1GEE - JenaLib

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF GLUCOSE DEHYDROGENASE MUTANT Q252L COMPLEXED WITH NAD+

Authors :   K. Yamamoto, G. Kurisu, M. Kusunoki, S. Tabata, I. Urabe, S. Osaki

Date :   07 Nov 00 (Deposition) - 12 Aug 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Short-Chain Dehydrogenase/Reductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Yamamoto, G. Kurisu, M. Kusunoki, S. Tabata, I. Urabe, S. Osaki
Structural Analysis Of Stability-Increasing Mutants Of Glucose Dehydrogenase
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - GLUCOSE 1-DEHYDROGENASE
	Chains	:	A, B, E, F
	EC Number	:	1.1.1.47
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PKP1500
	Expression System Strain	:	KP3998
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	BACILLUS MEGATERIUM
	Organism Taxid	:	1404
	Strain	:	IWG3

		1	2	3	4
Asymmetric Unit	:	A	B	E	F
Biological Unit 1 (2x)	:	A	B
Biological Unit 2 (1x)	:			E	F
Biological Unit 3 (2x)	:			E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	NAD	4	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	NAD	4	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Biological Unit 3 (1, 4)

No.	Name	Count	Type	Full Name
1	NAD	4	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:14 , THR A:17 , GLY A:18 , LEU A:19 , ARG A:39 , GLY A:64 , ASP A:65 , VAL A:66 , ASN A:92 , ALA A:93 , GLY A:94 , THR A:115 , MET A:143 , SER A:144 , SER A:145 , TYR A:158 , LYS A:162 , PRO A:188 , GLY A:189 , ILE A:191 , THR A:193 , PRO A:194 , ILE A:195 , ASN A:196 , HOH A:1266 , HOH A:1274 , HOH A:1288 , HOH A:1297 , HOH A:1299 , HOH A:1305 , HOH A:1372	BINDING SITE FOR RESIDUE NAD A 1262
2	AC2	SOFTWARE	GLY B:14 , THR B:17 , GLY B:18 , LEU B:19 , GLY B:64 , ASP B:65 , VAL B:66 , ASN B:92 , ALA B:93 , GLY B:94 , THR B:115 , MET B:143 , SER B:144 , SER B:145 , TYR B:158 , LYS B:162 , PRO B:188 , GLY B:189 , ILE B:191 , THR B:193 , PRO B:194 , ILE B:195 , ASN B:196 , HOH B:2264 , HOH B:2281 , HOH B:2282 , HOH B:2322 , HOH B:2325 , HOH B:2332	BINDING SITE FOR RESIDUE NAD B 2262
3	AC3	SOFTWARE	GLY E:14 , THR E:17 , GLY E:18 , LEU E:19 , ARG E:39 , GLY E:64 , ASP E:65 , VAL E:66 , ASN E:92 , ALA E:93 , GLY E:94 , THR E:115 , MET E:143 , SER E:144 , SER E:145 , TYR E:158 , LYS E:162 , PRO E:188 , GLY E:189 , ILE E:191 , THR E:193 , PRO E:194 , ILE E:195 , ASN E:196 , HOH E:3266 , HOH E:3271 , HOH E:3296 , HOH E:3298 , HOH E:3340 , HOH E:3359	BINDING SITE FOR RESIDUE NAD E 3262
4	AC4	SOFTWARE	GLY F:14 , THR F:17 , GLY F:18 , LEU F:19 , GLY F:64 , ASP F:65 , VAL F:66 , ASN F:92 , ALA F:93 , GLY F:94 , THR F:115 , MET F:143 , SER F:144 , SER F:145 , TYR F:158 , LYS F:162 , PRO F:188 , GLY F:189 , ILE F:191 , THR F:193 , PRO F:194 , ILE F:195 , ASN F:196 , HOH F:4266 , HOH F:4281 , HOH F:4295 , HOH F:4316 , HOH F:4326 , HOH F:4329 , HOH F:4336 , HOH F:4371	BINDING SITE FOR RESIDUE NAD F 4262

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

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

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

Asymmetric Unit (1, 4)

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

Biological Unit 1 (1, 4)

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

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	DHG_BACME	145-173	2	- - E:145-173 F:145-173

Biological Unit 3 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	DHG_BACME	145-173	4	- - E:145-173 F:145-173

(no "Exon" information available for 1GEE)

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:261
 aligned with DHG_BACME | P40288 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:261
                                    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 
            DHG_BACME     1 MYKDLEGKVVVITGSSTGLGKSMAIRFATEKAKVVVNYRSKEDEANSVLEEIKKVGGEAIAVKGDVTVESDVINLVQSAIKEFGKLDVMINNAGLENPVSSHEMSLSDWNKVIDTNLTGAFLGSREAIKYFVENDIKGTVINMSSVHEKIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAINTPINAEKFADPEQRADVESMIPMGYIGEPEEIAAVAAWLASSEASYVTGITLFADGGMTQYPSFQAGRG 261
               SCOP domains d1geea_ A: Glucose dehydrogenase                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1geeA00 A:1-261 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh..eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh..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
                 1gee A   1 MYKDLEGKVVVITGSSTGLGKSMAIRFATEKAKVVVNYRSKEDEANSVLEEIKKVGGEAIAVKGDVTVESDVINLVQSAIKEFGKLDVMINNAGLENPVSSHEMSLSDWNKVIDTNLTGAFLGSREAIKYFVENDIKGTVINMSSVHEKIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAINTPINAEKFADPEQRADVESMIPMGYIGEPEEIAAVAAWLASSEASYVTGITLFADGGMTLYPSFQAGRG 261
                                    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

Chain B from PDB  Type:PROTEIN  Length:261
 aligned with DHG_BACME | P40288 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:261
                                    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 
            DHG_BACME     1 MYKDLEGKVVVITGSSTGLGKSMAIRFATEKAKVVVNYRSKEDEANSVLEEIKKVGGEAIAVKGDVTVESDVINLVQSAIKEFGKLDVMINNAGLENPVSSHEMSLSDWNKVIDTNLTGAFLGSREAIKYFVENDIKGTVINMSSVHEKIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAINTPINAEKFADPEQRADVESMIPMGYIGEPEEIAAVAAWLASSEASYVTGITLFADGGMTQYPSFQAGRG 261
               SCOP domains d1geeb_ B: Glucose dehydrogenase                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1geeB00 B:1-261 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh..eeee....hhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: B:145-173    ---------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gee B   1 MYKDLEGKVVVITGSSTGLGKSMAIRFATEKAKVVVNYRSKEDEANSVLEEIKKVGGEAIAVKGDVTVESDVINLVQSAIKEFGKLDVMINNAGLENPVSSHEMSLSDWNKVIDTNLTGAFLGSREAIKYFVENDIKGTVINMSSVHEKIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAINTPINAEKFADPEQRADVESMIPMGYIGEPEEIAAVAAWLASSEASYVTGITLFADGGMTLYPSFQAGRG 261
                                    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

Chain E from PDB  Type:PROTEIN  Length:261
 aligned with DHG_BACME | P40288 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:261
                                    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 
            DHG_BACME     1 MYKDLEGKVVVITGSSTGLGKSMAIRFATEKAKVVVNYRSKEDEANSVLEEIKKVGGEAIAVKGDVTVESDVINLVQSAIKEFGKLDVMINNAGLENPVSSHEMSLSDWNKVIDTNLTGAFLGSREAIKYFVENDIKGTVINMSSVHEKIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAINTPINAEKFADPEQRADVESMIPMGYIGEPEEIAAVAAWLASSEASYVTGITLFADGGMTQYPSFQAGRG 261
               SCOP domains d1geee_ E: Glucose dehydrogenase                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1geeE00 E:1-261 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh..eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: E:145-173    ---------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gee E   1 MYKDLEGKVVVITGSSTGLGKSMAIRFATEKAKVVVNYRSKEDEANSVLEEIKKVGGEAIAVKGDVTVESDVINLVQSAIKEFGKLDVMINNAGLENPVSSHEMSLSDWNKVIDTNLTGAFLGSREAIKYFVENDIKGTVINMSSVHEKIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAINTPINAEKFADPEQRADVESMIPMGYIGEPEEIAAVAAWLASSEASYVTGITLFADGGMTLYPSFQAGRG 261
                                    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

Chain F from PDB  Type:PROTEIN  Length:261
 aligned with DHG_BACME | P40288 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:261
                                    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 
            DHG_BACME     1 MYKDLEGKVVVITGSSTGLGKSMAIRFATEKAKVVVNYRSKEDEANSVLEEIKKVGGEAIAVKGDVTVESDVINLVQSAIKEFGKLDVMINNAGLENPVSSHEMSLSDWNKVIDTNLTGAFLGSREAIKYFVENDIKGTVINMSSVHEKIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAINTPINAEKFADPEQRADVESMIPMGYIGEPEEIAAVAAWLASSEASYVTGITLFADGGMTQYPSFQAGRG 261
               SCOP domains d1geef_ F: Glucose dehydrogenase                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1geeF00 F:1-261 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh..eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: F:145-173    ---------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gee F   1 MYKDLEGKVVVITGSSTGLGKSMAIRFATEKAKVVVNYRSKEDEANSVLEEIKKVGGEAIAVKGDVTVESDVINLVQSAIKEFGKLDVMINNAGLENPVSSHEMSLSDWNKVIDTNLTGAFLGSREAIKYFVENDIKGTVINMSSVHEKIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAINTPINAEKFADPEQRADVESMIPMGYIGEPEEIAAVAAWLASSEASYVTGITLFADGGMTLYPSFQAGRG 261
                                    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

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

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

Family: Tyrosine-dependent oxidoreductases (503)

Protein domain: Glucose dehydrogenase (4)

Bacillus megaterium [TaxId: 1404] (4)

1a	d1geea_	A:
1b	d1geeb_	B:
1c	d1geee_	E:
1d	d1geef_	F:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

Homologous Superfamily: NAD(P)-binding Rossmann-like Domain (1244)

Bacillus megaterium. Organism_taxid: 1404. Strain: iwg3. (4)

1a	1geeA00	A:1-261
1b	1geeB00	B:1-261
1c	1geeE00	E:1-261
1d	1geeF00	F:1-261

(no "Pfam Domain" information available for 1GEE)

Asymmetric Unit(hide GO term definitions)

Chain A,B,E,F (DHG_BACME | P40288)

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: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.
	GO:0030435	sporulation resulting in formation of a cellular spore	The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1gee)

Biological Units
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	1gee
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	DHG_BACME \| P40288	:	1g6k 1gco 1rwb

1g6k	1G6K CONTAINS GLUCOSE 1-DEHYDROGENASE (E96A).
1gco	1GCO CONTAINS WILD TYPE GLUCOSE 1-DEHYDROGENASE.

Description

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Ligands, Modified Residues, Ions (1, 4)

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