3F7J - JenaLib

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Title :   B.SUBTILIS YVGN

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

Date :   09 Nov 08 (Deposition) - 25 Nov 08 (Release) - 29 Jan 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: 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
	Synonym	:	PUTATIVE REDUCTASE PROTEIN, YVGN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 11)

No.	Name	Count	Type	Full Name
1	K	2	Ligand/Ion	POTASSIUM ION
2	NO3	9	Ligand/Ion	NITRATE ION

Biological Unit 1 (1, 5)

No.	Name	Count	Type	Full Name
1	K	-1	Ligand/Ion	POTASSIUM ION
2	NO3	5	Ligand/Ion	NITRATE ION

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	K	-1	Ligand/Ion	POTASSIUM ION
2	NO3	4	Ligand/Ion	NITRATE ION

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PHE A:25 , SER A:190 , PRO A:191 , LEU A:192 , MET A:193 , GLN A:194 , PRO A:231 , LYS A:232	BINDING SITE FOR RESIDUE NO3 A 277
02	AC2	SOFTWARE	LEU A:192 , GLY A:195 , LEU A:198 , ALA A:215 , ARG A:238 , HOH A:302 , HOH A:329 , HOH A:454	BINDING SITE FOR RESIDUE NO3 A 278
03	AC3	SOFTWARE	ASP A:117 , LYS A:118 , TYR A:119 , LYS A:120 , ASP A:121 , HOH A:570 , HOH A:666	BINDING SITE FOR RESIDUE NO3 A 279
04	AC4	SOFTWARE	TRP A:81 , ASN A:82 , LEU A:274 , PHE A:276 , HOH A:422 , HOH A:599 , HOH A:660 , TRP B:81 , LEU B:274 , K B:281	BINDING SITE FOR RESIDUE NO3 A 280
05	AC5	SOFTWARE	ASP A:177 , TYR A:178 , GLY A:181 , GLN A:182 , HOH A:577	BINDING SITE FOR RESIDUE NO3 A 281
06	AC6	SOFTWARE	PHE B:25 , SER B:190 , PRO B:191 , LEU B:192 , MET B:193 , GLN B:194 , PRO B:231 , LYS B:232 , HOH B:508	BINDING SITE FOR RESIDUE NO3 B 277
07	AC7	SOFTWARE	LEU B:192 , GLY B:195 , LEU B:198 , VAL B:214 , ALA B:215 , ARG B:238 , HOH B:295 , HOH B:301 , HOH B:395 , HOH B:467	BINDING SITE FOR RESIDUE NO3 B 278
08	AC8	SOFTWARE	ASP B:117 , LYS B:118 , TYR B:119 , LYS B:120 , ASP B:121 , HOH B:658	BINDING SITE FOR RESIDUE NO3 B 279
09	AC9	SOFTWARE	LYS A:55 , HOH A:356 , ALA B:52 , LYS B:55 , ARG B:100 , HOH B:307 , HOH B:334 , HOH B:421	BINDING SITE FOR RESIDUE NO3 B 280
10	BC1	SOFTWARE	NO3 A:280 , TRP B:81 , ASN B:82	BINDING SITE FOR RESIDUE K B 281
11	BC2	SOFTWARE	HOH A:486 , HOH B:668	BINDING SITE FOR RESIDUE K B 282

(no "SS Bond" information available for 3F7J)

(no "Cis Peptide Bond" information available for 3F7J)

(no "SAP(SNP)/Variant" information available for 3F7J)

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, 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 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	- 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 3F7J)

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

    Alignment length:276
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270      
             GR_BACSU     1 MPTSLKDTVKLHNGVEMPWFGLGVFKVENGNEATESVKAAIKNGYRSIDTAAIYKNEEGVGIGIKESGVAREELFITSKVWNEDQGYETTLAAFEKSLERLQLDYLDLYLIHWPGKDKYKDTWRALEKLYKDGKIRAIGVSNFQVHHLEELLKDAEIKPMVNQVEFHPRLTQKELRDYCKGQGIQLEAWSPLMQGQLLDNEVLTQIAEKHNKSVAQVILRWDLQHGVVTIPKSIKEHRIIENADIFDFELSQEDMDKIDALNKDERVGPNPDELLF 276
               SCOP domains d3f7ja_ A: automated matches                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 3f7jA00 A:1-276 NADP-dependent oxidoreductase                                                                                                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eee.....eee...ee......hhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhh.hhhhheeeeeehhhhhhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhh.....eeeee......hhhhhhhhhhhh.eeeee..hhhhh...hhhhhhhhhhhh.hhhhhhhhhhhhh..ee.....hhhhhhhhh.......hhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------ALDOKETO_REDUCTASE----------------------------------------------------------------ALDOKETO_REDUCTASE--------------------------------------------------------------------------------------ALDOKETO_REDUCTA------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3f7j A   1 MPTSLKDTVKLHNGVEMPWFGLGVFKVENGNEATESVKAAIKNGYRSIDTAAIYKNEEGVGIGIKESGVAREELFITSKVWNEDQGYETTLAAFEKSLERLQLDYLDLYLIHWPGKDKYKDTWRALEKLYKDGKIRAIGVSNFQVHHLEELLKDAEIKPMVNQVEFHPRLTQKELRDYCKGQGIQLEAWSPLMQGQLLDNEVLTQIAEKHNKSVAQVILRWDLQHGVVTIPKSIKEHRIIENADIFDFELSQEDMDKIDALNKDERVGPNPDELLF 276
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270

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

    Alignment length:276
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270      
             GR_BACSU     1 MPTSLKDTVKLHNGVEMPWFGLGVFKVENGNEATESVKAAIKNGYRSIDTAAIYKNEEGVGIGIKESGVAREELFITSKVWNEDQGYETTLAAFEKSLERLQLDYLDLYLIHWPGKDKYKDTWRALEKLYKDGKIRAIGVSNFQVHHLEELLKDAEIKPMVNQVEFHPRLTQKELRDYCKGQGIQLEAWSPLMQGQLLDNEVLTQIAEKHNKSVAQVILRWDLQHGVVTIPKSIKEHRIIENADIFDFELSQEDMDKIDALNKDERVGPNPDELLF 276
               SCOP domains d3f7jb_ B: automated matches                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 3f7jB00 B:1-276 NADP-dependent oxidoreductase                                                                                                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eee.....eee...ee.....hhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhh.hhhhheeeeeehhhhhhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhh.....eeeee......hhhhhhhhhhhh.eeeee..hhhhh...hhhhhhhhhhhh.hhhhhhhhhhhhh..ee.....hhhhhhhhh.......hhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------ALDOKETO_REDUCTASE----------------------------------------------------------------ALDOKETO_REDUCTASE--------------------------------------------------------------------------------------ALDOKETO_REDUCTA------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3f7j B   1 MPTSLKDTVKLHNGVEMPWFGLGVFKVENGNEATESVKAAIKNGYRSIDTAAIYKNEEGVGIGIKESGVAREELFITSKVWNEDQGYETTLAAFEKSLERLQLDYLDLYLIHWPGKDKYKDTWRALEKLYKDGKIRAIGVSNFQVHHLEELLKDAEIKPMVNQVEFHPRLTQKELRDYCKGQGIQLEAWSPLMQGQLLDNEVLTQIAEKHNKSVAQVILRWDLQHGVVTIPKSIKEHRIIENADIFDFELSQEDMDKIDALNKDERVGPNPDELLF 276
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270

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) (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	d3f7ja_	A:
1b	d3f7jb_	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. (5)

1a	3f7jA00	A:1-276
1b	3f7jB00	B:1-276

(no "Pfam Domain" information available for 3F7J)

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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3b3d	APOYTBE
3b3f	HOLOYVGN

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (2, 11)

Sites (11, 11)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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