3AY6 - JenaLib

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Title :   CRYSTAL STRUCTURE OF BACILLUS MEGATERIUM GLUCOSE DEHYDROGENASE 4 A258F MUTANT IN COMPLEX WITH NADH AND D-GLUCOSE

Authors :   T. Nishioka, Y. Yasutake, Y. Nishiya, T. Tamura

Date :   29 Apr 11 (Deposition) - 23 May 12 (Release) - 19 Sep 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Rossmann Fold, Oxidation-Reduction Process, Nucleotide Binding, Cytosol, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Nishioka, Y. Yasutake, Y. Nishiya, T. Tamura
Structure-Guided Mutagenesis For The Improvement Of Substrate Speciﬁ City Of Bacillus Megaterium Glucose 1-Dehydrogenase Iv
Febs J. V. 279 3264 2012
PubMed-ID: 22804868 | Reference-DOI: 10.1111/J.1742-4658.2012.08713.X

Molecule 1 - GLUCOSE 1-DEHYDROGENASE 4
	Chains	:	A, B, C, D
	EC Number	:	1.1.1.47
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21-CODONPLUS(DE3)-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	GDHIV
	Mutation	:	YES
	Organism Scientific	:	BACILLUS MEGATERIUM
	Organism Taxid	:	1404
	Strain	:	IAM 1030
	Synonym	:	GLCDH-IV

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 10)

No.	Name	Count	Type	Full Name
1	BGC	4	Ligand/Ion	BETA-D-GLUCOSE
2	CL	2	Ligand/Ion	CHLORIDE ION
3	NAI	4	Ligand/Ion	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY A:14 , THR A:17 , GLY A:18 , LEU A:19 , TYR A:39 , GLY A:64 , ASP A:65 , VAL A:66 , ASN A:92 , ALA A:93 , GLY A:94 , VAL A:95 , MET A:143 , SER A:144 , SER A:145 , TYR A:158 , LYS A:162 , PRO A:188 , GLY A:189 , ALA A:190 , MET A:191 , THR A:193 , PRO A:194 , ILE A:195 , ASN A:196 , BGC A:262 , HOH A:272 , HOH A:281 , HOH A:313 , HOH A:321 , HOH A:325 , HOH A:380	BINDING SITE FOR RESIDUE NAI A 263
02	AC2	SOFTWARE	GLU A:96 , SER A:145 , HIS A:147 , TRP A:152 , TYR A:158 , ALA A:190 , ASN A:196 , LYS A:199 , NAI A:263 , GLY C:261	BINDING SITE FOR RESIDUE BGC A 262
03	AC3	SOFTWARE	SER A:255 , SER C:255	BINDING SITE FOR RESIDUE CL A 264
04	AC4	SOFTWARE	GLU B:96 , SER B:145 , HIS B:147 , TRP B:152 , TYR B:158 , ASN B:196 , LYS B:199 , NAI B:263 , GLY D:261	BINDING SITE FOR RESIDUE BGC B 262
05	AC5	SOFTWARE	GLY B:14 , THR B:17 , GLY B:18 , LEU B:19 , TYR B:39 , GLY B:64 , ASP B:65 , VAL B:66 , ASN B:92 , ALA B:93 , GLY B:94 , VAL B:95 , THR B:115 , MET B:143 , SER B:144 , SER B:145 , TYR B:158 , LYS B:162 , PRO B:188 , GLY B:189 , ALA B:190 , MET B:191 , THR B:193 , PRO B:194 , ILE B:195 , ASN B:196 , BGC B:262 , HOH B:278 , HOH B:300 , HOH B:301 , HOH B:456	BINDING SITE FOR RESIDUE NAI B 263
06	AC6	SOFTWARE	PRO B:254 , SER B:255 , PRO D:254 , SER D:255	BINDING SITE FOR RESIDUE CL B 264
07	AC7	SOFTWARE	GLY C:14 , THR C:17 , GLY C:18 , LEU C:19 , TYR C:39 , GLY C:64 , ASP C:65 , VAL C:66 , ASN C:92 , ALA C:93 , GLY C:94 , VAL C:95 , MET C:143 , SER C:144 , TYR C:158 , LYS C:162 , PRO C:188 , GLY C:189 , MET C:191 , THR C:193 , PRO C:194 , ILE C:195 , ASN C:196 , BGC C:262 , HOH C:282 , HOH C:311 , HOH C:319 , HOH C:335	BINDING SITE FOR RESIDUE NAI C 263
08	AC8	SOFTWARE	GLY A:261 , GLU C:96 , SER C:145 , HIS C:147 , TYR C:158 , ASN C:196 , LYS C:199 , NAI C:263	BINDING SITE FOR RESIDUE BGC C 262
09	AC9	SOFTWARE	GLY B:261 , GLU D:96 , SER D:145 , HIS D:147 , TRP D:152 , TYR D:158 , ASN D:196 , LYS D:199 , NAI D:263	BINDING SITE FOR RESIDUE BGC D 262
10	BC1	SOFTWARE	GLY D:14 , THR D:17 , GLY D:18 , LEU D:19 , GLY D:64 , ASP D:65 , VAL D:66 , ASN D:92 , ALA D:93 , GLY D:94 , VAL D:95 , MET D:143 , SER D:144 , SER D:145 , TYR D:158 , LYS D:162 , PRO D:188 , GLY D:189 , MET D:191 , THR D:193 , PRO D:194 , ILE D:195 , ASN D:196 , BGC D:262 , HOH D:291 , HOH D:303 , HOH D:332	BINDING SITE FOR RESIDUE NAI D 263

(no "SS Bond" information available for 3AY6)

(no "Cis Peptide Bond" information available for 3AY6)

(no "SAP(SNP)/Variant" information available for 3AY6)

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	DHG4_BACME	145-173	4	A:145-173 B:145-173 C:145-173 D:145-173

(no "Exon" information available for 3AY6)

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
	(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:263
 aligned with DHG4_BACME | P39485 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:263
                              1                                                                                                                                                                                                                                                                    
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258   
           DHG4_BACME     - --MYTDLKDKVVVITGGSTGLGRAMAVRFGQEEAKVVINYYNNEEEALDAKKEVEEAGGQAIIVQGDVTKEEDVVNLVQTAIKEFGTLDVMINNAGVENPVPSHELSLDNWNKVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAMNTPINAEKFADPVQRADVESMIPMGYIGKPEEVAAVAAFLASSQASYVTGITLFADGGMTKYPSFQAGRG 261
               SCOP domains d3ay6a_ A: automated matches                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh..eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: A:145-173    ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ay6 A  -1 HHMYTDLKDKVVVITGGSTGLGRAMAVRFGQEEAKVVINYYNNEEEALDAKKEVEEAGGQAIIVQGDVTKEEDVVNLVQTAIKEFGTLDVMINNAGVENPVPSHELSLDNWNKVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAMNTPINAEKFADPVQRADVESMIPMGYIGKPEEVAAVAAFLASSQASYVTGITLFADGGMTKYPSFQFGRG 261
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258

Chain B from PDB  Type:PROTEIN  Length:267
 aligned with DHG4_BACME | P39485 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:267
                                  1                                                                                                                                                                                                                                                                    
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       
           DHG4_BACME     - ------MYTDLKDKVVVITGGSTGLGRAMAVRFGQEEAKVVINYYNNEEEALDAKKEVEEAGGQAIIVQGDVTKEEDVVNLVQTAIKEFGTLDVMINNAGVENPVPSHELSLDNWNKVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAMNTPINAEKFADPVQRADVESMIPMGYIGKPEEVAAVAAFLASSQASYVTGITLFADGGMTKYPSFQAGRG 261
               SCOP domains d3ay6b_ B: automated matches                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh..eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: B:145-173    ---------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ay6 B  -5 HHHHHHMYTDLKDKVVVITGGSTGLGRAMAVRFGQEEAKVVINYYNNEEEALDAKKEVEEAGGQAIIVQGDVTKEEDVVNLVQTAIKEFGTLDVMINNAGVENPVPSHELSLDNWNKVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAMNTPINAEKFADPVQRADVESMIPMGYIGKPEEVAAVAAFLASSQASYVTGITLFADGGMTKYPSFQFGRG 261
                                     4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254

Chain C from PDB  Type:PROTEIN  Length:262
 aligned with DHG4_BACME | P39485 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:262
                             1                                                                                                                                                                                                                                                                    
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259  
           DHG4_BACME     - -MYTDLKDKVVVITGGSTGLGRAMAVRFGQEEAKVVINYYNNEEEALDAKKEVEEAGGQAIIVQGDVTKEEDVVNLVQTAIKEFGTLDVMINNAGVENPVPSHELSLDNWNKVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAMNTPINAEKFADPVQRADVESMIPMGYIGKPEEVAAVAAFLASSQASYVTGITLFADGGMTKYPSFQAGRG 261
               SCOP domains d3ay6c_ C: automated matches                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh..eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: C:145-173    ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ay6 C   0 HMYTDLKDKVVVITGGSTGLGRAMAVRFGQEEAKVVINYYNNEEEALDAKKEVEEAGGQAIIVQGDVTKEEDVVNLVQTAIKEFGTLDVMINNAGVENPVPSHELSLDNWNKVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAMNTPINAEKFADPVQRADVESMIPMGYIGKPEEVAAVAAFLASSQASYVTGITLFADGGMTKYPSFQFGRG 261
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259

Chain D from PDB  Type:PROTEIN  Length:267
 aligned with DHG4_BACME | P39485 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:267
                                  1                                                                                                                                                                                                                                                                    
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       
           DHG4_BACME     - ------MYTDLKDKVVVITGGSTGLGRAMAVRFGQEEAKVVINYYNNEEEALDAKKEVEEAGGQAIIVQGDVTKEEDVVNLVQTAIKEFGTLDVMINNAGVENPVPSHELSLDNWNKVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAMNTPINAEKFADPVQRADVESMIPMGYIGKPEEVAAVAAFLASSQASYVTGITLFADGGMTKYPSFQAGRG 261
               SCOP domains d3ay6d_ D: automated matches                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh..eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: D:145-173    ---------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ay6 D  -5 HHHHHHMYTDLKDKVVVITGGSTGLGRAMAVRFGQEEAKVVINYYNNEEEALDAKKEVEEAGGQAIIVQGDVTKEEDVVNLVQTAIKEFGTLDVMINNAGVENPVPSHELSLDNWNKVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAMNTPINAEKFADPVQRADVESMIPMGYIGKPEEVAAVAAFLASSQASYVTGITLFADGGMTKYPSFQFGRG 261
                                     4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: NAD(P)-binding Rossmann-fold domains (1604)

Superfamily: NAD(P)-binding Rossmann-fold domains (1604)

Family: Tyrosine-dependent oxidoreductases (503)

Protein domain: automated matches (114)

Bacillus megaterium [TaxId: 1404] (5)

1a	d3ay6a_	A:
1b	d3ay6c_	C:
1c	d3ay6d_	D:
1d	d3ay6b_	B:

(no "CATH Domain" information available for 3AY6)

(no "Pfam Domain" information available for 3AY6)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (DHG4_BACME | P39485)

molecular function
	GO:0047936	glucose 1-dehydrogenase [NAD(P)] activity	Catalysis of the reaction: beta-D-glucose + NAD(P)+ = D-glucono-1,5-lactone + NAD(P)H.
	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: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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3ay6)

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	3ay6
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	DHG4_BACME \| P39485
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	1.1.1.47
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	DHG4_BACME \| P39485
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UniProtKB/Swiss-Prot
	DHG4_BACME \| P39485	:	3aus 3aut 3auu 3ay7

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

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