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Title :   CRYSTAL STRUCTURE OF E. COLI DIHYDROURIDINE SYNTHASE C (DUSC)

Authors :   R. T. Byrne, F. Whelan, A. Konevega, N. Aziz, M. Rodnina, A. A. Antson

Date :   16 Mar 13 (Deposition) - 06 Nov 13 (Release) - 27 May 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Oxidoreductase, Trna Modification (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. T. Byrne, H. T. Jenkins, D. T. Peters, F. Whelan, J. Stowell, N. Aziz, P. Kasatsky, M. V. Rodnina, E. V. Koonin, A. L. Konevega, A. A. Antson
Major Reorientation Of Trna Substrates Defines Specificity Of Dihydrouridine Synthases.
Proc. Natl. Acad. Sci. Usa V. 112 6033 2015
PubMed-ID: 25902496 | Reference-DOI: 10.1073/PNAS.1500161112

Molecule 1 - TRNA-DIHYDROURIDINE SYNTHASE C
	Atcc	:	700926
	Chains	:	A, B
	EC Number	:	1.3.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	ROSETTA PLYSS
	Expression System Vector	:	PET28A
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	ESCHERICHIA COLI K-12
	Organism Taxid	:	83333
	Strain	:	MG1655
	Synonym	:	DIHYDROURIDINE SYNTHASE C

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
2	FMN	2	Ligand/Ion	FLAVIN MONONUCLEOTIDE
3	NO3	2	Ligand/Ion	NITRATE ION

Biological Unit 1 (3, 4)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	FMN	1	Ligand/Ion	FLAVIN MONONUCLEOTIDE
3	NO3	1	Ligand/Ion	NITRATE ION

Biological Unit 2 (3, 4)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	FMN	1	Ligand/Ion	FLAVIN MONONUCLEOTIDE
3	NO3	1	Ligand/Ion	NITRATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:6 , PRO A:7 , MET A:8 , GLU A:9 , PHE A:33 , GLN A:68 , ASN A:95 , CYS A:98 , LYS A:139 , HIS A:168 , TYR A:176 , ASN A:200 , GLY A:201 , GLU A:202 , GLY A:224 , ARG A:225 , HOH A:2132 , HOH A:2215 , HOH A:2219 , ARG B:177	BINDING SITE FOR RESIDUE FMN A1316
2	AC2	SOFTWARE	ARG A:177 , ALA B:6 , PRO B:7 , MET B:8 , GLU B:9 , PHE B:33 , GLN B:68 , ASN B:95 , LYS B:139 , HIS B:168 , TYR B:176 , ASN B:200 , GLY B:201 , GLU B:202 , GLY B:224 , ARG B:225 , HOH B:2132 , HOH B:2196 , HOH B:2199	BINDING SITE FOR RESIDUE FMN B1316
3	AC3	SOFTWARE	TRP A:183 , GLN A:211 , HOH A:2196 , HOH A:2216 , HOH A:2303 , ARG B:281 , THR B:288	BINDING SITE FOR RESIDUE EDO A1317
4	AC4	SOFTWARE	ARG A:225 , ASN A:229 , TYR A:279 , LYS A:282 , HOH A:2236 , HOH A:2285 , GLU B:179	BINDING SITE FOR RESIDUE EDO A1318
5	AC5	SOFTWARE	ALA A:132 , ARG B:2 , ASP B:27 , TRP B:90	BINDING SITE FOR RESIDUE EDO B1317
6	AC6	SOFTWARE	ASP B:155 , GLN B:158 , GLN B:159 , HOH B:2306	BINDING SITE FOR RESIDUE EDO B1318
7	AC7	SOFTWARE	ASP A:182 , TRP A:183 , GLN A:184 , HOH A:2303 , HOH A:2304 , ARG B:281 , PHE B:291 , GLN B:292 , ARG B:295	BINDING SITE FOR RESIDUE NO3 A1319
8	AC8	SOFTWARE	ARG A:281 , GLN A:292 , ARG A:295 , HOH A:2289 , ILE B:181 , ASP B:182 , TRP B:183 , GLN B:184	BINDING SITE FOR RESIDUE NO3 B1319

(no "SS Bond" information available for 4BFA)

(no "Cis Peptide Bond" information available for 4BFA)

(no "SAP(SNP)/Variant" information available for 4BFA)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UPF0034	PS01136	Uncharacterized protein family UPF0034 signature.	DUSC_ECOLI	92-110	2	A:92-110 B:92-110

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UPF0034	PS01136	Uncharacterized protein family UPF0034 signature.	DUSC_ECOLI	92-110	1	A:92-110 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UPF0034	PS01136	Uncharacterized protein family UPF0034 signature.	DUSC_ECOLI	92-110	1	- B:92-110

(no "Exon" information available for 4BFA)

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
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Chain A from PDB  Type:PROTEIN  Length:317
 aligned with DUSC_ECOLI | P33371 from UniProtKB/Swiss-Prot  Length:315

    Alignment length:317
                              1                                                                                                                                                                                                                                                                                                                          
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       
           DUSC_ECOLI     - --MRVLLAPMEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRVQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMREAVPAHLPVSVKVRLGWDSGEKKFEIADAVQQAGATELVVHGRTKEQGYRAEHIDWQAIGDIRQRLNIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGALNIPNLSRVVKYNEPRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRKEYDEATELFQHVRVLNNSPDIARAIQAIDIEKL 315
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.......hhhhhhhhhhh....eeeeeeee......hhhhhhhhhhhhhhh........eeeeee..hhhhhhhhhhhhhhh....eeeee...........hhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.......hhhhhhhhhhhh...eeeee........hhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh..eeeehhhhhhh.hhhhhhhhh....hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------UPF0034            ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bfa A  -1 ASMRVLLAPMEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRVQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMREAVPAHLPVSVKVRLGWDSGEKKFEIADAVQQAGATELVVHGRTKEQGYRAEHIDWQAIGDIRQRLNIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGALNIPNLSRVVKYNEPRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRKEYDEATELFQHVRVLNNSPDIARAIQAIDIEKL 315
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308

Chain B from PDB  Type:PROTEIN  Length:307
 aligned with DUSC_ECOLI | P33371 from UniProtKB/Swiss-Prot  Length:315

    Alignment length:317
                              1                                                                                                                                                                                                                                                                                                                          
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       
           DUSC_ECOLI     - --MRVLLAPMEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRVQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMREAVPAHLPVSVKVRLGWDSGEKKFEIADAVQQAGATELVVHGRTKEQGYRAEHIDWQAIGDIRQRLNIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGALNIPNLSRVVKYNEPRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRKEYDEATELFQHVRVLNNSPDIARAIQAIDIEKL 315
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.......hhhhhhhhhhh....eeeeeeee......hhhhhhhhhhhhhhh........eeeeee..hhhhhhhhhhhhhhh....eeee..----------hhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeee.....hhhhhhhhhhhh...eeeeeeee.....hhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh..eeeehhhhhhh.hhhhhhhhh....hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------UPF0034            ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bfa B  -1 ASMRVLLAPMEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRVQLLGQFPQWLAENAARAVELGSWGVDLNCG----------GGATLLKDPELIYQGAKAMREAVPAHLPVSVKVRLGWDSGEKKFEIADAVQQAGATELVVHGRTKEQGYRAEHIDWQAIGDIRQRLNIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGALNIPNLSRVVKYNEPRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRKEYDEATELFQHVRVLNNSPDIARAIQAIDIEKL 315
                                     8        18        28        38        48        58        68        78        88        |-       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       
                                                                                                                             97        108

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 '\|'

(no "SCOP Domain" information available for 4BFA)

(no "CATH Domain" information available for 4BFA)

(no "Pfam Domain" information available for 4BFA)

Asymmetric Unit(hide GO term definitions)

Chain A,B (DUSC_ECOLI | P33371)

molecular function
	GO:0010181	FMN binding	Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0050660	flavin adenine dinucleotide binding	Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
	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:0000049	tRNA binding	Interacting selectively and non-covalently with transfer RNA.
	GO:0017150	tRNA dihydrouridine synthase activity	Catalysis of the reaction: tRNA-uracil + acceptor = tRNA-dihydrouridine + reduced acceptor.
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:0002943	tRNA dihydrouridine synthesis	The process whereby a uridine in a transfer RNA is converted to dihydrouridine.
	GO:0008033	tRNA processing	The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
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.

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	DUSC_ECOLI \| P33371	:	3w9z 4bf9 4yco 4ycp

4bf9	CRYSTAL STRUCTURE OF E. COLI DIHYDROURIDINE SYNTHASE C (DUSC) (SELENOMETHIONINE DERIVATIVE)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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Gene Ontology (11, 11)

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