1JEH - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF YEAST E3, LIPOAMIDE DEHYDROGENASE

Authors :   T. Toyoda, K. Suzuki, T. Sekigushi, J. Reed, A. Takenaka

Date :   18 Jun 01 (Deposition) - 11 Jul 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   2-Oxoglutarate Dehydrogenase Complex, Pyruvate Dehydrogenase Complex, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Toyoda, K. Suzuki, T. Sekiguchi, L. J. Reed, A. Takenaka
Crystal Structure Of Eucaryotic E3, Lipoamide Dehydrogenase From Yeast.
J. Biochem. (Tokyo) V. 123 668 1998
PubMed-ID: 9538259
(for further references see the PDB file header)

Molecule 1 - DIHYDROLIPOAMIDE DEHYDROGENASE
	Chains	:	A, B
	EC Number	:	1.8.1.4
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:11 , GLY A:12 , GLY A:14 , PRO A:15 , ALA A:16 , VAL A:34 , GLU A:35 , LYS A:36 , ARG A:37 , GLY A:42 , THR A:43 , CYS A:44 , VAL A:47 , GLY A:48 , CYS A:49 , SER A:52 , LYS A:53 , GLY A:118 , ALA A:152 , THR A:153 , GLY A:154 , SER A:173 , ILE A:194 , ARG A:285 , TYR A:288 , GLY A:291 , LEU A:292 , GLY A:324 , ASP A:325 , MET A:331 , LEU A:332 , ALA A:333 , HIS A:334 , TYR A:364 , HIS B:457 , PRO B:458	BINDING SITE FOR RESIDUE FAD A 480
2	AC2	SOFTWARE	HIS A:457 , PRO A:458 , ILE B:11 , GLY B:12 , GLY B:14 , PRO B:15 , ALA B:16 , GLU B:35 , LYS B:36 , ARG B:37 , GLY B:42 , THR B:43 , CYS B:44 , GLY B:48 , CYS B:49 , SER B:52 , LYS B:53 , ASN B:117 , GLY B:118 , ALA B:152 , THR B:153 , GLY B:154 , SER B:155 , SER B:173 , ARG B:285 , TYR B:288 , ALA B:290 , GLY B:291 , LEU B:292 , GLY B:324 , ASP B:325 , MET B:331 , LEU B:332 , ALA B:333 , HIS B:334 , TYR B:364 , HOH B:611	BINDING SITE FOR RESIDUE FAD B 580

Asymmetric/Biological Unit

No.	Residues
1	A:44	-	A:49
2	B:44	-	B:49

Asymmetric/Biological Unit

No.	Residues
1	His A:366	-	Pro A:367
2	His A:457	-	Pro A:458
3	His B:366	-	Pro B:367
4	His B:457	-	Pro B:458

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PYRIDINE_REDOX_1	PS00076	Pyridine nucleotide-disulphide oxidoreductases class-I active site.	DLDH_YEAST	62-72	2	A:41-51 B:41-51

Asymmetric/Biological Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YFL018C	1	YFL018C.1	VI:103121-101622	1500	DLDH_YEAST	1-499	499	2	A:1-478 B:1-478	478 478

Asymmetric/Biological Unit

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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
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Chain A from PDB  Type:PROTEIN  Length:478
 aligned with DLDH_YEAST | P09624 from UniProtKB/Swiss-Prot  Length:499

    Alignment length:478
                                    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       381       391       401       411       421       431       441       451       461       471       481       491        
           DLDH_YEAST    22 TINKSHDVVIIGGGPAGYVAAIKAAQLGFNTACVEKRGKLGGTCLNVGCIPSKALLNNSHLFHQMHTEAQKRGIDVNGDIKINVANFQKAKDDAVKQLTGGIELLFKKNKVTYYKGNGSFEDETKIRVTPVDGLEGTVKEDHILDVKNIIVATGSEVTPFPGIEIDEEKIVSSTGALSLKEIPKRLTIIGGGIIGLEMGSVYSRLGSKVTVVEFQPQIGASMDGEVAKATQKFLKKQGLDFKLSTKVISAKRNDDKNVVEIVVEDTKTNKQENLEAEVLLVAVGRRPYIAGLGAEKIGLEVDKRGRLVIDDQFNSKFPHIKVVGDVTFGPMLAHKAEEEGIAAVEMLKTGHGHVNYNNIPSVMYSHPEVAWVGKTEEQLKEAGIDYKIGKFPFAANSRAKTNQDTEGFVKILIDSKTERILGAHIIGPNAGEMIAEAGLALEYGASAEDVARVCHAHPTLSEAFKEANMAAYDKAIHC 499
               SCOP domains d1jeha1 A:1-160,A:283-355 Dihydrolipoamide dehydrogenase                                                                                                        d1jeha2 A:161-282 Dihydrolipoamide dehydrogenase                                                                          d1jeha1 A:1-160,A:283-355 Dihydrolipoamide dehydrogenase                 d1jeha3 A:356-478 Dihydrolipoamide dehydrogenase                                                                            SCOP domains
               CATH domains --1jehA01 A:3-157,A:284-357  [code=3.50.50.60, no name defined]                                                                                              1jehA02 A:158-283  [code=3.50.50.60, no name defined]                                                                         1jehA01 A:3-157,A:284-357  [code=3.50.50.60, no name defined]             1jehA03 A:358-478  [code=3.30.390.30, no name defined]                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee....hhhhhhhhhhhh...eeee......hhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee.eeeee....eeeeee...........eeeeeeeeee...eee............eehhhhhh.......eeeee..hhhhhhhhhhhhhhh.eeeeee.........hhhhhhhhhhhhhhh..eeee.eeeeeeee......eeeeeee.....eeeeee.eeee...eee.....hhhhhh.....................eee.........hhhhhhhhhhhhhhhhhh.....hhhhh.eee....eeeeee.hhhhhhhhh..eeeeeee...hhhhhhh.....eeeeeee.....eeeeeeee.hhhhhhhhhhhhhhh..hhhhhhh........hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------PYRIDINE_RE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-478 UniProt: 1-499 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                             Transcript 1
                 1jeh A   1 TINKSHDVVIIGGGPAGYVAAIKAAQLGFNTACVEKRGKLGGTCLNVGCIPSKALLNNSHLFHQMHTEAQKRGIDVNGDIKINVANFQKAKDDAVKQLTGGIELLFKKNKVTYYKGNGSFEDETKIRVTPVDGLEGTVKEDHILDVKNIIVATGSEVTPFPGIEIDEEKIVSSTGALSLKEIPKRLTIIGGGIIGLEMGSVYSRLGSKVTVVEFQPQIGASMDGEVAKATQKFLKKQGLDFKLSTKVISAKRNDDKNVVEIVVEDTKTNKQENLEAEVLLVAVGRRPYIAGLGAEKIGLEVDKRGRLVIDDQFNSKFPHIKVVGDVTFGPMLAHKAEEEGIAAVEMLKTGHGHVNYNNIPSVMYSHPEVAWVGKTEEQLKEAGIDYKIGKFPFAANSRAKTNQDTEGFVKILIDSKTERILGAHIIGPNAGEMIAEAGLALEYGASAEDVARVCHAHPTLSEAFKEANMAAYDKAIHC 478
                                    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       460       470

Chain B from PDB  Type:PROTEIN  Length:478
 aligned with DLDH_YEAST | P09624 from UniProtKB/Swiss-Prot  Length:499

    Alignment length:478
                                    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       381       391       401       411       421       431       441       451       461       471       481       491        
           DLDH_YEAST    22 TINKSHDVVIIGGGPAGYVAAIKAAQLGFNTACVEKRGKLGGTCLNVGCIPSKALLNNSHLFHQMHTEAQKRGIDVNGDIKINVANFQKAKDDAVKQLTGGIELLFKKNKVTYYKGNGSFEDETKIRVTPVDGLEGTVKEDHILDVKNIIVATGSEVTPFPGIEIDEEKIVSSTGALSLKEIPKRLTIIGGGIIGLEMGSVYSRLGSKVTVVEFQPQIGASMDGEVAKATQKFLKKQGLDFKLSTKVISAKRNDDKNVVEIVVEDTKTNKQENLEAEVLLVAVGRRPYIAGLGAEKIGLEVDKRGRLVIDDQFNSKFPHIKVVGDVTFGPMLAHKAEEEGIAAVEMLKTGHGHVNYNNIPSVMYSHPEVAWVGKTEEQLKEAGIDYKIGKFPFAANSRAKTNQDTEGFVKILIDSKTERILGAHIIGPNAGEMIAEAGLALEYGASAEDVARVCHAHPTLSEAFKEANMAAYDKAIHC 499
               SCOP domains d1jehb1 B:1-160,B:283-355 Dihydrolipoamide dehydrogenase                                                                                                        d1jehb2 B:161-282 Dihydrolipoamide dehydrogenase                                                                          d1jehb1 B:1-160,B:283-355 Dihydrolipoamide dehydrogenase                 d1jehb3 B:356-478 Dihydrolipoamide dehydrogenase                                                                            SCOP domains
               CATH domains --1jehB01 B:3-157,B:284-357  [code=3.50.50.60, no name defined]                                                                                              1jehB02 B:158-283  [code=3.50.50.60, no name defined]                                                                         1jehB01 B:3-157,B:284-357  [code=3.50.50.60, no name defined]             1jehB03 B:358-478  [code=3.30.390.30, no name defined]                                                                    CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Pyr_redox-1jehB01 B:185-270                                                           ----------------------------------------------------------------------------------------Pyr_redox_dim-1jehB05 B:359-468                                                                               ---------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Pyr_redox-1jehB02 B:185-270                                                           ----------------------------------------------------------------------------------------Pyr_redox_dim-1jehB06 B:359-468                                                                               ---------- Pfam domains (2)
           Pfam domains (3) ------Pyr_redox_2-1jehB03 B:7-331                                                                                                                                                                                                                                                                                                          --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) ------Pyr_redox_2-1jehB04 B:7-331                                                                                                                                                                                                                                                                                                          --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author ....eeeeeee..hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.eeeeee..eeeee............eeeeeeeeee...eee..............hhhhhhh......eeeee..hhhhhhhhhhhhhhh.eeeeee.........hhhhhhhhhhhhhhh.eeeee.eeeeeeeee....eeeeeeee.....eeeeee.eeee...eee................................eee.hhhh....hhhhhhhhhhhhhhhhhhh..........eee....eeeeee.hhhhhhhh...eeeeeee...hhhhhhh.....eeeeeee.....eeeeeeee.hhhhhhhhhhhhhhhh.hhhhhhh........hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------PYRIDINE_RE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:1-478 UniProt: 1-499 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                             Transcript 1
                 1jeh B   1 TINKSHDVVIIGGGPAGYVAAIKAAQLGFNTACVEKRGKLGGTCLNVGCIPSKALLNNSHLFHQMHTEAQKRGIDVNGDIKINVANFQKAKDDAVKQLTGGIELLFKKNKVTYYKGNGSFEDETKIRVTPVDGLEGTVKEDHILDVKNIIVATGSEVTPFPGIEIDEEKIVSSTGALSLKEIPKRLTIIGGGIIGLEMGSVYSRLGSKVTVVEFQPQIGASMDGEVAKATQKFLKKQGLDFKLSTKVISAKRNDDKNVVEIVVEDTKTNKQENLEAEVLLVAVGRRPYIAGLGAEKIGLEVDKRGRLVIDDQFNSKFPHIKVVGDVTFGPMLAHKAEEEGIAAVEMLKTGHGHVNYNNIPSVMYSHPEVAWVGKTEEQLKEAGIDYKIGKFPFAANSRAKTNQDTEGFVKILIDSKTERILGAHIIGPNAGEMIAEAGLALEYGASAEDVARVCHAHPTLSEAFKEANMAAYDKAIHC 478
                                    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       460       470

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Enolase-like; domain 1 (252)

Homologous Superfamily: [code=3.30.390.30, no name defined] (99)

Baker's yeast (Saccharomyces cerevisiae) (3)

1a	1jehA03	A:358-478
1b	1jehB03	B:358-478

Architecture: 3-Layer(bba) Sandwich (528)

Topology: FAD/NAD(P)-binding domain (373)

Homologous Superfamily: [code=3.50.50.60, no name defined] (373)

Baker's yeast (Saccharomyces cerevisiae) (22)

2a	1jehA01	A:3-157,A:284-357
2b	1jehB01	B:3-157,B:284-357
2c	1jehA02	A:158-283
2d	1jehB02	B:158-283

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (DLDH_YEAST | P09624)

molecular function
	GO:0004148	dihydrolipoyl dehydrogenase activity	Catalysis of the reaction: protein N6-(dihydrolipoyl)lysine + NAD+ = protein N6-(lipoyl)lysine + NADH + H+.
	GO:0050660	flavin adenine dinucleotide binding	Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
	GO:0004375	glycine dehydrogenase (decarboxylating) activity	Catalysis of the reaction: glycine + lipoylprotein = S-aminomethyldihydrolipoylprotein + CO2.
	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:0016668	oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a sulfur-containing group acts as a hydrogen or electron donor and reduces NAD or NADP.
	GO:0004591	oxoglutarate dehydrogenase (succinyl-transferring) activity	Catalysis of the reaction: 2-oxoglutarate + lipoamide = S-succinyldihydrolipoamide + CO2.
	GO:0004738	pyruvate dehydrogenase activity	Catalysis of the oxidative decarboxylation of pyruvate.
biological process
	GO:0006103	2-oxoglutarate metabolic process	The chemical reactions and pathways involving oxoglutarate, the dianion of 2-oxoglutaric acid. It is a key constituent of the TCA cycle and a key intermediate in amino-acid metabolism.
	GO:0006564	L-serine biosynthetic process	The chemical reactions and pathways resulting in the formation of L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid.
	GO:0045454	cell redox homeostasis	Any process that maintains the redox environment of a cell or compartment within a cell.
	GO:0006546	glycine catabolic process	The chemical reactions and pathways resulting in the breakdown of glycine, aminoethanoic acid.
	GO:0042743	hydrogen peroxide metabolic process	The chemical reactions and pathways involving hydrogen peroxide (H2O2), a potentially harmful byproduct of aerobic cellular respiration which can cause damage to DNA.
	GO:0006550	isoleucine catabolic process	The chemical reactions and pathways resulting in the breakdown of isoleucine, (2R,3R)-2-amino-3-methylpentanoic acid.
	GO:0006552	leucine catabolic process	The chemical reactions and pathways resulting in the breakdown of leucine, 2-amino-4-methylpentanoic acid.
	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:0006090	pyruvate metabolic process	The chemical reactions and pathways involving pyruvate, 2-oxopropanoate.
	GO:0006574	valine catabolic process	The chemical reactions and pathways resulting in the breakdown of valine, 2-amino-3-methylbutanoic acid.
cellular component
	GO:0005960	glycine cleavage complex	A protein complex that catalyzes the reversible oxidation of glycine. In E. coli, it has four components: dihydrolipoamide dehydrogenase, glycine dehydrogenase (decarboxylating), lipoyl-GcvH-protein and aminomethyltransferase, also known as L, P, H, and T.
	GO:0005759	mitochondrial matrix	The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
	GO:0042645	mitochondrial nucleoid	The region of a mitochondrion to which the DNA is confined.
	GO:0009353	mitochondrial oxoglutarate dehydrogenase complex	A complex of multiple copies of three enzymatic components: oxoglutarate dehydrogenase (lipoamide) ; EC:1.2.4.2 (E1), dihydrolipoamide S-succinyltransferase ; EC:2.3.1.61 (E2) and dihydrolipoamide dehydrogenase ; EC:1.8.1.4 (E3); catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and carbon dioxide (CO2) within the mitochondrial matrix. An example of this complex is found in Mus musculus.
	GO:0005967	mitochondrial pyruvate dehydrogenase complex	Complex that carries out the oxidative decarboxylation of pyruvate to form acetyl-CoA in eukaryotes; includes subunits possessing three catalytic activities: pyruvate dehydrogenase (E1), dihydrolipoamide S-acetyltransferase (E2), and dihydrolipoamide dehydrogenase (E3). The This Eukaryotic form usually contains more subunits than its bacterial counterpart; for example, one known complex contains 30 E1 dimers, 60 E2 monomers, and 6 E3 dimers as well as a few copies of pyruvate dehydrogenase kinase and pyruvate dehydrogenase phosphatase.
	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/Biological Unit
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		His A:457 - Pro A:458	[ RasMol ]
		His B:366 - Pro B:367	[ RasMol ]
		His B:457 - Pro B:458	[ RasMol ]

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	1jeh
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(no "Related Entries Specified in the PDB File" available for 1JEH)

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