1Z44 - JenaLib

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Title :   CRYSTAL STRUCTURE OF OXIDIZED YQJM FROM BACILLUS SUBTILIS COMPLEXED WITH P-NITROPHENOL

Authors :   K. Kitzing, T. B. Fitzpatrick, C. Wilken, J. Sawa, G. P. Bourenkov, P. Ma T. Clausen

Date :   15 Mar 05 (Deposition) - 17 May 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

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

Keywords :   Flavin, Fmn, P-Nitrophenol, Beta-Alpha-Barrel, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Kitzing, T. B. Fitzpatrick, C. Wilken, J. Sawa, G. P. Bourenkov, P. Macheroux, T. Clausen
The 1. 3 A Crystal Structure Of The Flavoprotein Yqjm Reveal A Novel Class Of Old Yellow Enzymes
J. Biol. Chem. V. 280 27904 2005
PubMed-ID: 15890652 | Reference-DOI: 10.1074/JBC.M502587200

Molecule 1 - PROBABLE NADH-DEPENDENT FLAVIN OXIDOREDUCTASE YQJM
	Chains	:	A, B
	EC Number	:	1.-.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21A
	Expression System Strain	:	BL21-CODON-PLUS(DE3)-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Synonym	:	YQJM

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 27)

No.	Name	Count	Type	Full Name
1	FMN	2	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	MSE	20	Mod. Amino Acid	SELENOMETHIONINE
3	NPO	3	Ligand/Ion	P-NITROPHENOL
4	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (4, 54)

No.	Name	Count	Type	Full Name
1	FMN	4	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	MSE	40	Mod. Amino Acid	SELENOMETHIONINE
3	NPO	6	Ligand/Ion	P-NITROPHENOL
4	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 2 (4, 27)

No.	Name	Count	Type	Full Name
1	FMN	2	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	MSE	20	Mod. Amino Acid	SELENOMETHIONINE
3	NPO	3	Ligand/Ion	P-NITROPHENOL
4	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:312 , HOH A:1741 , ARG B:318 , LYS B:322 , HOH B:1691	BINDING SITE FOR RESIDUE SO4 B 1508
2	AC2	SOFTWARE	ARG A:318 , HOH A:1740 , ARG B:312 , HOH B:1607 , HOH B:1688	BINDING SITE FOR RESIDUE SO4 A 1509
3	AC3	SOFTWARE	SER A:23 , PRO A:24 , MSE A:25 , CYS A:26 , ALA A:60 , GLN A:102 , HIS A:164 , HIS A:167 , ARG A:215 , VAL A:283 , MSE A:285 , GLY A:307 , ARG A:308 , NPO A:1506 , HOH A:1512 , HOH A:1518 , HOH A:1564 , HOH A:1567 , HOH A:1585 , ARG B:336	BINDING SITE FOR RESIDUE FMN A 1500
4	AC4	SOFTWARE	ARG A:336 , SER B:23 , PRO B:24 , MSE B:25 , CYS B:26 , ALA B:60 , GLN B:102 , HIS B:164 , HIS B:167 , ARG B:215 , VAL B:283 , MSE B:285 , GLY B:307 , ARG B:308 , NPO B:1505 , HOH B:1527 , HOH B:1533 , HOH B:1572 , HOH B:1585 , HOH B:1627	BINDING SITE FOR RESIDUE FMN B 1501
5	AC5	SOFTWARE	ARG A:336 , TYR B:28 , HIS B:164 , HIS B:167 , TYR B:169 , FMN B:1501	BINDING SITE FOR RESIDUE NPO B 1505
6	AC6	SOFTWARE	TYR A:28 , ILE A:69 , HIS A:164 , HIS A:167 , TYR A:169 , FMN A:1500 , ARG B:336	BINDING SITE FOR RESIDUE NPO A 1506
7	AC7	SOFTWARE	MSE A:42 , ALA A:43 , ILE A:46 , MSE B:42 , ALA B:43 , ILE B:46	BINDING SITE FOR RESIDUE NPO B 1507

(no "SS Bond" information available for 1Z44)

(no "Cis Peptide Bond" information available for 1Z44)

(no "SAP(SNP)/Variant" information available for 1Z44)

(no "PROSITE Motif" information available for 1Z44)

(no "Exon" information available for 1Z44)

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:337
 aligned with NAMA_BACSU | P54550 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:337
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       
           NAMA_BACSU     2 ARKLFTPITIKDMTLKNRIVMSPMCMYSSHEKDGKLTPFHMAHYISRAIGQVGLIIVEASAVNPQGRITDQDLGIWSDEHIEGFAKLTEQVKEQGSKIGIQLAHAGRKAELEGDIFAPSAIAFDEQSATPVEMSAEKVKETVQEFKQAAARAKEAGFDVIEIHAAHGYLIHEFLSPLSNHRTDEYGGSPENRYRFLREIIDEVKQVWDGPLFVRVSASDYTDKGLDIADHIGFAKWMKEQGVDLIDCSSGALVHADINVFPGYQVSFAEKIREQADMATGAVGMITDGSMAEEILQNGRADLIFIGRELLRDPFFARTAAKQLNTEIPAPVQYERGW 338
               SCOP domains d1z44a_ A: NADPH dehydrogenase NamA                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.eee..........................hhhhhhhhhhhhhh...eeeeeeee.hhhhh.....ee..hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhh......ee.............ee.hhhhhhhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhh............hhhhhhhhhhhhhhhhh......eeeeee.........hhhhhhhhhhhhhhhh..eeeee...............hhhhhhhhhhhhh.eeee.....hhhhhhhhhhh....eeeehhhhhhh.hhhhhhhhhh......hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z44 A   2 ARKLFTPITIKDmTLKNRIVmSPmCmYSSHEKDGKLTPFHmAHYISRAIGQVGLIIVEASAVNPQGRITDQDLGIWSDEHIEGFAKLTEQVKEQGSKIGIQLAHAGRKAELEGDIFAPSAIAFDEQSATPVEmSAEKVKETVQEFKQAAARAKEAGFDVIEIHAAHGYLIHEFLSPLSNHRTDEYGGSPENRYRFLREIIDEVKQVWDGPLFVRVSASDYTDKGLDIADHIGFAKWmKEQGVDLIDCSSGALVHADINVFPGYQVSFAEKIREQADmATGAVGmITDGSmAEEILQNGRADLIFIGRELLRDPFFARTAAKQLNTEIPAPVQYERGW 338
                                    11  |     21|  | |  31        41|       51        61        71        81        91       101       111       121       131  |    141       151       161       171       181       191       201       211       221       231      |241       251       261       271      |281   |   291       301       311       321       331       
                                       14-MSE  22-MSE|             42-MSE                                                                                     134-MSE                                                                                                 238-MSE                                 278-MSE  |     |                                               
                                                  25-MSE                                                                                                                                                                                                                                                             285-MSE |                                               
                                                    27-MSE                                                                                                                                                                                                                                                                 291-MSE

Chain B from PDB  Type:PROTEIN  Length:337
 aligned with NAMA_BACSU | P54550 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:337
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       
           NAMA_BACSU     2 ARKLFTPITIKDMTLKNRIVMSPMCMYSSHEKDGKLTPFHMAHYISRAIGQVGLIIVEASAVNPQGRITDQDLGIWSDEHIEGFAKLTEQVKEQGSKIGIQLAHAGRKAELEGDIFAPSAIAFDEQSATPVEMSAEKVKETVQEFKQAAARAKEAGFDVIEIHAAHGYLIHEFLSPLSNHRTDEYGGSPENRYRFLREIIDEVKQVWDGPLFVRVSASDYTDKGLDIADHIGFAKWMKEQGVDLIDCSSGALVHADINVFPGYQVSFAEKIREQADMATGAVGMITDGSMAEEILQNGRADLIFIGRELLRDPFFARTAAKQLNTEIPAPVQYERGW 338
               SCOP domains d1z44b_ B: NADPH dehydrogenase NamA                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --Oxidored_FMN-1z44B01 B:4-327                                                                                                                                                                                                                                                                                                        ----------- Pfam domains (1)
           Pfam domains (2) --Oxidored_FMN-1z44B02 B:4-327                                                                                                                                                                                                                                                                                                        ----------- Pfam domains (2)
         Sec.struct. author .hhhhh.eee..........................hhhhhhhhhhhhhh...eeeeeeee.hhhhh.....ee..hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhh......ee.............ee.hhhhhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh............hhhhhhhhhhhhhhhhhhhh...eeeeee.........hhhhhhhhhhhhhhhh..eeeee...............hhhhhhhhhhhhh..eee.....hhhhhhhhhhh....eeee.hhhhhh.hhhhhhhhhh......hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z44 B   2 ARKLFTPITIKDmTLKNRIVmSPmCmYSSHEKDGKLTPFHmAHYISRAIGQVGLIIVEASAVNPQGRITDQDLGIWSDEHIEGFAKLTEQVKEQGSKIGIQLAHAGRKAELEGDIFAPSAIAFDEQSATPVEmSAEKVKETVQEFKQAAARAKEAGFDVIEIHAAHGYLIHEFLSPLSNHRTDEYGGSPENRYRFLREIIDEVKQVWDGPLFVRVSASDYTDKGLDIADHIGFAKWmKEQGVDLIDCSSGALVHADINVFPGYQVSFAEKIREQADmATGAVGmITDGSmAEEILQNGRADLIFIGRELLRDPFFARTAAKQLNTEIPAPVQYERGW 338
                                    11  |     21|  | |  31        41|       51        61        71        81        91       101       111       121       131  |    141       151       161       171       181       191       201       211       221       231      |241       251       261       271      |281   |   291       301       311       321       331       
                                       14-MSE  22-MSE|             42-MSE                                                                                     134-MSE                                                                                                 238-MSE                                 278-MSE  |     |                                               
                                                  25-MSE                                                                                                                                                                                                                                                             285-MSE |                                               
                                                    27-MSE                                                                                                                                                                                                                                                                 291-MSE

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

)

Protein Domains( (-)

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Organisms( (-)

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

Fold: TIM beta/alpha-barrel (3956)

Superfamily: FMN-linked oxidoreductases (290)

Family: FMN-linked oxidoreductases (242)

Protein domain: NADPH dehydrogenase NamA (4)

Bacillus subtilis [TaxId: 1423] (4)

1a	d1z44a_	A:
1b	d1z44b_	B:

(no "CATH Domain" information available for 1Z44)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: Oxidored_FMN (38)

Bacillus subtilis (4)

1a	Oxidored_FMN-1z44B01	B:4-327
1b	Oxidored_FMN-1z44B02	B:4-327

Asymmetric Unit(hide GO term definitions)

Chain A,B (NAMA_BACSU | P54550)

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: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:0003959	NADPH dehydrogenase activity	Catalysis of the reaction: NADPH + H+ + acceptor = NADP+ + reduced acceptor.
	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: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:0018548	pentaerythritol trinitrate reductase activity	Catalysis of the reaction: pentaerythritol trinitrate + NADPH = NADP+ + nitrate + pentaerythritol dinitrate.
	GO:0052690	trichloro-p-hydroquinone reductive dehalogenase activity	Catalysis of the reaction: 2,3,6-trichlorohydroquinone + 2 glutathione = 2,6-dichlorohydroquinone + glutathione disulfide + HCl.
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: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:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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	1z44
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UniProtKB/Swiss-Prot
	NAMA_BACSU \| P54550	:	1z41 1z42 1z48

1z41	OXIDIZED YQJM
1z42	OXIDIZED YQJM COMPLEXED WITH P-HYDROXYBENZALDEHYDE
1z48	REDUCED YQJM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 27)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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