1MG5 - JenaLib

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Title :   CRYSTAL STRUCTURE OF DROSOPHILA MELANOGASTER ALCOHOL DEHYDROGENASE COMPLEXED WITH NADH AND ACETATE AT 1.6 A

Authors :   J. Benach, S. Atrian, R. Gonzalez-Duarte, R. Ladenstein

Date :   14 Aug 02 (Deposition) - 14 Oct 03 (Release) - 30 Oct 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.63

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

Keywords :   Sdr, Adh, Drosophila Melanogaster, Nadh, Acetate, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Benach, J. O. Winberg, J. S. Svendsen, S. Atrian, R. Gonzalez-Duarte, R. Ladenstein
Drosophila Alcohol Dehydrogenase: Acetate-Enzyme Interactions And Novel Insights Into The Effects Of Electrostatics On Catalysis
J. Mol. Biol. V. 345 579 2005
PubMed-ID: 15581900 | Reference-DOI: 10.1016/J.JMB.2004.10.028
(for further references see the PDB file header)

Molecule 1 - ALCOHOL DEHYDROGENASE
	Chains	:	A, B
	EC Number	:	1.1.1.1
	Organism Common	:	FRUIT FLY
	Organism Scientific	:	DROSOPHILA MELANOGASTER
	Organism Taxid	:	7227
	Other Details	:	ADH-SLOW ALLELE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	NAI	2	Ligand/Ion	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:139 , THR A:141 , TYR A:152 , ILE A:184 , NAI A:850	BINDING SITE FOR RESIDUE ACT A 900
2	AC2	SOFTWARE	SER B:139 , THR B:141 , TYR B:152 , ILE B:184 , NAI B:851	BINDING SITE FOR RESIDUE ACT B 901
3	AC3	SOFTWARE	ALA A:13 , GLY A:16 , GLY A:17 , ILE A:18 , ASP A:38 , ARG A:39 , ILE A:40 , TYR A:63 , ASP A:64 , VAL A:65 , GLY A:92 , ALA A:93 , GLY A:94 , ARG A:103 , ILE A:137 , GLY A:138 , SER A:139 , TYR A:152 , LYS A:156 , PRO A:182 , GLY A:183 , ILE A:184 , THR A:185 , THR A:187 , LEU A:189 , ACT A:900 , HOH A:903 , HOH A:930 , HOH A:959 , HOH A:989 , HOH A:1028 , HOH A:1033 , HOH A:1067	BINDING SITE FOR RESIDUE NAI A 850
4	AC4	SOFTWARE	ALA B:13 , GLY B:16 , GLY B:17 , ILE B:18 , ASP B:38 , ARG B:39 , ILE B:40 , TYR B:63 , ASP B:64 , VAL B:65 , GLY B:92 , ALA B:93 , GLY B:94 , ARG B:103 , VAL B:107 , ILE B:137 , GLY B:138 , SER B:139 , TYR B:152 , LYS B:156 , PRO B:182 , GLY B:183 , ILE B:184 , THR B:185 , THR B:187 , LEU B:189 , ACT B:901 , HOH B:906 , HOH B:912 , HOH B:964 , HOH B:970 , HOH B:1009 , HOH B:1010	BINDING SITE FOR RESIDUE NAI B 851

(no "SS Bond" information available for 1MG5)

(no "Cis Peptide Bond" information available for 1MG5)

Asymmetric/Biological Unit (7, 14)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_ADH_DROME_001 *	N	9	V	ADH_DROME	---	---	A/B	N	8	V
2	UniProt	VAR_ADH_DROME_002 *	A	46	D	ADH_DROME	---	---	A/B	A	45	D
3	UniProt	VAR_ADH_DROME_003 *	A	46	V	ADH_DROME	---	---	A/B	A	45	V
4	UniProt	VAR_ADH_DROME_004 *	A	52	E	ADH_DROME	---	---	A/B	A	51	E
5	UniProt	VAR_ADH_DROME_005 *	A	71	S	ADH_DROME	---	---	A/B	A	70	S
6	UniProt	VAR_ADH_DROME_006 *	K	193	T	ADH_DROME	---	---	A/B	K	192	T
7	UniProt	VAR_ADH_DROME_007 *	P	215	S	ADH_DROME	---	---	A/B	P	214	S
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	ADH_DROME	140-168	2	A:139-167 B:139-167

(no "Exon" information available for 1MG5)

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:255
 aligned with ADH_DROME | P00334 from UniProtKB/Swiss-Prot  Length:256

    Alignment length:255
                                    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     
            ADH_DROME     2 SFTLTNKNVIFVAGLGGIGLDTSKELLKRDLKNLVILDRIENPAAIAELKAINPKVTVTFYPYDVTVPIAETTKLLKTIFAQLKTVDVLINGAGILDDHQIERTIAVNYTGLVNTTTAILDFWDKRKGGPGGIICNIGSVTGFNAIYQVPVYSGTKAAVVNFTSSLAKLAPITGVTAYTVNPGITRTTLVHKFNSWLDVEPQVAEKLLAHPTQPSLACAENFVKAIELNQNGAIWKLDLGTLEAIQWTKHWDSGI 256
               SCOP domains d1mg5a_ A: Drosophila alcohol dehydrogenase                                                                                                                                                                                                                     SCOP domains
               CATH domains 1mg5A00 A:1-255 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee...hhhhhhhhhhhh.....eeeeee...hhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeee..ee........hhhhh..hhhhhhhh...eehhhhhhhhhhhhhhh....eeeee..eeee........... Sec.struct. author
             SAPs(SNPs) (1) -------V------------------------------------D-----E------------------S-------------------------------------------------------------------------------------------------------------------------T---------------------S----------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------------------------------------V------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs) (2)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: A:139-167    ---------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mg5 A   1 SFTLTNKNVIFVAGLGGIGLDTSKELLKRDLKNLVILDRIENPAAIAELKAINPKVTVTFYPYDVTVPIAETTKLLKTIFAQLKTVDVLINGAGILDDHQIERTIAVNYTGLVNTTTAILDFWDKRKGGPGGIICNIGSVTGFNAIYQVPVYSGTKAAVVNFTSSLAKLAPITGVTAYTVNPGITRTTLVHKFNSWLDVEPQVAEKLLAHPTQPSLACAENFVKAIELNQNGAIWKLDLGTLEAIQWTKHWDSGI 255
                                    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

Chain B from PDB  Type:PROTEIN  Length:255
 aligned with ADH_DROME | P00334 from UniProtKB/Swiss-Prot  Length:256

    Alignment length:255
                                    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     
            ADH_DROME     2 SFTLTNKNVIFVAGLGGIGLDTSKELLKRDLKNLVILDRIENPAAIAELKAINPKVTVTFYPYDVTVPIAETTKLLKTIFAQLKTVDVLINGAGILDDHQIERTIAVNYTGLVNTTTAILDFWDKRKGGPGGIICNIGSVTGFNAIYQVPVYSGTKAAVVNFTSSLAKLAPITGVTAYTVNPGITRTTLVHKFNSWLDVEPQVAEKLLAHPTQPSLACAENFVKAIELNQNGAIWKLDLGTLEAIQWTKHWDSGI 256
               SCOP domains d1mg5b_ B: Drosophila alcohol dehydrogenase                                                                                                                                                                                                                     SCOP domains
               CATH domains 1mg5B00 B:1-255 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                             CATH domains
           Pfam domains (1) ------adh_short-1mg5B01 B:7-170                                                                                                                                           ------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------adh_short-1mg5B02 B:7-170                                                                                                                                           ------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .......eeeee...hhhhhhhhhhhh.....eeeeee...hhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeee..eehhhhhh..hhhhh..hhhhhhhh...eehhhhhhhhhhhhhhh....eeeee..eeee........... Sec.struct. author
             SAPs(SNPs) (1) -------V------------------------------------D-----E------------------S-------------------------------------------------------------------------------------------------------------------------T---------------------S----------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------------------------------------V------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs) (2)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: B:139-167    ---------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mg5 B   1 SFTLTNKNVIFVAGLGGIGLDTSKELLKRDLKNLVILDRIENPAAIAELKAINPKVTVTFYPYDVTVPIAETTKLLKTIFAQLKTVDVLINGAGILDDHQIERTIAVNYTGLVNTTTAILDFWDKRKGGPGGIICNIGSVTGFNAIYQVPVYSGTKAAVVNFTSSLAKLAPITGVTAYTVNPGITRTTLVHKFNSWLDVEPQVAEKLLAHPTQPSLACAENFVKAIELNQNGAIWKLDLGTLEAIQWTKHWDSGI 255
                                    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

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: Drosophila alcohol dehydrogenase (9)

Fruit fly (Drosophila melanogaster) [TaxId: 7227] (1)

1a	d1mg5a_	A:
1b	d1mg5b_	B:

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)

Fruit fly (Drosophila melanogaster) (1)

1a	1mg5A00	A:1-255
1b	1mg5B00	B:1-255

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: adh_short (92)

Drosophila melanogaster (Fruit fly) (2)

1a	adh_short-1mg5B01	B:7-170
1b	adh_short-1mg5B02	B:7-170

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (ADH_DROME | P00334)

molecular function
	GO:0008774	acetaldehyde dehydrogenase (acetylating) activity	Catalysis of the reaction: acetaldehyde + CoA + NAD+ = acetyl-CoA + NADH + H+.
	GO:0004022	alcohol dehydrogenase (NAD) activity	Catalysis of the reaction: an alcohol + NAD+ = an aldehyde or ketone + NADH + 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.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
	GO:0006117	acetaldehyde metabolic process	The chemical reactions and pathways involving acetaldehyde, a colorless, flammable liquid intermediate in the metabolism of alcohol.
	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:0048149	behavioral response to ethanol	Any process that results in a change in the behavior of an organism as a result of an ethanol stimulus.
	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:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	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.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005811	lipid droplet	An intracellular non-membrane-bounded organelle comprising a matrix of coalesced lipids surrounded by a phospholipid monolayer. May include associated proteins.
	GO:0005875	microtubule associated complex	Any multimeric complex connected to a microtubule.
	GO:0043234	protein complex	A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

Asymmetric/Biological Unit
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1a4u	DROSOPHILA LEBANONENSIS ALCOHOL DEHYDROGENASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (7, 14)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

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