1JQ5 - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   BACILLUS STEAROTHERMOPHILUS GLYCEROL DEHYDROGENASE COMPLEX WITH NAD+

Authors :   S. N. Ruzheinikov, J. Burke, S. Sedelnikova, P. J. Baker, R. Taylor, P. A. Bullough, N. M. Muir, M. G. Gore, D. W. Rice

Date :   03 Aug 01 (Deposition) - 01 Oct 01 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym. Unit : A
Biol. Unit 1: A  (8x)

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

Reference :   S. N. Ruzheinikov, J. Burke, S. Sedelnikova, P. J. Baker, R. Taylor, P. A. Bullough, N. M. Muir, M. G. Gore, D. W. Rice
Glycerol Dehydrogenase. Structure, Specificity, And Mechanism Of A Family Iii Polyol Dehydrogenase.
Structure V. 9 789 2001
PubMed-ID: 11566129 | Reference-DOI: 10.1016/S0969-2126(01)00645-1
(for further references see the PDB file header)

Molecule 1 - GLYCEROL DEHYDROGENASE
	Chains	:	A
	EC Number	:	1.1.1.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PKK233-2
	Expression System Strain	:	JM103
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	GLDA OR GLD
	Mutation	:	YES
	Organism Scientific	:	GEOBACILLUS STEAROTHERMOPHILUS
	Organism Taxid	:	1422

		1
Asymmetric Unit	:	A
Biological Unit 1 (8x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

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

Biological Unit 1 (1, 8)

No.	Name	Count	Type	Full Name
1	NAD	8	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:173 , HIS A:256 , HIS A:274 , HOH A:402	BINDING SITE FOR RESIDUE ZN A 371
2	AC2	SOFTWARE	GLU A:268 , HIS A:271	BINDING SITE FOR RESIDUE ZN A 372
3	AC3	SOFTWARE	ASP A:39 , ILE A:45 , GLY A:95 , GLY A:96 , LYS A:97 , ASP A:100 , THR A:118 , SER A:121 , THR A:122 , ASP A:123 , ALA A:124 , SER A:127 , LEU A:129 , VAL A:131 , TYR A:133 , ALA A:162 , PRO A:163 , LEU A:166 , PHE A:247 , HIS A:274 , HOH A:405 , HOH A:406 , HOH A:408 , HOH A:410 , HOH A:411 , HOH A:412 , HOH A:413 , HOH A:414	BINDING SITE FOR RESIDUE NAD A 401

(no "SS Bond" information available for 1JQ5)

(no "Cis Peptide Bond" information available for 1JQ5)

(no "SAP(SNP)/Variant" information available for 1JQ5)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_IRON_1	PS00913	Iron-containing alcohol dehydrogenases signature 1.	GLDA_GEOSE	152-180	1	A:152-180
2	ADH_IRON_2	PS00060	Iron-containing alcohol dehydrogenases signature 2.	GLDA_GEOSE	243-263	1	A:243-263

Biological Unit 1 (2, 16)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_IRON_1	PS00913	Iron-containing alcohol dehydrogenases signature 1.	GLDA_GEOSE	152-180	8	A:152-180
2	ADH_IRON_2	PS00060	Iron-containing alcohol dehydrogenases signature 2.	GLDA_GEOSE	243-263	8	A:243-263

(no "Exon" information available for 1JQ5)

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:366
 aligned with GLDA_GEOSE | P32816 from UniProtKB/Swiss-Prot  Length:370

    Alignment length:366
                                    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      
           GLDA_GEOSE     2 AAERVFISPAKYVQGKNVITKIANYLEGIGNKTVVIADEIVWKIAGHTIVNELKKGNIAAEEVVFSGEASRNEVERIANIARKAEAAIVIGVGGGKTLDTAKAVADELDAYIVIVPTAASTDAPTSALSVIYSDDGVFESYRFYKKNPDLVLVDTKIIANAPPRLLASGIADALATWVEARSVIKSGGKTMAGGIPTIAAEAIAEKCEQTLFKYGKLAYESVKAKVVTPALEAVVEANTLLSGLGFESGGLAAAHAIHNGFTALEGEIHHLTHGEKVAFGTLVQLALEEHSQQEIERYIELYLSLDLPVTLEDIKLKDASREDILKVAKAATAEGETIHNAFNVTADDVADAIFAADQYAKAYKEK 367
               SCOP domains d1jq5a_ A: Glycerol dehydrogenase                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --------1jq5A01 A:10-161  [code=3.40.50.1970, no name defined]                                                                                                  1jq5A02 A:162-367 Dehydroquinate synthase-like - alpha domain                                                                                                                                                  CATH domains
               Pfam domains --------Fe-ADH-1jq5A01 A:10-350                                                                                                                                                                                                                                                                                                                              ----------------- Pfam domains
         Sec.struct. author ..........eeeee.hhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhh.eeeeee...........eeeee.....eeeeee......eeeeehhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..............hhhhhhhhhhhhh...hhhhhh...hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ADH_IRON_1  PDB: A:152-180   --------------------------------------------------------------ADH_IRON_2           -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jq5 A   2 AAERVFISPAKYVQGKNVITKIANYLEGIGNKTVVIADEIVWKIAGHTIVNELKKGNIAAEEVVFSGEASRNEVERIANIARKAEAAIVIGVGGGKTLDTAKAVADELDAYIVIVPTAASTDAPTSALSVIYSDDGVFESYRFYKKNPDLVLVDTKIIANAPPRLLASGIADALATWVEARSVIKSGGKTMAGGIPTIAAEAIAEKCEQTLFKYGKLAYESVKAKVVTPALEAVVEANTLLSGLGFESGGLAAAHAIHNGFTALEGEIHHLTHGEKVAFGTLVQLALEEHSQQEIERYIELYLCLDLPVTLEDIKLKDASREDILKVAKAATAEGETIHNAFNVTADDVADAIFAADQYAKAYKEK 367
                                    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

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(

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Folds(

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Superfamilies( (-)

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Families(

)

Protein Domains( (-)

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Organisms( (-)

)

Class: Multi-domain proteins (alpha and beta) (2421)

Fold: Dehydroquinate synthase-like (30)

Superfamily: Dehydroquinate synthase-like (30)

Family: Iron-containing alcohol dehydrogenase (11)

Protein domain: Glycerol dehydrogenase (4)

Bacillus stearothermophilus [TaxId: 1422] (3)

d1jq5a_

Asymmetric Unit

Clans(

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Families(

)

Organisms( (-)

)

Clan: DHQS (27)

Family: Fe-ADH (12)

Geobacillus stearothermophilus (Bacillus stearothermophilus) (3)

Fe-ADH-1jq5A01

A:10-350

Asymmetric Unit(hide GO term definitions)

Chain A (GLDA_GEOSE | P32816)

molecular function
	GO:0008888	glycerol dehydrogenase [NAD+] activity	Catalysis of the reaction: glycerol + NAD(+) = glycerone + H(+) + NADH.
	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.
biological process
	GO:0019588	anaerobic glycerol catabolic process	The anaerobic chemical reactions and pathways resulting in the breakdown of glycerol, yielding energy in the form of ATP.
	GO:0006071	glycerol metabolic process	The chemical reactions and pathways involving glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.
	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 Unit
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Biological Unit
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		Biological Unit 1	[ Jena3D ]

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	1jq5
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	1.1.1.6
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UniProtKB/Swiss-Prot
	GLDA_GEOSE \| P32816	:	1jpu 1jqa

1jpu	1JPU CONTAINS THE SAME PROTEIN NATIVE FORM.
1jqa	THE SAME PROTEIN IN COMPLEX WITH GLYCEROL.

Description

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Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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