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Asym./Biol. Unit (Jmol Viewer)

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Title :   MOUSE CLASS II ALCOHOL DEHYDROGENASE COMPLEX WITH NADH AND INHIBITOR

Authors :   S. Svensson, J. O. Hoog, G. Schneider, T. Sandalova

Date :   16 Jun 00 (Deposition) - 12 Sep 00 (Release) - 30 Oct 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.08

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

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

Reference :   S. Svensson, J. O. Hoeoeg, G. Schneider, T. Sandalova
Crystal Structure Of Mouse Class Ii Alcohol Dehydrogenase Reveal Determinants Of Substrate Specificity And Catalytic Efficiency
J. Mol. Biol. V. 302 441 2000
PubMed-ID: 10970744 | Reference-DOI: 10.1006/JMBI.2000.4039
(for further references see the PDB file header)

Molecule 1 - ALCOHOL DEHYDROGENASE, CLASS II
	Chains	:	A, B
	EC Number	:	1.1.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Gene	:	ADH-2
	Organ	:	LIVER
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 8)

No.	Name	Count	Type	Full Name
1	CXF	2	Ligand/Ion	CYCLOHEXYLFORMAMIDE
2	NAI	2	Ligand/Ion	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
3	ZN	4	Ligand/Ion	ZINC ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:46 , HIS A:67 , CYS A:178 , CXF A:378	BINDING SITE FOR RESIDUE ZN A 380
2	AC2	SOFTWARE	CYS A:97 , CYS A:100 , CYS A:103 , CYS A:111 , GLY A:112	BINDING SITE FOR RESIDUE ZN A 381
3	AC3	SOFTWARE	CYS B:46 , HIS B:67 , CYS B:178 , CXF B:378	BINDING SITE FOR RESIDUE ZN B 380
4	AC4	SOFTWARE	CYS B:97 , CYS B:100 , CYS B:103 , CYS B:111 , GLY B:112	BINDING SITE FOR RESIDUE ZN B 381
5	AC5	SOFTWARE	PRO A:47 , THR A:48 , CYS A:178 , SER A:182 , GLY A:203 , GLY A:205 , CYS A:206 , VAL A:207 , ASP A:227 , ILE A:228 , LYS A:232 , CYS A:272 , THR A:275 , THR A:278 , VAL A:296 , GLY A:297 , THR A:319 , PHE A:320 , PHE A:321 , ARG A:371 , CXF A:378 , HOH A:2136 , HOH A:2179 , HOH A:2180 , HOH A:2184 , HOH A:2185 , HOH A:2186 , ASP B:362	BINDING SITE FOR RESIDUE NAI A 377
6	AC6	SOFTWARE	CYS A:46 , THR A:48 , HIS A:67 , PHE A:93 , MET A:145 , CYS A:178 , NAI A:377 , ZN A:380	BINDING SITE FOR RESIDUE CXF A 378
7	AC7	SOFTWARE	PRO B:47 , THR B:48 , CYS B:178 , SER B:182 , GLY B:203 , GLY B:205 , CYS B:206 , VAL B:207 , ASP B:227 , ILE B:228 , LYS B:232 , CYS B:272 , THR B:278 , VAL B:296 , GLY B:297 , THR B:319 , PHE B:320 , PHE B:321 , ARG B:371 , CXF B:378 , HOH B:2096 , HOH B:2103 , HOH B:2132 , HOH B:2134 , HOH B:2176 , HOH B:2177 , HOH B:2180 , HOH B:2181 , HOH B:2182 , HOH B:2183	BINDING SITE FOR RESIDUE NAI B 377
8	AC8	SOFTWARE	CYS B:46 , THR B:48 , HIS B:67 , PHE B:93 , CYS B:178 , NAI B:377 , ZN B:380	BINDING SITE FOR RESIDUE CXF B 378

(no "SS Bond" information available for 1E3I)

Asymmetric/Biological Unit

No.	Residues
1	Phe A:61	-	Pro A:62
2	Phe B:61	-	Pro B:62

(no "SAP(SNP)/Variant" information available for 1E3I)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_ZINC	PS00059	Zinc-containing alcohol dehydrogenases signature.	ADH4_MOUSE	67-81	2	A:66-80 B:66-80

(no "Exon" information available for 1E3I)

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:376
 aligned with ADH4_MOUSE | Q9QYY9 from UniProtKB/Swiss-Prot  Length:377

    Alignment length:376
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371      
           ADH4_MOUSE     2 GTQGKVIKCKAAIAWKTGSPLCIEEIEVSPPKACEVRIQVIATCVCPTDINATDPKKKALFPVVLGHECAGIVESVGPGVTNFKPGDKVIPFFAPQCKRCKLCLSPLTNLCGKLRNFKYPTIDQELMEDRTSRFTCKGRSIYHFMGVSSFSQYTVVSEANLARVDDEANLERVCLIGCGFSSGYGAAINTAKVTPSSTCAVFGLGCVGLSAIIGCKIAGASRIIAIDINGEKFPKAKALGATDCLNPRELDKPVQDVITELTAGGVDYSLDCAGTAQTLKAAVDCTVLGWGSCTVVGAKVDKMTIPTVDVILGRSINGTFFGGWKSVDSVPNLVSDYKNKKFDLDLLVTHALPFESINDAIDLMKEGKSIRTILTF 377
               SCOP domains d1e3ia1 A:1-167,A:342-376 Alcohol dehydrogenase                                                                                                                        d1e3ia2 A:168-341 Alcohol dehydrogenase                                                                                                                                       d1e3ia1 A:1-167,A:342-376           SCOP domains
               CATH domains 1e3iA01 A:1-182,A:320-376 Medium-chain alcohol dehydrogenases, catalytic domain                                                                                                       1e3iA02 A:183-319 NAD(P)-binding Rossmann-like Domain                                                                                    1e3iA01 A:1-182,A:320-376                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee........eeeeeee......eeeeeeeeee.hhhhhhh...............eeeeeeeee...........eeee........hhhhhh.............hhhhh..........eee..eee...........eeeee...eee.....hhhhhhhhhhhhhhhhhhhhh........eeeee..hhhhhhhhhhhhhh...eeeee..hhhhhhhhhhh...eeehhhhh..hhhhhhhhhh.....eeee...hhhhhhhhhhh......eeee......eeeeehhhhhh..eeee.hhhhhhhhhhhhhhhhhhhh...hhhh.eeeeee..hhhhhhhhhhh....eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------ADH_ZINC       -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e3i A   1 GTQGKVIKCKAAIAWKTGSPLCIEEIEVSPPKACEVRIQVIATCVCPTDINATDPKKKALFPVVLGHECAGIVESVGPGVTNFKPGDKVIPFFAPQCKRCKLCLSPLTNLCGKLRNFKYPTIDQELMEDRTSRFTCKGRSIYHFMGVSSFSQYTVVSEANLARVDDEANLERVCLIGCGFSSGYGAAINTAKVTPGSTCAVFGLGCVGLSAIIGCKIAGASRIIAIDINGEKFPKAKALGATDCLNPRELDKPVQDVITELTAGGVDYSLDCAGTAQTLKAAVDCTVLGWGSCTVVGAKVDEMTIPTVDVILGRSINGTFFGGWKSVDSVPNLVSDYKNKKFDLDLLVTHALPFESINDAIDLMKEGKSIRTILTF 376
                                    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

Chain B from PDB  Type:PROTEIN  Length:373
 aligned with ADH4_MOUSE | Q9QYY9 from UniProtKB/Swiss-Prot  Length:377

    Alignment length:373
                                    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       264       274       284       294       304       314       324       334       344       354       364       374   
           ADH4_MOUSE     5 GKVIKCKAAIAWKTGSPLCIEEIEVSPPKACEVRIQVIATCVCPTDINATDPKKKALFPVVLGHECAGIVESVGPGVTNFKPGDKVIPFFAPQCKRCKLCLSPLTNLCGKLRNFKYPTIDQELMEDRTSRFTCKGRSIYHFMGVSSFSQYTVVSEANLARVDDEANLERVCLIGCGFSSGYGAAINTAKVTPSSTCAVFGLGCVGLSAIIGCKIAGASRIIAIDINGEKFPKAKALGATDCLNPRELDKPVQDVITELTAGGVDYSLDCAGTAQTLKAAVDCTVLGWGSCTVVGAKVDKMTIPTVDVILGRSINGTFFGGWKSVDSVPNLVSDYKNKKFDLDLLVTHALPFESINDAIDLMKEGKSIRTILTF 377
               SCOP domains d1e3ib1 B:4-167,B:342-376 Alcohol dehydrogenase                                                                                                                     d1e3ib2 B:168-341 Alcohol dehydrogenase                                                                                                                                       d1e3ib1 B:4-167,B:342-376           SCOP domains
               CATH domains 1e3iB01 B:4-182,B:320-376 Medium-chain alcohol dehydrogenases, catalytic domain                                                                                                    1e3iB02 B:183-319 NAD(P)-binding Rossmann-like Domain                                                                                    1e3iB01 B:4-182,B:320-376                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.......eeeeeee......eeeeeeeeee.hhhhhhh..........ee...eeeeeeeee...........eeee........hhhhhh.............hhhhh..........eee..eee...........eeeee...eeee.......hhhhhhhhhhhhhhhhhh........eeeee..hhhhhhhhhhhhhh...eeeee..hhhhhhhhhhh...eeehhhhh..hhhhhhhhhh.....eeee...hhhhhhhhhhh......eeee......eeeeehhhhhh..eeee.hhhhhhhhhhhhhhhhhhhh...hhhh.eeeeee..hhhhhhhhhhh....eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------ADH_ZINC       -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e3i B   4 GKVIKCKAAIAWKTGSPLCIEEIEVSPPKACEVRIQVIATCVCPTDINATDPKKKALFPVVLGHECAGIVESVGPGVTNFKPGDKVIPFFAPQCKRCKLCLSPLTNLCGKLRNFKYPTIDQELMEDRTSRFTCKGRSIYHFMGVSSFSQYTVVSEANLARVDDEANLERVCLIGCGFSSGYGAAINTAKVTPGSTCAVFGLGCVGLSAIIGCKIAGASRIIAIDINGEKFPKAKALGATDCLNPRELDKPVQDVITELTAGGVDYSLDCAGTAQTLKAAVDCTVLGWGSCTVVGAKVDEMTIPTVDVILGRSINGTFFGGWKSVDSVPNLVSDYKNKKFDLDLLVTHALPFESINDAIDLMKEGKSIRTILTF 376
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373

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: GroES-like (132)

Superfamily: GroES-like (130)

Family: Alcohol dehydrogenase-like, N-terminal domain (114)

Protein domain: Alcohol dehydrogenase (77)

Mouse (Mus musculus), class II [TaxId: 10090] (3)

1a	d1e3ia1	A:1-167,A:342-376
1b	d1e3ib1	B:4-167,B:342-376

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: Alcohol dehydrogenase-like, C-terminal domain (115)

Protein domain: Alcohol dehydrogenase (77)

Mouse (Mus musculus), class II [TaxId: 10090] (3)

2a	d1e3ia2	A:168-341
2b	d1e3ib2	B:168-341

Asymmetric/Biological 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)

House mouse (Mus musculus) (11)

1a	1e3iA02	A:183-319
1b	1e3iB02	B:183-319

Architecture: Alpha-Beta Complex (3881)

Topology: Quinone Oxidoreductase; Chain A, domain 1 (131)

Homologous Superfamily: Medium-chain alcohol dehydrogenases, catalytic domain (131)

House mouse (Mus musculus) (3)

2a	1e3iB01	B:4-182,B:320-376
2b	1e3iA01	A:1-182,A:320-376

(no "Pfam Domain" information available for 1E3I)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (ADH4_MOUSE | Q9QYY9)

molecular function
	GO:0051287	NAD binding	Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
	GO:0003960	NADPH:quinone reductase activity	Catalysis of the reaction: NADPH + H+ + quinone = NADP+ + semiquinone.
	GO:0004022	alcohol dehydrogenase (NAD) activity	Catalysis of the reaction: an alcohol + NAD+ = an aldehyde or ketone + NADH + H+.
	GO:0004024	alcohol dehydrogenase activity, zinc-dependent	Catalysis of the reaction: an alcohol + NAD+ = an aldehyde or ketone + NADH + H+, requiring the presence of zinc.
	GO:0004032	alditol:NADP+ 1-oxidoreductase activity	Catalysis of the reaction: an alditol + NADP+ = an aldose + NADPH + H+.
	GO:0005503	all-trans retinal binding	Interacting selectively and non-covalently with all-trans retinal, a compound that plays an important role in the visual process in most vertebrates. All-trans retinal (trans r., visual yellow) results from the bleaching of rhodopsin by light, in which the 11-cis form is converted to the all-trans form. Retinal is one of the forms of vitamin A.
	GO:0019115	benzaldehyde dehydrogenase activity	Catalysis of the reaction: benzaldehyde + NAD(P)+ + H2O = benzoate + NAD(P)H + H+.
	GO:0035276	ethanol binding	Interacting selectively and non-covalently with ethanol, CH(3)-CH(2)-OH.
	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:0016620	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP.
	GO:0019841	retinol binding	Interacting selectively and non-covalently with retinol, vitamin A1, 2,6,6-trimethyl-1-(9'-hydroxy-3',7'-dimethylnona-1',3',5',7'-tetraenyl)cyclohex-1-ene, one of the three components that makes up vitamin A. Retinol is an intermediate in the vision cycle and it also plays a role in growth and differentiation.
	GO:0004745	retinol dehydrogenase activity	Catalysis of the reaction: retinol + NAD+ = retinal + NADH + H+.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0046164	alcohol catabolic process	The chemical reactions and pathways resulting in the breakdown of alcohols, any of a class of compounds containing one or more hydroxyl groups attached to a saturated carbon atom.
	GO:0006066	alcohol metabolic process	The chemical reactions and pathways involving alcohols, any of a class of compounds containing one or more hydroxyl groups attached to a saturated carbon atom.
	GO:0006081	cellular aldehyde metabolic process	The chemical reactions and pathways involving aldehydes, any organic compound with the formula R-CH=O, as carried out by individual cells.
	GO:0006067	ethanol metabolic process	The chemical reactions and pathways involving ethanol, CH3-CH2-OH, a colorless, water-miscible, flammable liquid produced by alcoholic fermentation.
	GO:0006069	ethanol oxidation	An ethanol metabolic process in which ethanol is converted to acetyl-CoA via acetaldehyde and acetate.
	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:1901661	quinone metabolic process	The chemical reactions and pathways involving quinone.
	GO:0001523	retinoid metabolic process	The chemical reactions and pathways involving retinoids, any member of a class of isoprenoids that contain or are derived from four prenyl groups linked head-to-tail. Retinoids include retinol and retinal and structurally similar natural derivatives or synthetic compounds, but need not have vitamin A activity.
	GO:0042572	retinol metabolic process	The chemical reactions and pathways involving retinol, one of the three compounds that makes up vitamin A.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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	1e3i
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Description

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Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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