3D3F - JenaLib

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Title :   CRYSTAL STRUCTURE OF YVGN AND COFACTOR NADPH FROM BACILLUS SUBTILIS

Authors :   Y. F. Zhou, J. Lei, X. D. Su

Date :   10 May 08 (Deposition) - 28 Apr 09 (Release) - 29 Jan 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A  (1x)
Biol. Unit 3: B  (1x)

Keywords :   Aldo-Keto Reductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Lei, Y. F. Zhou, L. F. Li, X. -D. Su
Structural And Biochemical Analyses Of Yvgn And Ytbe From Bacillus Subtilis
Protein Sci. V. 18 1792 2009
PubMed-ID: 19585557 | Reference-DOI: 10.1002/PRO.178

Molecule 1 - YVGN PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	YVGN
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Strain	:	168
	Synonym	:	PUTATIVE REDUCTASE PROTEIN, YVGN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	NDP	2	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	NDP	2	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	NDP	1	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	NDP	1	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:23 , VAL A:24 , PHE A:25 , ASP A:49 , TYR A:54 , LYS A:79 , HIS A:112 , SER A:141 , ASN A:142 , GLN A:163 , TRP A:189 , SER A:190 , PRO A:191 , LEU A:192 , MET A:193 , GLN A:194 , LEU A:198 , ALA A:215 , ILE A:230 , PRO A:231 , LYS A:232 , SER A:233 , ILE A:234 , LYS A:235 , ARG A:238 , GLU A:241 , ASN A:242 , HOH A:284 , HOH A:296	BINDING SITE FOR RESIDUE NDP A 1
2	AC2	SOFTWARE	GLY B:23 , VAL B:24 , PHE B:25 , ASP B:49 , TYR B:54 , LYS B:79 , HIS B:112 , SER B:141 , ASN B:142 , GLN B:163 , TRP B:189 , SER B:190 , PRO B:191 , LEU B:192 , MET B:193 , GLN B:194 , LEU B:198 , ILE B:230 , PRO B:231 , LYS B:232 , SER B:233 , ILE B:234 , LYS B:235 , ARG B:238 , ASN B:242 , HOH B:321	BINDING SITE FOR RESIDUE NDP B 1

(no "SS Bond" information available for 3D3F)

(no "Cis Peptide Bond" information available for 3D3F)

(no "SAP(SNP)/Variant" information available for 3D3F)

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALDOKETO_REDUCTASE_1	PS00798	Aldo/keto reductase family signature 1.	GR_BACSU	44-61	2	A:44-61 B:44-61
2	ALDOKETO_REDUCTASE_2	PS00062	Aldo/keto reductase family signature 2.	GR_BACSU	126-143	2	A:126-143 B:126-143
3	ALDOKETO_REDUCTASE_3	PS00063	Aldo/keto reductase family putative active site signature.	GR_BACSU	230-245	2	A:230-245 B:230-245

Biological Unit 1 (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALDOKETO_REDUCTASE_1	PS00798	Aldo/keto reductase family signature 1.	GR_BACSU	44-61	2	A:44-61 B:44-61
2	ALDOKETO_REDUCTASE_2	PS00062	Aldo/keto reductase family signature 2.	GR_BACSU	126-143	2	A:126-143 B:126-143
3	ALDOKETO_REDUCTASE_3	PS00063	Aldo/keto reductase family putative active site signature.	GR_BACSU	230-245	2	A:230-245 B:230-245

Biological Unit 2 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALDOKETO_REDUCTASE_1	PS00798	Aldo/keto reductase family signature 1.	GR_BACSU	44-61	1	A:44-61 -
2	ALDOKETO_REDUCTASE_2	PS00062	Aldo/keto reductase family signature 2.	GR_BACSU	126-143	1	A:126-143 -
3	ALDOKETO_REDUCTASE_3	PS00063	Aldo/keto reductase family putative active site signature.	GR_BACSU	230-245	1	A:230-245 -

Biological Unit 3 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALDOKETO_REDUCTASE_1	PS00798	Aldo/keto reductase family signature 1.	GR_BACSU	44-61	1	- B:44-61
2	ALDOKETO_REDUCTASE_2	PS00062	Aldo/keto reductase family signature 2.	GR_BACSU	126-143	1	- B:126-143
3	ALDOKETO_REDUCTASE_3	PS00063	Aldo/keto reductase family putative active site signature.	GR_BACSU	230-245	1	- B:230-245

(no "Exon" information available for 3D3F)

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:275
 aligned with GR_BACSU | O32210 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:275
                                    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     
             GR_BACSU     2 PTSLKDTVKLHNGVEMPWFGLGVFKVENGNEATESVKAAIKNGYRSIDTAAIYKNEEGVGIGIKESGVAREELFITSKVWNEDQGYETTLAAFEKSLERLQLDYLDLYLIHWPGKDKYKDTWRALEKLYKDGKIRAIGVSNFQVHHLEELLKDAEIKPMVNQVEFHPRLTQKELRDYCKGQGIQLEAWSPLMQGQLLDNEVLTQIAEKHNKSVAQVILRWDLQHGVVTIPKSIKEHRIIENADIFDFELSQEDMDKIDALNKDERVGPNPDELLF 276
               SCOP domains d3d3fa_ A: automated matches                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 3d3fA00 A:2-276 NADP-dependent oxidoreductase                                                                                                                                                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee.....eee...ee......hhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhh..hhhhheeeeeehhhhhhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhh.....eeeee......hhhhhhhhhhh..eeeee..hhhhh...hhhhhhhhhhhh.hhhhhhhhhhhhhh.ee.....hhhhhhhhhh......hhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------ALDOKETO_REDUCTASE----------------------------------------------------------------ALDOKETO_REDUCTASE--------------------------------------------------------------------------------------ALDOKETO_REDUCTA------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d3f A   2 PTSLKDTVKLHNGVEMPWFGLGVFKVENGNEATESVKAAIKNGYRSIDTAAIYKNEEGVGIGIKESGVAREELFITSKVWNEDQGYETTLAAFEKSLERLQLDYLDLYLIHWPGKDKYKDTWRALEKLYKDGKIRAIGVSNFQVHHLEELLKDAEIKPMVNQVEFHPRLTQKELRDYCKGQGIQLEAWSPLMQGQLLDNEVLTQIAEKHNKSVAQVILRWDLQHGVVTIPKSIKEHRIIENADIFDFELSQEDMDKIDALNKDERVGPNPDELLF 276
                                    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

Chain B from PDB  Type:PROTEIN  Length:275
 aligned with GR_BACSU | O32210 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:275
                                    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     
             GR_BACSU     2 PTSLKDTVKLHNGVEMPWFGLGVFKVENGNEATESVKAAIKNGYRSIDTAAIYKNEEGVGIGIKESGVAREELFITSKVWNEDQGYETTLAAFEKSLERLQLDYLDLYLIHWPGKDKYKDTWRALEKLYKDGKIRAIGVSNFQVHHLEELLKDAEIKPMVNQVEFHPRLTQKELRDYCKGQGIQLEAWSPLMQGQLLDNEVLTQIAEKHNKSVAQVILRWDLQHGVVTIPKSIKEHRIIENADIFDFELSQEDMDKIDALNKDERVGPNPDELLF 276
               SCOP domains d3d3fb_ B: automated matches                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 3d3fB00 B:2-276 NADP-dependent oxidoreductase                                                                                                                                                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee.....eee...ee......hhhhhhhhhhhhhh...eee......hhhhhhhhhhhh..hhhhheeeeeehhhhhhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhh.......eeeee......hhhhhhhhhhhh.eeeee..hhhhh...hhhhhhhhhhhh.hhhhhhhhhhhhh..ee.....hhhhhhhhhh......hhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------ALDOKETO_REDUCTASE----------------------------------------------------------------ALDOKETO_REDUCTASE--------------------------------------------------------------------------------------ALDOKETO_REDUCTA------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d3f B   2 PTSLKDTVKLHNGVEMPWFGLGVFKVENGNEATESVKAAIKNGYRSIDTAAIYKNEEGVGIGIKESGVAREELFITSKVWNEDQGYETTLAAFEKSLERLQLDYLDLYLIHWPGKDKYKDTWRALEKLYKDGKIRAIGVSNFQVHHLEELLKDAEIKPMVNQVEFHPRLTQKELRDYCKGQGIQLEAWSPLMQGQLLDNEVLTQIAEKHNKSVAQVILRWDLQHGVVTIPKSIKEHRIIENADIFDFELSQEDMDKIDALNKDERVGPNPDELLF 276
                                    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

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(

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Superfamilies( (-)

)

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)

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)

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

Fold: TIM beta/alpha-barrel (3956)

Superfamily: NAD(P)-linked oxidoreductase (286)

Family: automated matches (35)

Protein domain: automated matches (35)

Bacillus subtilis [TaxId: 1423] (3)

1a	d3d3fa_	A:
1b	d3d3fb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: NADP-dependent oxidoreductase (181)

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

1a	3d3fA00	A:2-276
1b	3d3fB00	B:2-276

(no "Pfam Domain" information available for 3D3F)

Asymmetric Unit(hide GO term definitions)

Chain A,B (GR_BACSU | O32210)

molecular function
	GO:0043892	methylglyoxal reductase (NADPH-dependent) activity	Catalysis of the reaction: lactaldehyde + NADP+ = methylglyoxal + NADPH + H+.
	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: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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