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Title :   CRYSTAL STRUCTURE OF PUTATIVE NITROREDUCTASE YDFN (2632848) FROM BACILLUS SUBTILIS AT 1.65 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   19 Nov 07 (Deposition) - 04 Dec 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

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

Keywords :   2632848, Putative Nitroreductase Ydfn, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Flavoprotein, Fmn, Nad, Nadp, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Nitroreductase Ydfn (2632848) From Bacillus Subtilis At 1. 65 A Resolution
To Be Published
PubMed: search

Molecule 1 - PUTATIVE NAD(P)H NITROREDUCTASE YDFN
	Chains	:	A, B
	EC Number	:	1.-.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	MH4A
	Expression System Strain	:	HK100
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	2632848, YDFN, BSU05480
	Mutation	:	YES
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Strain	:	168

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 26)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	FMN	2	Ligand/Ion	FLAVIN MONONUCLEOTIDE
3	MSE	20	Mod. Amino Acid	SELENOMETHIONINE
4	NI	1	Ligand/Ion	NICKEL (II) ION
5	PGO	2	Ligand/Ion	S-1,2-PROPANEDIOL

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:6 , GLU A:10 , HIS B:0 , HOH B:450	BINDING SITE FOR RESIDUE NI A 400
2	AC2	SOFTWARE	TYR A:94 , FMN B:300	BINDING SITE FOR RESIDUE ACT A 401
3	AC3	SOFTWARE	ARG A:11 , ARG A:12 , SER A:13 , GLN A:68 , LYS A:70 , CYS A:154 , PRO A:155 , MSE A:156 , ILE A:157 , GLY A:158 , ARG A:193 , ARG A:196 , HOH A:468 , HOH A:472 , PRO B:39 , SER B:40 , ALA B:41 , ASN B:43 , LEU B:137	BINDING SITE FOR RESIDUE FMN A 300
4	AC4	SOFTWARE	PRO A:39 , SER A:40 , ALA A:41 , ASN A:43 , ASN A:134 , LEU A:137 , ACT A:401 , HOH A:488 , ARG B:11 , ARG B:12 , SER B:13 , GLN B:68 , LYS B:70 , CYS B:154 , PRO B:155 , MSE B:156 , ILE B:157 , GLY B:158 , ARG B:193 , ARG B:196 , HOH B:335	BINDING SITE FOR RESIDUE FMN B 300
5	AC5	SOFTWARE	PRO B:22 , ILE B:23 , LEU B:53 , SER B:75	BINDING SITE FOR RESIDUE PGO B 301
6	AC6	SOFTWARE	LEU A:18 , SER A:19 , GLY A:20 , HIS A:21 , SER A:73 , SER A:75	BINDING SITE FOR RESIDUE PGO A 402

(no "SS Bond" information available for 3BEM)

(no "Cis Peptide Bond" information available for 3BEM)

(no "SAP(SNP)/Variant" information available for 3BEM)

(no "PROSITE Motif" information available for 3BEM)

(no "Exon" information available for 3BEM)

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
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Chain A from PDB  Type:PROTEIN  Length:207
 aligned with MHQN_BACSU | P96692 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:207
                             1                                                                                                                                                                                                                 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       
           MHQN_BACSU     - -MAEFTHLVNERRSASNFLSGHPITKEDLNEMFELVALAPSAFNLQHTKYVTVLDQDVKEKLKQAANGQYKVVSSSAVLLVLGDKQAYQQAADIYEGLKVLGILNKQEYDHMVQDTVSFYENRGEQFKRDEAIRNASLSAMMFMLSAKEKGWDTCPMIGFDAEAVKRILNIDDQFEVVMMITIGKEKTESRRPRGYRKPVNEFVEYM 206
               SCOP domains d3bema_ A: automated matches                                                                                                                                                                                    SCOP domains
               CATH domains 3bemA00 A:0-205 NADH Oxidase                                                                                                                                                                                  - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh............hhhhhhhhhhhhh...hhhhh..eeeeee.hhhhhhhhhhh....hhhhhh.eeeeeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhh....eeeeeeeeee..hhhhh.......hhhh.eeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bem A   0 HmAEFTHLVNERRSASNFLSGHPITKEDLNEmFELVALAPSAFNLQHTKYVTVLDQDVKEKLKQAANGQYKVVSSSAVLLVLGDKQAYQQAADIYEGLKVLGILNKQEYDHmVQDTVSFYENRGEQFKRDEAIRNASLSAmmFmLSAAAAGWDTCPmIGFDAEAVKRILNIDDQFEVVmmITIGKEKTESRRPRGYRKPVNEFVEYm 206
                             |       9        19        29 |      39        49        59        69        79        89        99       109 |     119       129       139|| |   149      |159       169       179       189       199      |
                             |                            31-MSE                                                                         111-MSE                      140-MSE         156-MSE               178-MSE                     206-MSE
                             1-MSE                                                                                                                                     141-MSE                               179-MSE                       
                                                                                                                                                                         143-MSE

Chain B from PDB  Type:PROTEIN  Length:210
 aligned with MHQN_BACSU | P96692 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:210
                                1                                                                                                                                                                                                                 
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206
           MHQN_BACSU     - ----MAEFTHLVNERRSASNFLSGHPITKEDLNEMFELVALAPSAFNLQHTKYVTVLDQDVKEKLKQAANGQYKVVSSSAVLLVLGDKQAYQQAADIYEGLKVLGILNKQEYDHMVQDTVSFYENRGEQFKRDEAIRNASLSAMMFMLSAKEKGWDTCPMIGFDAEAVKRILNIDDQFEVVMMITIGKEKTESRRPRGYRKPVNEFVEYM 206
               SCOP domains d3bemb_ B: automated matches                                                                                                                                                                                       SCOP domains
               CATH domains 3bemB00 B:-3-205 NADH Oxidase                                                                                                                                                                                    - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh............hhhhhhhhhhhhh...hhhhh..eeeeee.hhhhhhhhhhhh...hhhhhh.eeeeeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhh....eeeeeeeeee..hhhhh.......hhhh.eeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3bem B  -3 HHHHmAEFTHLVNERRSASNFLSGHPITKEDLNEmFELVALAPSAFNLQHTKYVTVLDQDVKEKLKQAANGQYKVVSSSAVLLVLGDKQAYQQAADIYEGLKVLGILNKQEYDHmVQDTVSFYENRGEQFKRDEAIRNASLSAmmFmLSAAAAGWDTCPmIGFDAEAVKRILNIDDQFEVVmmITIGKEKTESRRPRGYRKPVNEFVEYm 206
                                |    6        16        26    |   36        46        56        66        76        86        96       106    |  116       126       136   || |146       156       166       176 ||    186       196       206
                                |                            31-MSE                                                                         111-MSE                      140-MSE         156-MSE               178-MSE                     206-MSE
                                1-MSE                                                                                                                                     141-MSE                               179-MSE                       
                                                                                                                                                                            143-MSE

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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(

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Folds(

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Superfamilies( (-)

)

Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a+b) (23004)

Fold: FMN-dependent nitroreductase-like (52)

Superfamily: FMN-dependent nitroreductase-like (52)

Family: automated matches (22)

Protein domain: automated matches (22)

Bacillus subtilis [TaxId: 1423] (2)

1a	d3bema_	A:
1b	d3bemb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: NADH Oxidase (36)

Homologous Superfamily: NADH Oxidase (36)

Bacillus subtilis. Organism_taxid: 1423. Strain: 168. (1)

1a	3bemB00	B:-3-205
1b	3bemA00	A:0-205

(no "Pfam Domain" information available for 3BEM)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (MHQN_BACSU | P96692)

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.
biological process
	GO:0019439	aromatic compound catabolic process	The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
	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:0009636	response to toxic substance	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 a toxic stimulus.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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Ligands, Modified Residues, Ions (5, 26)

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