1TA9 - JenaLib

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Title :   CRYSTAL STRUCTURE OF GLYCEROL DEHYDROGENASE FROM SCHIZOSACCHAROMYCES POMBE

Authors :   A. M. Mulichak

Date :   19 May 04 (Deposition) - 16 Aug 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (4x)

Keywords :   Glycerol Dehydrogenase, Schizosaccharomyces Pombe, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. M. Mulichak
Crystal Structure Of Glycerol Dehydrogenase From Schyzosaccharomyces Pombe
To Be Published
PubMed: search

Molecule 1 - GLYCEROL DEHYDROGENASE
	Chains	:	A, B
	EC Number	:	1.1.1.6
	Organism Common	:	FISSION YEAST
	Organism Scientific	:	SCHIZOSACCHAROMYCES POMBE
	Organism Taxid	:	4896

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (4x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 9)

No.	Name	Count	Type	Full Name
1	ALA	2	Mod. Amino Acid	ALANINE
2	GOL	3	Ligand/Ion	GLYCEROL
3	K	2	Ligand/Ion	POTASSIUM ION
4	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 20)

No.	Name	Count	Type	Full Name
1	ALA	8	Mod. Amino Acid	ALANINE
2	GOL	12	Ligand/Ion	GLYCEROL
3	K	-1	Ligand/Ion	POTASSIUM ION
4	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP B:232 , HIS B:315 , HIS B:333 , GOL B:1402	BINDING SITE FOR RESIDUE ZN B 1501
2	AC2	SOFTWARE	ASP A:232 , HIS A:315 , HIS A:333 , GOL A:1401	BINDING SITE FOR RESIDUE ZN A 1502
3	AC3	SOFTWARE	ASP A:182 , ASP A:232 , SER A:235 , THR A:236 , SER A:302 , HIS A:315 , GOL A:1401 , HOH A:1540	BINDING SITE FOR RESIDUE K A 1503
4	AC4	SOFTWARE	ASP B:182 , ASP B:232 , SER B:235 , THR B:236 , HIS B:315 , GOL B:1402 , HOH B:1526	BINDING SITE FOR RESIDUE K B 1504
5	AC5	SOFTWARE	ALA A:130 , VAL A:190 , ILE A:191 , TYR A:192 , ALA A:1505 , HOH A:1623	BINDING SITE FOR RESIDUE ALA A 1504
6	AC6	SOFTWARE	ALA A:130 , ALA A:1504 , HOH A:1740	BINDING SITE FOR RESIDUE ALA A 1505
7	AC7	SOFTWARE	ASP A:182 , ASP A:232 , HIS A:315 , HIS A:333 , ZN A:1502 , K A:1503 , HOH A:1814 , HOH A:1871	BINDING SITE FOR RESIDUE GOL A 1401
8	AC8	SOFTWARE	ASP B:182 , ASP B:232 , HIS B:315 , HIS B:333 , ZN B:1501 , K B:1504 , HOH B:1749	BINDING SITE FOR RESIDUE GOL B 1402
9	AC9	SOFTWARE	LYS A:162 , ALA A:165 , LEU A:170 , SER A:172 , SER A:187 , TYR A:204 , LEU A:206 , ASN A:207 , PRO A:208 , HOH A:1530 , HOH A:1611 , HOH A:1881	BINDING SITE FOR RESIDUE GOL A 1403

(no "SS Bond" information available for 1TA9)

(no "Cis Peptide Bond" information available for 1TA9)

(no "SAP(SNP)/Variant" information available for 1TA9)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_IRON_1	PS00913	Iron-containing alcohol dehydrogenases signature 1.	GLD1_SCHPO	211-239	2	A:211-239 B:211-239

Biological Unit 1 (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_IRON_1	PS00913	Iron-containing alcohol dehydrogenases signature 1.	GLD1_SCHPO	211-239	8	A:211-239 B:211-239

(no "Exon" information available for 1TA9)

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:389
 aligned with GLD1_SCHPO | O13702 from UniProtKB/Swiss-Prot  Length:450

    Alignment length:393
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447   
           GLD1_SCHPO    58 FEESKDRIFTSPQKYVQGRHAFTRSYMYVKKWATKSAVVLADQNVWNICANKIVDSLSQNGMTVTKLVFGGEASLVELDKLRKQCPDDTQVIIGVGGGKTMDSAKYIAHSMNLPSIICPTTASSDAATSSLSVIYTPDGQFQKYSFYPLNPNLIFIDTDVIVRAPVRFLISGIGDALSTWVETESVIRSNSTSFAGGVASIAGRYIARACKDTLEKYALSAILSNTRGVCTEAFENVVEANTLMSGLGFENGGLAAAHAIHNGMTAIHGPVHRLMHGEKVAYGTLVQVVLEDWPLEDFNNLASFMAKCHLPITLEELGIPNVTDEELLMVGRATLRPDESIHNMSKKFNPSQIADAIKAVDSYSQKWQEQTGWTERFRLPPSRHSPHLTDIHP 450
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -----------1ta9A01 A:69-220  [code=3.40.50.1970, no name defined]                                                                                                  1ta9A02 A:221-450 Dehydroquinate synthase-like - alpha domain                                                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee...eeeee.hhhhhhhhhhh.....eeeeeeehhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhh.......eeeeeehhhhhhhhhhhhhhh...eeeee...........eeee.----...eeee......eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhh....hhhhhhhhhhhhh...hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh..................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------ADH_IRON_1  PDB: A:211-239   ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ta9 A  58 FEESKDRIFTSPQKYVQGRHAFTRSYMYVKKWATKSAVVLADQNVWNICANKIVDSLSQNGMTVTKLVFGGEASLVELDKLRKQCPDDTQVIIGVGGGKTMDSAKYIAHSMNLPSIICPTTASSDAATSSLSVIY----QFQKYSFYPLNPNLIFIDTDVIVRAPVRFLISGIGDALSTWVETESVIRSNSTSFAGGVASIAGRYIARACKDTLEKYALSAILSNTRGVCTEAFENVVEANTLMSGLGFENGGLAAAHAIHNGMTAIHGPVHRLMHGEKVAYGTLVQVVLEDWPLEDFNNLASFMAKCHLPITLEELGIPNVTDEELLMVGRATLRPDESIHNMSKKFNPSQIADAIKAVDSYSQKWQEQTGWTERFRLPPSRHSPHLTDIHP 450
                                    67        77        87        97       107       117       127       137       147       157       167       177       187    |  197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447   
                                                                                                                                                                192  197

Chain B from PDB  Type:PROTEIN  Length:394
 aligned with GLD1_SCHPO | O13702 from UniProtKB/Swiss-Prot  Length:450

    Alignment length:394
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446    
           GLD1_SCHPO    57 EFEESKDRIFTSPQKYVQGRHAFTRSYMYVKKWATKSAVVLADQNVWNICANKIVDSLSQNGMTVTKLVFGGEASLVELDKLRKQCPDDTQVIIGVGGGKTMDSAKYIAHSMNLPSIICPTTASSDAATSSLSVIYTPDGQFQKYSFYPLNPNLIFIDTDVIVRAPVRFLISGIGDALSTWVETESVIRSNSTSFAGGVASIAGRYIARACKDTLEKYALSAILSNTRGVCTEAFENVVEANTLMSGLGFENGGLAAAHAIHNGMTAIHGPVHRLMHGEKVAYGTLVQVVLEDWPLEDFNNLASFMAKCHLPITLEELGIPNVTDEELLMVGRATLRPDESIHNMSKKFNPSQIADAIKAVDSYSQKWQEQTGWTERFRLPPSRHSPHLTDIHP 450
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------1ta9B01 B:69-220  [code=3.40.50.1970, no name defined]                                                                                                  1ta9B02 B:221-450 Dehydroquinate synthase-like - alpha domain                                                                                                                                                                          CATH domains
           Pfam domains (1) ------------Fe-ADH-1ta9B01 B:69-410                                                                                                                                                                                                                                                                                                                               ---------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------Fe-ADH-1ta9B02 B:69-410                                                                                                                                                                                                                                                                                                                               ---------------------------------------- Pfam domains (2)
         Sec.struct. author .......eeee...eeeee.hhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhh.......eeeeeehhhhhhhhhhhhhhh...eeeee...........eeeee.....eeeeee......eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhh....hhhhhhhhhhhhh...hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh..................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------ADH_IRON_1  PDB: B:211-239   ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ta9 B  57 EFEESKDRIFTSPQKYVQGRHAFTRSYMYVKKWATKSAVVLADQNVWNICANKIVDSLSQNGMTVTKLVFGGEASLVELDKLRKQCPDDTQVIIGVGGGKTMDSAKYIAHSMNLPSIICPTTASSDAATSSLSVIYTPDGQFQKYSFYPLNPNLIFIDTDVIVRAPVRFLISGIGDALSTWVETESVIRSNSTSFAGGVASIAGRYIARACKDTLEKYALSAILSNTRGVCTEAFENVVEANTLMSGLGFENGGLAAAHAIHNGMTAIHGPVHRLMHGEKVAYGTLVQVVLEDWPLEDFNNLASFMAKCHLPITLEELGIPNVTDEELLMVGRATLRPDESIHNMSKKFNPSQIADAIKAVDSYSQKWQEQTGWTERFRLPPSRHSPHLTDIHP 450
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446

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 '\|'

(no "SCOP Domain" information available for 1TA9)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1970, no name defined] (28)

Fission yeast (Schizosaccharomyces pombe) (1)

1a	1ta9B01	B:69-220
1b	1ta9A01	A:69-220

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Dehydroquinate synthase-like, alpha domain (24)

Homologous Superfamily: Dehydroquinate synthase-like - alpha domain (24)

Fission yeast (Schizosaccharomyces pombe) (1)

2a	1ta9A02	A:221-450
2b	1ta9B02	B:221-450

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: DHQS (27)

Family: Fe-ADH (12)

Schizosaccharomyces pombe (strain ATCC 38366 / 972) (Fission yeast) (1)

1a	Fe-ADH-1ta9B01	B:69-410
1b	Fe-ADH-1ta9B02	B:69-410

Asymmetric Unit(hide GO term definitions)

Chain A,B (GLD1_SCHPO | O13702)

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.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0019564	aerobic glycerol catabolic process	The chemical reactions and pathways resulting in the breakdown of glycerol, 1,2,3-propanetriol, in the presence of oxygen.
	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.
cellular component
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

Asymmetric Unit
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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