIDEKPNFRTHVVELPDHMLDGLETGASVAHNGCCLTVTEINGNHVSFDLMKETLRITNLGDLKVGDWVNVERAAKFSDEIGGH 97
                                    10        20        30        40        50        60        70        80        90

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 '\|'

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Reductase/isomerase/elongation factor common domain (381)

Superfamily: Riboflavin synthase domain-like (130)

Family: Riboflavin synthase (5)

Protein domain: Riboflavin synthase (5)

Escherichia coli [TaxId: 562] (4)

1a	d1i18a_	A:
1b	d1i18b_	B:

NMR Structure

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Elongation Factor Tu (Ef-tu); domain 3 (323)

Homologous Superfamily: [code=2.40.30.20, no name defined] (40)

Escherichia coli. Organism_taxid: 562. (2)

1a	1i18A00	A:1-97
1b	1i18B00	B:1-97

(no "Pfam Domain" information available for 1I18)

NMR Structure(hide GO term definitions)

Chain A,B (RISA_SHIFL | P0AFU9)

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).

Chain A,B (RISA_ECOLI | P0AFU8)

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.

NMR Structure
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UniProtKB/Swiss-Prot
	RISA_ECOLI \| P0AFU8	:	1hze 1i8d 1pkv
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1hze	SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF RIBOFLAVIN SYNTHASE FROM E. COLI

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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