1C9U - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

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Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE SOLUBLE QUINOPROTEIN GLUCOSE DEHYDROGENASE IN COMPLEX WITH PQQ

Authors :   A. Oubrie, H. J. Rozeboom, B. W. Dijkstra

Date :   03 Aug 99 (Deposition) - 04 Feb 00 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Beta-Propeller, Superbarrel, Cofactor Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Oubrie, H. J. Rozeboom, K. H. Kalk, A. J. Olsthoorn, J. A. Duine, B. W. Dijkstra
Structure And Mechanism Of Soluble Quinoprotein Glucose Dehydrogenase.
Embo J. V. 18 5187 1999
PubMed-ID: 10508152 | Reference-DOI: 10.1093/EMBOJ/18.19.5187
(for further references see the PDB file header)

Molecule 1 - SOLUBLE QUINOPROTEIN GLUCOSE DEHYDROGENASE
	Cellular Location	:	PERIPLASM
	Chains	:	A, B
	EC Number	:	1.1.99.17
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	ACINETOBACTER CALCOACETICUS
	Organism Taxid	:	471

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 12)

No.	Name	Count	Type	Full Name
1	CA	6	Ligand/Ion	CALCIUM ION
2	GOL	4	Ligand/Ion	GLYCEROL
3	PQQ	2	Ligand/Ion	PYRROLOQUINOLINE QUINONE

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ALA A:269 , TYR A:271 , ASP A:273 , GLU A:309 , HOH A:1020 , HOH A:1056	BINDING SITE FOR RESIDUE CA A 1001
02	AC2	SOFTWARE	GLU A:253 , TYR A:263 , HOH A:1018 , HOH A:1042 , HOH A:1082 , HOH A:1215	BINDING SITE FOR RESIDUE CA A 1002
03	AC3	SOFTWARE	GLY A:247 , PRO A:248 , PQQ A:1004 , HOH A:1049 , HOH A:1198	BINDING SITE FOR RESIDUE CA A 1003
04	AC4	SOFTWARE	ALA B:269 , TYR B:271 , ASP B:273 , GLU B:309 , HOH B:1028 , HOH B:1030	BINDING SITE FOR RESIDUE CA B 1001
05	AC5	SOFTWARE	GLU B:253 , TYR B:263 , HOH B:1027 , HOH B:1040 , HOH B:1051	BINDING SITE FOR RESIDUE CA B 1002
06	AC6	SOFTWARE	GLY B:247 , PRO B:248 , PQQ B:1004 , HOH B:1066 , HOH B:1297	BINDING SITE FOR RESIDUE CA B 1003
07	AC7	SOFTWARE	GLN A:76 , HIS A:144 , ARG A:228 , ASN A:229 , GLN A:231 , GLN A:246 , GLY A:247 , PRO A:248 , TYR A:343 , TRP A:346 , THR A:348 , LEU A:376 , LYS A:377 , ARG A:406 , ARG A:408 , CA A:1003 , GOL A:1005 , HOH A:1178	BINDING SITE FOR RESIDUE PQQ A 1004
08	AC8	SOFTWARE	GLN B:76 , HIS B:144 , ARG B:228 , ASN B:229 , GLN B:231 , GLN B:246 , GLY B:247 , PRO B:248 , TYR B:343 , TRP B:346 , THR B:348 , LEU B:376 , LYS B:377 , ARG B:406 , ARG B:408 , CA B:1003 , GOL B:1005 , HOH B:1158 , HOH B:1240 , HOH B:1297	BINDING SITE FOR RESIDUE PQQ B 1004
09	AC9	SOFTWARE	TYR A:343 , TRP A:346 , PQQ A:1004 , HOH A:1118 , HOH A:1198 , HOH A:1218	BINDING SITE FOR RESIDUE GOL A 1005
10	BC1	SOFTWARE	PQQ B:1004 , HOH B:1246 , HOH B:1253	BINDING SITE FOR RESIDUE GOL B 1005
11	BC2	SOFTWARE	GLN A:179 , HIS A:180 , THR A:181 , ASN A:216 , LYS A:299 , HOH A:1175	BINDING SITE FOR RESIDUE GOL A 1006
12	BC3	SOFTWARE	LEU A:4 , ASP A:335 , CYS A:345 , TRP A:346 , ARG A:378 , HOH A:1102 , HOH A:1122 , HOH A:1250	BINDING SITE FOR RESIDUE GOL A 1007

Asymmetric/Biological Unit

No.	Residues
1	A:338	-	A:345
2	B:338	-	B:345

Asymmetric/Biological Unit

No.	Residues
1	Trp A:265	-	Pro A:266
2	Leu A:324	-	Tyr A:325
3	Trp B:265	-	Pro B:266
4	Leu B:324	-	Tyr B:325

(no "SAP(SNP)/Variant" information available for 1C9U)

(no "PROSITE Motif" information available for 1C9U)

(no "Exon" information available for 1C9U)

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:444
 aligned with DHGB_ACICA | P13650 from UniProtKB/Swiss-Prot  Length:478

    Alignment length:450
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474
           DHGB_ACICA    25 DVPLTPSQFAKAKSENFDKKVILSNLNKPHALLWGPDNQIWLTERATGKILRVNPESGSVKTVFQVPEIVNDADGQNGLLGFAFHPDFKNNPYIYISGTFKNPKSTDKELPNQTIIRRYTYNKSTDTLEKPVDLLAGLPSSKDHQSGRLVIGPDQKIYYTIGDQGRNQLAYLFLPNQAQHTPTQQELNGKDYHTYMGKVLRLNLDGSIPKDNPSFNGVVSHIYTLGHRNPQGLAFTPNGKLLQSEQGPNSDDEINLIVKGGNYGWPNVAGYKDDSGYAYANYSAAANKSIKDLAQNGVKVAAGVPVTKESEWTGKNFVPPLKTLYTVQDTYNYNDPTCGEMTYICWPTVAPSSAYVYKGGKKAITGWENTLLVPSLKRGVIFRIKLDPTYSTTYDDAVPMFKSNNRYRDVIASPDGNVLYVLTDTAGNVQKDDGSVTNTLENPGSLIKFT 474
               SCOP domains d1c9ua_ A: Soluble quinoprotein glucose dehydrogenase                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1c9uA00 A:1-450 TolB, C-terminal domain                                                                                                                                                                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhh.......eeeee.....eeeeee.....eeeee....eeeee......eeeeee.............eeeeee........eeeeeeeee...------.eeeeeeeeeee....eeeeeeeeeeee.......eeeeee.....eeeee......hhhhh..........hhhhhhh........eeeee...................eeee...eeeeeee.....eeeeee.....eeeeee.....................ee.hhhh....................eehhhhh.........eee..........hhhhh.hhhhhh........ee.............eeeee......eeeee............eee......eeeeee......eeeee.....ee.....ee........eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1c9u A   1 DVPLTPSQFAKAKSENFDKKVILSNLNKPHALLWGPDNQIWLTERATGKILRVNPESGSVKTVFQVPEIVNDADGQNGLLGFAFHPDFKNNPYIYISGTFKNPK------PNQTIIRRYTYNKSTDTLEKPVDLLAGLPSSKDHQSGRLVIGPDQKIYYTIGDQGRNQLAYLFLPNQAQHTPTQQELNGKDYHTYMGKVLRLNLDGSIPKDNPSFNGVVSHIYTLGHRNPQGLAFTPNGKLLQSEQGPNSDDEINLIVKGGNYGWPNVAGYKDDSGYAYANYSAAANKSIKDLAQNGVKVAAGVPVTKESEWTGKNFVPPLKTLYTVQDTYNYNDPTCGEMTYICWPTVAPSSAYVYKGGKKAITGWENTLLVPSLKRGVIFRIKLDPTYSTTYDDAVPMFKSNNRYRDVIASPDGNVLYVLTDTAGNVQKDDGSVTNTLENPGSLIKFT 450
                                    10        20        30        40        50        60        70        80        90       100   |     -|      120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450
                                                                                                                                 104    111

Chain B from PDB  Type:PROTEIN  Length:452
 aligned with DHGB_ACICA | P13650 from UniProtKB/Swiss-Prot  Length:478

    Alignment length:452
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474  
           DHGB_ACICA    25 DVPLTPSQFAKAKSENFDKKVILSNLNKPHALLWGPDNQIWLTERATGKILRVNPESGSVKTVFQVPEIVNDADGQNGLLGFAFHPDFKNNPYIYISGTFKNPKSTDKELPNQTIIRRYTYNKSTDTLEKPVDLLAGLPSSKDHQSGRLVIGPDQKIYYTIGDQGRNQLAYLFLPNQAQHTPTQQELNGKDYHTYMGKVLRLNLDGSIPKDNPSFNGVVSHIYTLGHRNPQGLAFTPNGKLLQSEQGPNSDDEINLIVKGGNYGWPNVAGYKDDSGYAYANYSAAANKSIKDLAQNGVKVAAGVPVTKESEWTGKNFVPPLKTLYTVQDTYNYNDPTCGEMTYICWPTVAPSSAYVYKGGKKAITGWENTLLVPSLKRGVIFRIKLDPTYSTTYDDAVPMFKSNNRYRDVIASPDGNVLYVLTDTAGNVQKDDGSVTNTLENPGSLIKFTYK 476
               SCOP domains d1c9ub_ B: Soluble quinoprotein glucose dehydrogenase                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1c9uB00 B:1-452 TolB, C-terminal domain                                                                                                                                                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhh.....eeeeeee.....eeeeee.....eeeee....eeeee........eeee.............eeeeee........eeeeeeeee..........eeeeeeeeeee....eeeeeeeeeeee.......eeeeee.....eeeee......hhhhh..........hhhhhhh........eeeee...........ee..ee..eeee...eeeeeee.....eeeeee.....eeeee......................ee.hhhh....................eehhhhh.........eee..............................eee............eeeee......eeeeee......eeeeee........eeeeee.....eeeeee.....ee.....ee........eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1c9u B   1 DVPLTPSQFAKAKSENFDKKVILSNLNKPHALLWGPDNQIWLTERATGKILRVNPESGSVKTVFQVPEIVNDADGQNGLLGFAFHPDFKNNPYIYISGTFKNPKSTDKELPNQTIIRRYTYNKSTDTLEKPVDLLAGLPSSKDHQSGRLVIGPDQKIYYTIGDQGRNQLAYLFLPNQAQHTPTQQELNGKDYHTYMGKVLRLNLDGSIPKDNPSFNGVVSHIYTLGHRNPQGLAFTPNGKLLQSEQGPNSDDEINLIVKGGNYGWPNVAGYKDDSGYAYANYSAAANKSIKDLAQNGVKVAAGVPVTKESEWTGKNFVPPLKTLYTVQDTYNYNDPTCGEMTYICWPTVAPSSAYVYKGGKKAITGWENTLLVPSLKRGVIFRIKLDPTYSTTYDDAVPMFKSNNRYRDVIASPDGNVLYVLTDTAGNVQKDDGSVTNTLENPGSLIKFTYK 452
                                    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       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450

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: All beta proteins (24004)

Fold: 6-bladed beta-propeller (327)

Superfamily: Soluble quinoprotein glucose dehydrogenase (4)

Family: Soluble quinoprotein glucose dehydrogenase (4)

Protein domain: Soluble quinoprotein glucose dehydrogenase (4)

Acinetobacter calcoaceticus [TaxId: 471] (4)

1a	d1c9ua_	A:
1b	d1c9ub_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: 6 Propellor (215)

Topology: Neuraminidase (215)

Homologous Superfamily: TolB, C-terminal domain (42)

Acinetobacter calcoaceticus. Organism_taxid: 471. (4)

1a	1c9uA00	A:1-450
1b	1c9uB00	B:1-452

(no "Pfam Domain" information available for 1C9U)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (DHGB_ACICA | P13650)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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.
	GO:0016901	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces a quinone or a similar acceptor molecule.
	GO:0048038	quinone binding	Interacting selectively and non-covalently with a quinone, any member of a class of diketones derivable from aromatic compounds by conversion of two CH groups into CO groups with any necessary rearrangement of double bonds.
	GO:0008876	quinoprotein glucose dehydrogenase activity	Catalysis of the reaction: D-glucose + ubiquinone = D-glucono-1,5-lactone + ubiquinol.
biological process
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	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
		Leu A:324 - Tyr A:325	[ RasMol ]
		Leu B:324 - Tyr B:325	[ RasMol ]
		Trp A:265 - Pro A:266	[ RasMol ]
		Trp B:265 - Pro B:266	[ RasMol ]

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	1c9u
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	1.1.99.17
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UniProtKB/Swiss-Prot
	DHGB_ACICA \| P13650	:	1cq1 1cru 1qbi

1cq1	SOLUBLE QUINOPROTEIN GLUCOSE DEHYDROGENASE FROM ACINETOBACTER CALCOACETICUS IN COMPLEX WITH PQQH2 AND GLUCOSE
1cru	SOLUBLE QUINOPROTEIN GLUCOSE DEHYDROGENASE FROM ACINETOBACTER CALCOACETICUS IN COMPLEX WITH PQQ AND METHYLHYDRAZINE
1qbi	1QBI CONTAINS THE SAME PROTEIN IN THE APO-FORM, WITHOUT PQQ

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 12)

Sites (12, 12)

SS Bonds (2, 2)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (1, 2)

CATH Domains (1, 2)

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Gene Ontology (8, 8)

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