1ICV - JenaLib

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Title :   THE STRUCTURE OF ESCHERICHIA COLI NITROREDUCTASE COMPLEXED WITH NICOTINIC ACID

Authors :   A. L. Lovering, E. I. Hyde, P. F. Searle, S. A. White

Date :   02 Apr 01 (Deposition) - 18 Apr 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Alpha-Beta, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. L. Lovering, E. I. Hyde, P. F. Searle, S. A. White
The Structure Of Escherichia Coli Nitroreductase Complexed With Nicotinic Acid: Three Crystal Forms At 1. 7 A, 1. 8 A And 2. 4 A Resolution.
J. Mol. Biol. V. 309 203 2001
PubMed-ID: 11491290 | Reference-DOI: 10.1006/JMBI.2001.4653
(for further references see the PDB file header)

Molecule 1 - OXYGEN-INSENSITIVE NAD(P)H NITROREDUCTASE
	Chains	:	A, B, C, D
	EC Number	:	1.6.99.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET11C
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	NFSB
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	DIHYDROPTERIDINE REDUCTASE

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 24)

No.	Name	Count	Type	Full Name
1	FMN	4	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	MSE	16	Mod. Amino Acid	SELENOMETHIONINE
3	NIO	4	Ligand/Ion	NICOTINIC ACID

Biological Unit 1 (3, 12)

No.	Name	Count	Type	Full Name
1	FMN	2	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
3	NIO	2	Ligand/Ion	NICOTINIC ACID

Biological Unit 2 (3, 12)

No.	Name	Count	Type	Full Name
1	FMN	2	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
3	NIO	2	Ligand/Ion	NICOTINIC ACID

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:10 , HIS A:11 , SER A:12 , LYS A:14 , ASN A:71 , LYS A:74 , TYR A:144 , PRO A:163 , ILE A:164 , GLU A:165 , GLY A:166 , ASN A:200 , LYS A:205 , ARG A:207 , HOH A:712 , HOH A:715 , HOH A:748 , PRO B:38 , SER B:39 , SER B:40 , ASN B:42 , LEU B:145 , NIO B:702 , HOH B:714	BINDING SITE FOR RESIDUE FMN A 701
2	AC2	SOFTWARE	PHE A:70 , GLY A:166 , FMN A:701 , SER B:40 , THR B:41 , PHE B:124 , HOH B:869	BINDING SITE FOR RESIDUE NIO B 702
3	AC3	SOFTWARE	PRO A:38 , SER A:39 , SER A:40 , ASN A:42 , GLN A:142 , LEU A:145 , NIO A:704 , ARG B:10 , HIS B:11 , SER B:12 , LYS B:14 , ASN B:71 , LYS B:74 , TYR B:144 , PRO B:163 , ILE B:164 , GLU B:165 , GLY B:166 , ASN B:200 , LYS B:205 , ARG B:207 , HOH B:717 , HOH B:744 , HOH B:813	BINDING SITE FOR RESIDUE FMN B 703
4	AC4	SOFTWARE	SER A:40 , THR A:41 , PHE A:124 , GLU B:165 , GLY B:166 , FMN B:703	BINDING SITE FOR RESIDUE NIO A 704
5	AC5	SOFTWARE	ARG C:10 , HIS C:11 , SER C:12 , LYS C:14 , ASN C:71 , LYS C:74 , TYR C:144 , PRO C:163 , ILE C:164 , GLU C:165 , GLY C:166 , ASN C:200 , LYS C:205 , ARG C:207 , HOH C:717 , HOH C:725 , HOH C:727 , HOH C:743 , PRO D:38 , SER D:39 , SER D:40 , ASN D:42 , GLN D:142 , LEU D:145 , NIO D:706	BINDING SITE FOR RESIDUE FMN C 705
6	AC6	SOFTWARE	GLY C:166 , FMN C:705 , SER D:40 , THR D:41 , PHE D:124	BINDING SITE FOR RESIDUE NIO D 706
7	AC7	SOFTWARE	PRO C:38 , SER C:39 , SER C:40 , ASN C:42 , GLN C:142 , LEU C:145 , NIO C:708 , ARG D:10 , HIS D:11 , SER D:12 , LYS D:14 , PHE D:70 , ASN D:71 , LYS D:74 , TYR D:144 , PRO D:163 , ILE D:164 , GLU D:165 , GLY D:166 , LYS D:205 , ARG D:207 , HOH D:708 , HOH D:740 , HOH D:742	BINDING SITE FOR RESIDUE FMN D 707
8	AC8	SOFTWARE	SER C:40 , THR C:41 , PHE C:124 , HOH C:793 , GLY D:166 , FMN D:707	BINDING SITE FOR RESIDUE NIO C 708

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

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

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

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

(no "Exon" information available for 1ICV)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:216
 aligned with NFSB_ECOLI | P38489 from UniProtKB/Swiss-Prot  Length:217

    Alignment length:216
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211      
           NFSB_ECOLI     2 DIISVALKRHSTKAFDASKKLTPEQAEQIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGNYVFNERKMLDASHVVVFCAKTAMDDVWLKLVVDQEDADGRFATPEAKAANDKGRKFFADMHRKDLHDDAEWMAKQVYLNVGNFLLGVAALGLDAVPIEGFDAAILDAEFGLKEKGYTSLVVVPVGHHSVEDFNATLPKSRLPQNITLTEV 217
               SCOP domains d1icva_ A: Oxygen-insensitive NAD(P)H nitroreductase                                                                                                                                                                     SCOP domains
               CATH domains 1icvA00 A:2-217 NADH Oxidase                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhh............hhhhhhhhhhhhhh..hhhhh..eeeeee.hhhhhhhhhhhhh..hhhhhhhhhhh.eeeeeeee...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..ee......hhhhhhhhhhhhhhheeeeeeeeee.....hhhhh......hhhhheee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1icv A   2 DIISVALKRHSTKAFDASKKLTPEQAEQIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGNYVFNERKmLDASHVVVFCAKTAmDDVWLKLVVDQEDADGRFATPEAKAANDKGRKFFADmHRKDLHDDAEWmAKQVYLNVGNFLLGVAALGLDAVPIEGFDAAILDAEFGLKEKGYTSLVVVPVGHHSVEDFNATLPKSRLPQNITLTEV 217
                                    11        21        31        41        51        61        71   |    81        91       101       111       121     | 131       141       151       161       171       181       191       201       211      
                                                                                                    75-MSE         90-MSE                              127-MSE     139-MSE

Chain B from PDB  Type:PROTEIN  Length:216
 aligned with NFSB_ECOLI | P38489 from UniProtKB/Swiss-Prot  Length:217

    Alignment length:216
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211      
           NFSB_ECOLI     2 DIISVALKRHSTKAFDASKKLTPEQAEQIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGNYVFNERKMLDASHVVVFCAKTAMDDVWLKLVVDQEDADGRFATPEAKAANDKGRKFFADMHRKDLHDDAEWMAKQVYLNVGNFLLGVAALGLDAVPIEGFDAAILDAEFGLKEKGYTSLVVVPVGHHSVEDFNATLPKSRLPQNITLTEV 217
               SCOP domains d1icvb_ B: Oxygen-insensitive NAD(P)H nitroreductase                                                                                                                                                                     SCOP domains
               CATH domains 1icvB00 B:2-217 NADH Oxidase                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhh............hhhhhhhhhhhhhh..hhhhh..eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..ee......hhhhhhhhhhhhhh.eeeeeeeeee.....hhhhh......hhhhheee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1icv B   2 DIISVALKRHSTKAFDASKKLTPEQAEQIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGNYVFNERKmLDASHVVVFCAKTAmDDVWLKLVVDQEDADGRFATPEAKAANDKGRKFFADmHRKDLHDDAEWmAKQVYLNVGNFLLGVAALGLDAVPIEGFDAAILDAEFGLKEKGYTSLVVVPVGHHSVEDFNATLPKSRLPQNITLTEV 217
                                    11        21        31        41        51        61        71   |    81        91       101       111       121     | 131       141       151       161       171       181       191       201       211      
                                                                                                    75-MSE         90-MSE                              127-MSE     139-MSE

Chain C from PDB  Type:PROTEIN  Length:216
 aligned with NFSB_ECOLI | P38489 from UniProtKB/Swiss-Prot  Length:217

    Alignment length:216
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211      
           NFSB_ECOLI     2 DIISVALKRHSTKAFDASKKLTPEQAEQIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGNYVFNERKMLDASHVVVFCAKTAMDDVWLKLVVDQEDADGRFATPEAKAANDKGRKFFADMHRKDLHDDAEWMAKQVYLNVGNFLLGVAALGLDAVPIEGFDAAILDAEFGLKEKGYTSLVVVPVGHHSVEDFNATLPKSRLPQNITLTEV 217
               SCOP domains d1icvc_ C: Oxygen-insensitive NAD(P)H nitroreductase                                                                                                                                                                     SCOP domains
               CATH domains 1icvC00 C:2-217 NADH Oxidase                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhh............hhhhhhhhhhhhhh..hhhhh..eeeeee.hhhhhhhhhhhhh..hhhhhhhhhhh.eeeeeeee...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..ee......hhhhhhhhhhhhhhheeeeeeeeee.....hhhhh......hhhhheee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1icv C   2 DIISVALKRHSTKAFDASKKLTPEQAEQIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGNYVFNERKmLDASHVVVFCAKTAmDDVWLKLVVDQEDADGRFATPEAKAANDKGRKFFADmHRKDLHDDAEWmAKQVYLNVGNFLLGVAALGLDAVPIEGFDAAILDAEFGLKEKGYTSLVVVPVGHHSVEDFNATLPKSRLPQNITLTEV 217
                                    11        21        31        41        51        61        71   |    81        91       101       111       121     | 131       141       151       161       171       181       191       201       211      
                                                                                                    75-MSE         90-MSE                              127-MSE     139-MSE

Chain D from PDB  Type:PROTEIN  Length:216
 aligned with NFSB_ECOLI | P38489 from UniProtKB/Swiss-Prot  Length:217

    Alignment length:216
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211      
           NFSB_ECOLI     2 DIISVALKRHSTKAFDASKKLTPEQAEQIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGNYVFNERKMLDASHVVVFCAKTAMDDVWLKLVVDQEDADGRFATPEAKAANDKGRKFFADMHRKDLHDDAEWMAKQVYLNVGNFLLGVAALGLDAVPIEGFDAAILDAEFGLKEKGYTSLVVVPVGHHSVEDFNATLPKSRLPQNITLTEV 217
               SCOP domains d1icvd_ D: Oxygen-insensitive NAD(P)H nitroreductase                                                                                                                                                                     SCOP domains
               CATH domains 1icvD00 D:2-217 NADH Oxidase                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhh............hhhhhhhhhhhhhh..hhhhh..eeeeee.hhhhhhhhhhhhh..hhhhhhhhhhh.eeeeeeee...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..ee......hhhhhhhhh.hhhh.eeeeeeeeee.....hhhhh......hhhhheee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1icv D   2 DIISVALKRHSTKAFDASKKLTPEQAEQIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGNYVFNERKmLDASHVVVFCAKTAmDDVWLKLVVDQEDADGRFATPEAKAANDKGRKFFADmHRKDLHDDAEWmAKQVYLNVGNFLLGVAALGLDAVPIEGFDAAILDAEFGLKEKGYTSLVVVPVGHHSVEDFNATLPKSRLPQNITLTEV 217
                                    11        21        31        41        51        61        71   |    81        91       101       111       121     | 131       141       151       161       171       181       191       201       211      
                                                                                                    75-MSE         90-MSE                              127-MSE     139-MSE

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) (23004)

Fold: FMN-dependent nitroreductase-like (52)

Superfamily: FMN-dependent nitroreductase-like (52)

Family: NADH oxidase/flavin reductase (29)

Protein domain: Oxygen-insensitive NAD(P)H nitroreductase (14)

Escherichia coli, minor form, NfnB [TaxId: 562] (9)

1a	d1icva_	A:
1b	d1icvb_	B:
1c	d1icvc_	C:
1d	d1icvd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: NADH Oxidase (36)

Homologous Superfamily: NADH Oxidase (36)

Escherichia coli. Organism_taxid: 562. (7)

1a	1icvA00	A:2-217
1b	1icvB00	B:2-217
1c	1icvC00	C:2-217
1d	1icvD00	D:2-217

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (NFSB_ECOLI | P38489)

molecular function
	GO:0004155	6,7-dihydropteridine reductase activity	Catalysis of the reaction: NADP+ + 5,6,7,8-tetrahydropteridine = NADPH + H+ + 6,7-dihydropteridine.
	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:0018545	NAD(P)H nitroreductase activity	Catalysis of the conversion of a nitrate group to an amino or hydroxylamino group on toluene or a toluene derivative.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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:0046256	2,4,6-trinitrotoluene catabolic process	The chemical reactions and pathways resulting in the breakdown of 2,4,6-trinitrotoluene, 1-methyl-2,4,6-trinitrobenzene, a highly explosive pale yellow crystalline solid.
	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.
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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1icv)

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	1icv
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	NFSB_ECOLI \| P38489
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	1.6.99.7
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UniProtKB/Swiss-Prot
	NFSB_ECOLI \| P38489	:	1ds7 1icr 1icu 1idt 1oo5 1oo6 1oon 1ooq 1yki 1ylr 1ylu 3x21 3x22

1icr	1ICR WAS SOLVED USING THE TETRAGONAL CRYSTAL FORM.
1icu	1ICU WAS SOLVED USING THE MONOCLINIC CRYSTAL FORM.

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (3, 24)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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SCOP Domains (1, 4)

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