4DY4 - JenaLib

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Title :   HIGH RESOLUTION STRUCTURE OF E.COLI WRBA WITH FMN

Authors :   I. Kishko, J. Brynda, I. Kuta Smatanova, R. Ettrich, J. Carey

Date :   28 Feb 12 (Deposition) - 06 Mar 13 (Release) - 06 Mar 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.20

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

Keywords :   Rossmann Fold, Nadh Oxidoreductase, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. Kishko, J. Brynda, I. Kuta Smatanova, R. Ettrich, J. Carey
High Resolution Structure Of E. Coli Wrba With Fmn
To Be Published
PubMed: search

Molecule 1 - FLAVOPROTEIN WRBA
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	WRBA, ECOK1_09050, APECO1_95
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	405955
	Synonym	:	TRP REPRESSOR-BINDING PROTEIN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	FMN	2	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	PEG	3	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 1 (2, 10)

No.	Name	Count	Type	Full Name
1	FMN	4	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	PEG	6	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:9 , MET A:10 , TYR A:11 , GLY A:12 , HIS A:13 , ILE A:14 , PRO A:76 , THR A:77 , ARG A:78 , PHE A:79 , GLY A:80 , SER A:112 , THR A:113 , GLY A:114 , THR A:115 , GLY A:116 , GLY A:117 , ALA A:165 , HOH A:313 , HOH A:330 , HOH A:390 , ASP C:91 , HIS C:132	BINDING SITE FOR RESIDUE FMN A 201
2	AC2	SOFTWARE	LEU A:96 , TRP A:97 , GLY A:100 , ALA A:101 , LEU A:102 , TYR A:103 , HIS A:133 , HOH A:304 , HOH A:340	BINDING SITE FOR RESIDUE PEG A 202
3	AC3	SOFTWARE	TRP A:97 , HOH A:315 , PHE C:79 , FMN C:201	BINDING SITE FOR RESIDUE PEG A 203
4	AC4	SOFTWARE	ASP A:91 , HIS A:132 , PEG A:203 , SER C:9 , MET C:10 , TYR C:11 , GLY C:12 , HIS C:13 , ILE C:14 , PRO C:76 , THR C:77 , ARG C:78 , PHE C:79 , GLY C:80 , SER C:112 , THR C:113 , GLY C:114 , THR C:115 , GLY C:116 , GLY C:117 , HOH C:313 , HOH C:327 , HOH C:349 , HOH C:377	BINDING SITE FOR RESIDUE FMN C 201
5	AC5	SOFTWARE	PRO C:39 , VAL C:59 , HOH C:347 , HOH C:417	BINDING SITE FOR RESIDUE PEG C 202

(no "SS Bond" information available for 4DY4)

(no "Cis Peptide Bond" information available for 4DY4)

(no "SAP(SNP)/Variant" information available for 4DY4)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FLAVODOXIN_LIKE	PS50902	Flavodoxin-like domain profile.	NQOR_ECOK1	4-189	2	A:3-188 C:3-188

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FLAVODOXIN_LIKE	PS50902	Flavodoxin-like domain profile.	NQOR_ECOK1	4-189	4	A:3-188 C:3-188

(no "Exon" information available for 4DY4)

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:194
 aligned with E2QJP6_ECOLX | E2QJP6 from UniProtKB/TrEMBL  Length:198

    Alignment length:197
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       
         E2QJP6_ECOLX     2 AKVLVLYYSMYGHIETMARAVAEGASKVDGAEVVVKRVPETMPPQLFEKAGGKTQTAPVATPQELADYDAIIFGTPTRFGNMSGQMRTFLDQTGGLWASGALYGKLASVFSSTGTGGGQEQTITSTWTTLAHHGMVIVPIGYAAQELFDVSQVRGGTPYGATTIAGGDGSRQPSQEELSIARYQGEYVAGLAVKLNG 198
               SCOP domains d4dy4a_ A: automated matches                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhh...........hhhhhhh.eeeeeee......hhhhhhhhh.hhhhhhhh.....eeeeeee.....hhhhhhhhhhhhhhhh..ee......hhhhh....---..................hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dy4 A   1 AKVLVLYYSMYGHIETMARAVAEGASKVDGAEVVVKRVPETMPPQLFEKAGGKTQTAPVATPQELADYDAIIFGTPTRFGNMSGQMRTFLDQTGGLWASGALYGKLASVFSSTGTGGGQEQTITSTWTTLAHHGMVIVPIGYAAQELFDVSQ---GTPYGATTIAGGDGSRQPSQEELSIARYQGEYVAGLAVKLNG 197
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150 |   | 160       170       180       190       
                                                                                                                                                                                 152 156

Chain A from PDB  Type:PROTEIN  Length:194
 aligned with NQOR_ECOK1 | A1A9Q9 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:197
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       
           NQOR_ECOK1     2 AKVLVLYYSMYGHIETMARAVAEGASKVDGAEVVVKRVPETMPPQLFEKAGGKTQTAPVATPQELADYDAIIFGTPTRFGNMSGQMRTFLDQTGGLWASGALYGKLASVFSSTGTGGGQEQTITSTWTTLAHHGMVIVPIGYAAQELFDVSQVRGGTPYGATTIAGGDGSRQPSQEELSIARYQGEYVAGLAVKLNG 198
               SCOP domains d4dy4a_ A: automated matches                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhh...........hhhhhhh.eeeeeee......hhhhhhhhh.hhhhhhhh.....eeeeeee.....hhhhhhhhhhhhhhhh..ee......hhhhh....---..................hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --FLAVODOXIN_LIKE  PDB: A:3-188 UniProt: 4-189                                                                                                                                              --------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dy4 A   1 AKVLVLYYSMYGHIETMARAVAEGASKVDGAEVVVKRVPETMPPQLFEKAGGKTQTAPVATPQELADYDAIIFGTPTRFGNMSGQMRTFLDQTGGLWASGALYGKLASVFSSTGTGGGQEQTITSTWTTLAHHGMVIVPIGYAAQELFDVSQ---GTPYGATTIAGGDGSRQPSQEELSIARYQGEYVAGLAVKLNG 197
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150 |   | 160       170       180       190       
                                                                                                                                                                                 152 156

Chain C from PDB  Type:PROTEIN  Length:181
 aligned with E2QJP6_ECOLX | E2QJP6 from UniProtKB/TrEMBL  Length:198

    Alignment length:197
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       
         E2QJP6_ECOLX     2 AKVLVLYYSMYGHIETMARAVAEGASKVDGAEVVVKRVPETMPPQLFEKAGGKTQTAPVATPQELADYDAIIFGTPTRFGNMSGQMRTFLDQTGGLWASGALYGKLASVFSSTGTGGGQEQTITSTWTTLAHHGMVIVPIGYAAQELFDVSQVRGGTPYGATTIAGGDGSRQPSQEELSIARYQGEYVAGLAVKLNG 198
               SCOP domains d4dy4c_ C: automated matches                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhh...........hhhhhhh.eeeeeee......hhhhhhhhh.hhhhhhhh.....eeeeeeee....hhhhhhhhhhhhhhhh..ee......-------------.....eee...---...hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dy4 C   1 AKVLVLYYSMYGHIETMARAVAEGASKVDGAEVVVKRVPETMPPQLFEKAGGKTQTAPVATPQELADYDAIIFGTPTRFGNMSGQMRTFLDQTGGLWASGALYGKLASVFSSTGTGGGQEQTITSTWTTLAHHGMVIVPIGYA-------------TPYGATTIAGG---RQPSQEELSIARYQGEYVAGLAVKLNG 197
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140  |      -      |160      |  -|      180       190       
                                                                                                                                                                        143           157       167 171

Chain C from PDB  Type:PROTEIN  Length:181
 aligned with NQOR_ECOK1 | A1A9Q9 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:197
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       
           NQOR_ECOK1     2 AKVLVLYYSMYGHIETMARAVAEGASKVDGAEVVVKRVPETMPPQLFEKAGGKTQTAPVATPQELADYDAIIFGTPTRFGNMSGQMRTFLDQTGGLWASGALYGKLASVFSSTGTGGGQEQTITSTWTTLAHHGMVIVPIGYAAQELFDVSQVRGGTPYGATTIAGGDGSRQPSQEELSIARYQGEYVAGLAVKLNG 198
               SCOP domains d4dy4c_ C: automated matches                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhh...........hhhhhhh.eeeeeee......hhhhhhhhh.hhhhhhhh.....eeeeeeee....hhhhhhhhhhhhhhhh..ee......-------------.....eee...---...hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --FLAVODOXIN_LIKE  PDB: C:3-188 UniProt: 4-189                                                                                                                                              --------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dy4 C   1 AKVLVLYYSMYGHIETMARAVAEGASKVDGAEVVVKRVPETMPPQLFEKAGGKTQTAPVATPQELADYDAIIFGTPTRFGNMSGQMRTFLDQTGGLWASGALYGKLASVFSSTGTGGGQEQTITSTWTTLAHHGMVIVPIGYA-------------TPYGATTIAGG---RQPSQEELSIARYQGEYVAGLAVKLNG 197
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140  |      -      |160      |  -|      180       190       
                                                                                                                                                                        143           157       167 171

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Flavodoxin-like (1057)

Superfamily: Flavoproteins (208)

Family: WrbA-like (12)

Protein domain: automated matches (3)

Escherichia coli [TaxId: 405955] (2)

1a	d4dy4a_	A:
1b	d4dy4c_	C:

(no "CATH Domain" information available for 4DY4)

(no "Pfam Domain" information available for 4DY4)

Asymmetric Unit(hide GO term definitions)

Chain A,C (NQOR_ECOK1 | A1A9Q9)

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:0051287	NAD binding	Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
	GO:0003955	NAD(P)H dehydrogenase (quinone) activity	Catalysis of the reaction: NAD(P)H + H+ + a quinone = NAD(P)+ + a hydroquinone.
	GO:0050661	NADP binding	Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
	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:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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.
biological process
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	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.

Chain A,C (E2QJP6_ECOLX | E2QJP6)

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:0051287	NAD binding	Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
	GO:0003955	NAD(P)H dehydrogenase (quinone) activity	Catalysis of the reaction: NAD(P)H + H+ + a quinone = NAD(P)+ + a hydroquinone.
	GO:0050661	NADP binding	Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
	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:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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.
biological process
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	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.

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