2Z9D - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

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Title :   THE CRYSTAL STRUCTURE OF AZOR (AZOREDUCTASE) FROM ESCHERICHIA COLI: OXIDIZED AZOR IN ORTHORHOMBIC CRYSTALS

Authors :   K. Ito

Date :   18 Sep 07 (Deposition) - 11 Mar 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym./Biol. Unit : A,B

Keywords :   Azoreductase, Flavoprotein, Fmn, Nad, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Ito, M. Nakanishi, W. C. Lee, Y. Zhi, H. Sasaki, S. Zenno, K. Saigo, Y. Kitade, M. Tanokura
Expansion Of Substrate Specificity And Catalytic Mechanism Of Azoreductase By X-Ray Crystallography And Site-Directed Mutagenesis
J. Biol. Chem. V. 283 13889 2008
PubMed-ID: 18337254 | Reference-DOI: 10.1074/JBC.M710070200
(for further references see the PDB file header)

Molecule 1 - FMN-DEPENDENT NADH-AZOREDUCTASE
	Chains	:	A, B
	EC Number	:	1.7.1.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	AZOR
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	FMN-DEPENDENT NADH-AZO COMPOUND OXIDOREDUCTASE, AZO-DYE REDUCTASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	FMN	2	Ligand/Ion	FLAVIN MONONUCLEOTIDE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:9 , LEU A:11 , SER A:15 , GLN A:16 , SER A:17 , ASP A:62 , PRO A:94 , MET A:95 , TYR A:96 , ASN A:97 , PHE A:98 , SER A:139 , ARG A:140 , GLY A:141 , GLY A:142 , HIS A:144 , HOH A:457 , LEU B:50 , ARG B:59	BINDING SITE FOR RESIDUE FMN A 401
2	AC2	SOFTWARE	LEU A:50 , ARG A:59 , SER B:9 , LEU B:11 , SER B:15 , GLN B:16 , SER B:17 , ASP B:62 , PRO B:94 , MET B:95 , TYR B:96 , ASN B:97 , PHE B:98 , SER B:139 , ARG B:140 , GLY B:141 , GLY B:142 , HIS B:144 , HOH B:436	BINDING SITE FOR RESIDUE FMN B 402

(no "SS Bond" information available for 2Z9D)

(no "Cis Peptide Bond" information available for 2Z9D)

(no "SAP(SNP)/Variant" information available for 2Z9D)

(no "PROSITE Motif" information available for 2Z9D)

(no "Exon" information available for 2Z9D)

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
	(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:200
 aligned with AZOR_ECOLI | P41407 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:200
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201
           AZOR_ECOLI     2 SKVLVLKSSILAGYSQSNQLSDYFVEQWREKHSADEITVRDLAANPIPVLDGELVGALRPSDAPLTPRQQEALALSDELIAELKAHDVIVIAAPMYNFNISTQLKNYFDLVARAGVTFRYTENGPEGLVTGKKAIVITSRGGIHKDGPTDLVTPYLSTFLGFIGITDVKFVFAEGIAYGPEMAAKAQSDAKAAIDSIVSA 201
               SCOP domains d2z9da_ A: ACP phosphodiesterase AcpD                                                                                                                                                                    SCOP domains
               CATH domains 2z9dA00 A:1-200  [code=3.40.50.360, no name defined]                                                                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhhhhhhhhhhh...eeeeee.........hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.eeeee..ee..eehhhhhhhhhhhh.....eeee..eeee.....eeeeeee...........hhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z9d A   1 SKVLVLKSSILAGYSQSNQLSDYFVEQWREKHSADEITVRDLAANPIPVLDGELVGALRPSDAPLTPRQQEALALSDELIAELKAHDVIVIAAPMYNFNISTQLKNYFDLVARAGVTFRYTENGPEGLVTGKKAIVITSRGGIHKDGPTDLVTPYLSTFLGFIGITDVKFVFAEGIAYGPEMAAKAQSDAKAAIDSIVSA 200
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

Chain B from PDB  Type:PROTEIN  Length:200
 aligned with AZOR_ECOLI | P41407 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:200
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201
           AZOR_ECOLI     2 SKVLVLKSSILAGYSQSNQLSDYFVEQWREKHSADEITVRDLAANPIPVLDGELVGALRPSDAPLTPRQQEALALSDELIAELKAHDVIVIAAPMYNFNISTQLKNYFDLVARAGVTFRYTENGPEGLVTGKKAIVITSRGGIHKDGPTDLVTPYLSTFLGFIGITDVKFVFAEGIAYGPEMAAKAQSDAKAAIDSIVSA 201
               SCOP domains d2z9db_ B: ACP phosphodiesterase AcpD                                                                                                                                                                    SCOP domains
               CATH domains 2z9dB00 B:1-200  [code=3.40.50.360, no name defined]                                                                                                                                                     CATH domains
           Pfam domains (1) Flavodoxin_2-2z9dB01 B:1-198                                                                                                                                                                          -- Pfam domains (1)
           Pfam domains (2) Flavodoxin_2-2z9dB02 B:1-198                                                                                                                                                                          -- Pfam domains (2)
         Sec.struct. author .eeeeee...hhhhhhhhhhhhhhhhhhhhhh...eeeeee.........hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.eeeee..ee..eehhhhhhhhhhhh.....eeee..eeee.....eeeeeee...........hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z9d B   1 SKVLVLKSSILAGYSQSNQLSDYFVEQWREKHSADEITVRDLAANPIPVLDGELVGALRPSDAPLTPRQQEALALSDELIAELKAHDVIVIAAPMYNFNISTQLKNYFDLVARAGVTFRYTENGPEGLVTGKKAIVITSRGGIHKDGPTDLVTPYLSTFLGFIGITDVKFVFAEGIAYGPEMAAKAQSDAKAAIDSIVSA 200
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Flavodoxin-like (1057)

Superfamily: Flavoproteins (208)

Family: Quinone reductase (65)

Protein domain: ACP phosphodiesterase AcpD (8)

Escherichia coli [TaxId: 562] (7)

1a	d2z9da_	A:
1b	d2z9db_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.360, no name defined] (150)

Escherichia coli. Organism_taxid: 562. (5)

1a	2z9dA00	A:1-200
1b	2z9dB00	B:1-200

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Flavoprotein (71)

Family: Flavodoxin_2 (35)

Escherichia coli (strain K12) (7)

1a	Flavodoxin_2-2z9dB01	B:1-198
1b	Flavodoxin_2-2z9dB02	B:1-198

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (AZOR_ECOLI | P41407)

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:0008752	FMN reductase activity	Catalysis of the reaction: FMNH2 + NAD(P)+ = FMN + NAD(P)H + H+.
	GO:0050446	azobenzene reductase activity	Catalysis of the reaction: N,N-dimethyl-1,4-phenylenediamine + aniline + NADP+ = 4-(dimethylamino)azobenzene + NADPH + H+.
	GO:0009055	electron carrier activity	Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	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:0016652	oxidoreductase activity, acting on NAD(P)H, NAD(P) as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which NADH or NADPH acts as a hydrogen or electron donor and reduces NAD+ or NADP.
	GO:0016655	oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which NADH or NADPH acts as a hydrogen or electron donor and reduces a quinone or a similar acceptor molecule.
	GO:0016661	oxidoreductase activity, acting on other nitrogenous compounds as donors	Catalysis of an oxidation-reduction (redox) reaction in which a nitrogenous group, excluding NH and NH2 groups, acts as a hydrogen or electron donor and reduces a hydrogen or electron 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:0006979	response to oxidative stress	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
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.

Asymmetric/Biological Unit
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	2z9d
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	AZOR_ECOLI \| P41407	:	1tik 1v4b 2d5i 2z98 2z9b 2z9c

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Ligands, Modified Residues, Ions (1, 2)

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