1RWB - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   COOPERATIVE EFFECT OF TWO SURFACE AMINO ACID MUTATIONS (Q252L AND E170K) OF GLUCOSE DEHYDROGENASE FROM BACILLUS MEGATERIUM IWG3 FOR THE STABILIZATION OF OLIGOMERIC STATE

Authors :   S. -H. Baik, F. Michel, R. Haser, S. Harayama

Date :   16 Dec 03 (Deposition) - 30 Dec 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. H. Baik, F. Michel, N. Aghajari, R. Haser, S. Harayama
Cooperative Effect Of Two Surface Amino Acid Mutations (Q252L And E170K) In Glucose Dehydrogenase From Bacillus Megaterium Iwg3 On Stabilization Of Its Oligomeric State.
Appl. Environ. Microbiol. V. 71 3285 2005
PubMed-ID: 15933031 | Reference-DOI: 10.1128/AEM.71.6.3285-3293.2005

Molecule 1 - GLUCOSE 1-DEHYDROGENASE
	Chains	:	A, B, E, F
	EC Number	:	1.1.1.47
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	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 (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, 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 , ASN A:196 , HOH A:602 , HOH A:649 , HOH A:712 , HOH A:736	BINDING SITE FOR RESIDUE NAD A 601
2	AC2	SOFTWARE	GLY B:14 , THR B:17 , GLY B:18 , LEU B:19 , ARG B:39 , 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 , ILE B:195 , ASN B:196 , HOH B:708 , HOH B:769 , HOH B:805	BINDING SITE FOR RESIDUE NAD B 701
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 , LEU E:95 , 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 , ASN E:196 , HOH E:802 , HOH E:825 , HOH E:869	BINDING SITE FOR RESIDUE NAD E 801
4	AC4	SOFTWARE	GLY F:14 , THR F:17 , GLY F:18 , LEU F:19 , ARG F:39 , 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:902 , HOH F:923 , HOH F:937 , HOH F:960 , HOH F:1030	BINDING SITE FOR RESIDUE NAD F 901

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

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

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

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, 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 1RWB)

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 d1rwba_ A: Glucose dehydrogenase                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1rwbA00 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....hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: A:145-173    ---------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rwb A   1 MYKDLEGKVVVITGSSTGLGKSMAIRFATEKAKVVVNYRSKEDEANSVLEEIKKVGGEAIAVKGDVTVESDVINLVQSAIKEFGKLDVMINNAGLENPVSSHEMSLSDWNKVIDTNLTGAFLGSREAIKYFVENDIKGTVINMSSVHEKIPWPLFVHYAASKGGMKLMTKTLALEYAPKGIRVNNIGPGAINTPINAEKFADPEQRADVESMIPMGYIGEPEEIAAVAAWLASSEASYVTGITLFADGGMTLYPSFQAGRG 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 d1rwbb_ B: Glucose dehydrogenase                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1rwbB00 B: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.........hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: B:145-173    ---------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rwb B   1 MYKDLEGKVVVITGSSTGLGKSMAIRFATEKAKVVVNYRSKEDEANSVLEEIKKVGGEAIAVKGDVTVESDVINLVQSAIKEFGKLDVMINNAGLENPVSSHEMSLSDWNKVIDTNLTGAFLGSREAIKYFVENDIKGTVINMSSVHEKIPWPLFVHYAASKGGMKLMTKTLALEYAPKGIRVNNIGPGAINTPINAEKFADPEQRADVESMIPMGYIGEPEEIAAVAAWLASSEASYVTGITLFADGGMTLYPSFQAGRG 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 d1rwbe_ E: Glucose dehydrogenase                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1rwbE00 E:1-261 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh..eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: E:145-173    ---------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rwb E   1 MYKDLEGKVVVITGSSTGLGKSMAIRFATEKAKVVVNYRSKEDEANSVLEEIKKVGGEAIAVKGDVTVESDVINLVQSAIKEFGKLDVMINNAGLENPVSSHEMSLSDWNKVIDTNLTGAFLGSREAIKYFVENDIKGTVINMSSVHEKIPWPLFVHYAASKGGMKLMTKTLALEYAPKGIRVNNIGPGAINTPINAEKFADPEQRADVESMIPMGYIGEPEEIAAVAAWLASSEASYVTGITLFADGGMTLYPSFQAGRG 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 d1rwbf_ F: Glucose dehydrogenase                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1rwbF00 F:1-261 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh..eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.......hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: F:145-173    ---------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rwb F   1 MYKDLEGKVVVITGSSTGLGKSMAIRFATEKAKVVVNYRSKEDEANSVLEEIKKVGGEAIAVKGDVTVESDVINLVQSAIKEFGKLDVMINNAGLENPVSSHEMSLSDWNKVIDTNLTGAFLGSREAIKYFVENDIKGTVINMSSVHEKIPWPLFVHYAASKGGMKLMTKTLALEYAPKGIRVNNIGPGAINTPINAEKFADPEQRADVESMIPMGYIGEPEEIAAVAAWLASSEASYVTGITLFADGGMTLYPSFQAGRG 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	d1rwba_	A:
1b	d1rwbb_	B:
1c	d1rwbe_	E:
1d	d1rwbf_	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	1rwbA00	A:1-261
1b	1rwbB00	B:1-261
1c	1rwbE00	E:1-261
1d	1rwbF00	F:1-261

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

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 1rwb)

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

(no "Related Entries Specified in the PDB File" available for 1RWB)

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Ligands, Modified Residues, Ions (1, 4)

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SS Bonds (0, 0)

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