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(-) Description

Title :  SNAPSHOTS OF CATALYSIS IN THE E1 SUBUNIT OF THE PYRUVATE DEHYDROGENASE MULTI-ENZYME COMPLEX
 
Authors :  X. Y. Pei, C. M. Titman, R. A. W. Frank, F. J. Leeper, B. F. Luisi
Date :  17 Jul 08  (Deposition) - 06 Jan 09  (Release) - 06 Jan 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J
Biol. Unit 1:  A,B,C,D,I  (1x)
Biol. Unit 2:  E,F,G,H,J  (1x)
Keywords :  Oxidoreductase, Pyruvate, Dehydrogenase, Dihydrolipoyl, Acetyl Transferase, Multienzyme Complex, Transferase, Glycolysis, Phosphoprotein, Thiamine Pyrophosphate, Acyltransferase, Oxidoreductase/Transferase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Y. Pei, C. M. Titman, R. A. Frank, F. J. Leeper, B. F. Luisi
Snapshots Of Catalysis In The E1 Subunit Of The Pyruvate Dehydrogenase Multienzyme Complex
Structure V. 16 1860 2008
PubMed-ID: 19081062  |  Reference-DOI: 10.1016/J.STR.2008.10.009
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PYRUVATE DEHYDROGENASE E1 COMPONENT SUBUNIT ALPHA
    Chains: A, C, E, G
    EC Number: 1.2.4.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKBSTE1A
    Expression System Strain: TG1 RECO
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PDHA
    Organism Scientific: BACILLUS STEAROTHERMOPHILUS
 
Molecule 2 - PYRUVATE DEHYDROGENASE E1 COMPONENT SUBUNIT BETA
    Chains: B, D, F, H
    EC Number: 1.2.4.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKBSTE1B
    Expression System Strain: TG1 RECO
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PDHB
    Organism Scientific: BACILLUS STEAROTHERMOPHILUS
 
Molecule 3 - DIHYDROLIPOYLLYSINE-RESIDUE ACETYLTRANSFERASE COMPONENT OF PYRUVATE DEHYDROGENASE COMPLEX
    Chains: I, J
    EC Number: 2.3.1.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKBSTE1A
    Expression System Strain: TG1 RECO
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PDHC
    Organism Scientific: BACILLUS STEAROTHERMOPHILUS
    Synonym: E2, DIHYDROLIPOAMIDE ACETYLTRANSFERASE COMPONENT OF PYRUVATE DEHYDROGENASE COMPLEX

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric Unit : ABCDEFGHIJ
Biological Unit 1 (1x): ABCD    I 
Biological Unit 2 (1x):     EFGH J

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
1K2Ligand/IonPOTASSIUM ION
2MG5Ligand/IonMAGNESIUM ION
3R1T4Ligand/Ion2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-[(1R)-1-HYDROXYETHYL]-3-METHYL-2-THIENYL}ETHYL TRIHYDROGENDIPHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION
2MG-1Ligand/IonMAGNESIUM ION
3R1T2Ligand/Ion2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-[(1R)-1-HYDROXYETHYL]-3-METHYL-2-THIENYL}ETHYL TRIHYDROGENDIPHOSPHATE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION
2MG-1Ligand/IonMAGNESIUM ION
3R1T2Ligand/Ion2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-[(1R)-1-HYDROXYETHYL]-3-METHYL-2-THIENYL}ETHYL TRIHYDROGENDIPHOSPHATE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:173 , ASN A:202 , PHE A:204 , R1T A:1370 , HOH A:1374BINDING SITE FOR RESIDUE MG A1368
02AC2SOFTWAREILE B:112 , THR B:113 , ALA B:160 , ASP B:163 , ASP B:165BINDING SITE FOR RESIDUE K B1325
03AC3SOFTWAREHOH B:1344BINDING SITE FOR RESIDUE MG D1326
04AC4SOFTWAREASP C:173 , ASN C:202 , PHE C:204 , R1T C:1370BINDING SITE FOR RESIDUE MG C1368
05AC5SOFTWAREILE D:112 , THR D:113 , ALA D:160 , ASP D:163 , ASP D:165BINDING SITE FOR RESIDUE K D1325
06AC6SOFTWARETYR A:102 , ARG A:103 , ILE A:142 , ILE A:144 , GLY A:172 , ASP A:173 , GLY A:174 , GLY A:175 , GLN A:178 , ASN A:202 , PHE A:204 , ALA A:205 , ILE A:206 , HIS A:271 , MG A:1368 , HOH A:1374 , HOH A:1375 , HOH A:1393 , GLU D:28 , LEU D:57 , GLU D:59 , GLN D:81 , PHE D:85 , HIS D:128BINDING SITE FOR RESIDUE R1T A1370
07AC7SOFTWAREASP E:173 , ASN E:202 , PHE E:204 , R1T E:1370 , HOH E:1382BINDING SITE FOR RESIDUE MG E1371
08AC8SOFTWAREGLU B:28 , LEU B:57 , GLU B:59 , GLN B:81 , PHE B:85 , HIS B:128 , TYR C:102 , ARG C:103 , ILE C:142 , ILE C:144 , GLY C:172 , ASP C:173 , GLY C:174 , GLY C:175 , GLN C:178 , ASN C:202 , PHE C:204 , ALA C:205 , ILE C:206 , HIS C:271 , MG C:1368 , HOH C:1417BINDING SITE FOR RESIDUE R1T C1370
09AC9SOFTWAREASP G:173 , ASN G:202 , PHE G:204 , R1T G:1370 , HOH G:1383BINDING SITE FOR RESIDUE MG G1371
10BC1SOFTWARETYR E:102 , ARG E:103 , ILE E:142 , ILE E:144 , GLY E:172 , ASP E:173 , GLY E:174 , GLY E:175 , ASN E:202 , PHE E:204 , ALA E:205 , ILE E:206 , HIS E:271 , MG E:1371 , HOH E:1373 , HOH E:1380 , HOH E:1382 , HOH E:1390 , GLU H:28 , LEU H:57 , GLU H:59 , GLN H:81 , PHE H:85 , HIS H:128BINDING SITE FOR RESIDUE R1T E1370
11BC2SOFTWAREGLU F:28 , LEU F:57 , GLU F:59 , GLN F:81 , PHE F:85 , HIS F:128 , TYR G:102 , ARG G:103 , ILE G:142 , ILE G:144 , GLY G:172 , ASP G:173 , GLY G:174 , GLY G:175 , ASN G:202 , PHE G:204 , ALA G:205 , ILE G:206 , HIS G:271 , MG G:1371 , HOH G:1376 , HOH G:1383BINDING SITE FOR RESIDUE R1T G1370

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3DUF)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Gln B:239 -Pro B:240
2Gln D:239 -Pro D:240
3Met I:132 -Pro I:133
4Asp E:277 -Pro E:278
5Gln F:239 -Pro F:240
6Gln H:239 -Pro H:240

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3DUF)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PSBDPS51826 Peripheral subunit-binding (PSBD) domain profile.ODP2_GEOSE130-167
 		  2I:130-165
J:130-165
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PSBDPS51826 Peripheral subunit-binding (PSBD) domain profile.ODP2_GEOSE130-167
 		  1I:130-165
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PSBDPS51826 Peripheral subunit-binding (PSBD) domain profile.ODP2_GEOSE130-167
 		  1-
J:130-165

(-) Exons   (0, 0)

(no "Exon" information available for 3DUF)

(-) Sequences/Alignments

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:365
 aligned with ODPA_GEOSE | P21873 from UniProtKB/Swiss-Prot  Length:369

    Alignment length:365
                                    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     
           ODPA_GEOSE     5 TFQFPFAEQLEKVAEQFPTFQILNEEGEVVNEEAMPELSDEQLKELMRRMVYTRILDQRSISLNRQGRLGFYAPTAGQEASQIASHFALEKEDFILPGYRDVPQIIWHGLPLYQAFLFSRGHFHGNQIPEGVNVLPPQIIIGAQYIQAAGVALGLKMRGKKAVAITYTGDGGTSQGDFYEGINFAGAFKAPAIFVVQNNRFAISTPVEKQTVAKTLAQKAVAAGIPGIQVDGMDPLAVYAAVKAARERAINGEGPTLIETLCFRYGPHTMSGDDPTRYRSKELENEWAKKDPLVRFRKFLEAKGLWSEEEENNVIEQAKEEIKEAIKKADETPKQKVTDLISIMFEELPFNLKEQYEIYKEKESK 369
               SCOP domains d3dufa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 3dufA00 A:4-368  [code=3.40.50.970, no name defined]                                                                                                                                                                                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh..ee..........hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhh......eee....hhhhhhhh..hhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhh...eeeeeee..ee..ee.hhh.....hhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhh....eeeeee...........hhhhh...hhhhhhhhh.hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh.....hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3duf A   4 TFQFPFAEQLEKVAEQFPTFQILNEEGEVVNEEAMPELSDEQLKELMRRMVYTRILDQRSISLNRQGRLGFYAPTAGQEASQIASHFALEKEDFILPGYRDVPQIIWHGLPLYQAFLFSRGHFHGNQIPEGVNVLPPQIIIGAQYIQAAGVALGLKMRGKKAVAITYTGDGGTSQGDFYEGINFAGAFKAPAIFVVQNNRFAISTPVEKQTVAKTLAQKAVAAGIPGIQVDGMDPLAVYAAVKAARERAINGEGPTLIETLCFRYGPHTMSGDDPTRYRSKELENEWAKKDPLVRFRKFLEAKGLWSEEEENNVIEQAKEEIKEAIKKADETPKQKVTDLISIMFEELPFNLKEQYEIYKEKESK 368
                                    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     


Chain B from PDB  Type:PROTEIN  Length:324
 aligned with ODPB_GEOSE | P21874 from UniProtKB/Swiss-Prot  Length:325

    Alignment length:324
                                    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    
           ODPB_GEOSE     2 AQMTMVQAITDALRIELKNDPNVLIFGEDVGVNGGVFRATEGLQAEFGEDRVFDTPLAESGIGGLAIGLALQGFRPVPEIQFFGFVYEVMDSICGQMARIRYRTGGRYHMPITIRSPFGGGVHTPELHSDSLEGLVAQQPGLKVVIPSTPYDAKGLLISAIRDNDPVIFLEHLKLYRSFRQEVPEGEYTIPIGKADIKREGKDITIIAYGAMVHESLKAAAELEKEGISAEVVDLRTVQPLDIETIIGSVEKTGRAIVVQEAQRQAGIAANVVAEINERAILSLEAPVLRVAAPDTVYPFAQAESVWLPNFKDVIETAKKVMNF 325
               SCOP domains d3dufb1 B:1-186 automated matches                                                                                                                                                         d3dufb2 B:187-324 automated matches                                                                                                        SCOP domains
               CATH domains 3dufB01 B:1-191  [code=3.40.50.970, no name defined]                                                                                                                                           3dufB02 B:192-324  [code=3.40.50.920, no name defined]                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eehhhhhhhhhhhhhhhhh..eeeee..............hhhhhhh...eee...hhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhh...hhhhhh........eeeeee.............hhhhhh.....eee...hhhhhhhhhhhhhhh...eeeeee.hhh....ee.............eeee....eeeee..hhhhhhhhhhhhhhh....eeeee..eee..hhhhhhhhhhhhh.eeeeeeee....hhhhhhhhhhhhh........eeeee......hhhhhhhhh.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3duf B   1 AQMTMVQAITDALRIELKNDPNVLIFGEDVGVNGGVFRATEGLQAEFGEDRVFDTPLAESGIGGLAIGLALQGFRPVPEIQFFGFVYEVMDSICGQMARIRYRTGGRYHMPITIRSPFGGGVHTPELHSDSLEGLVAQQPGLKVVIPSTPYDAKGLLISAIRDNDPVIFLEHLKLYRSFRQEVPEGEYTIPIGKADIKREGKDITIIAYGAMVHESLKAAAELEKEGISAEVVDLRTVQPLDIETIIGSVEKTGRAIVVQEAQRQAGIAANVVAEINERAILSLEAPVLRVAAPDTVYPFAQAESVWLPNFKDVIETAKKVMNF 324
                                    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    


Chain C from PDB  Type:PROTEIN  Length:365
 aligned with ODPA_GEOSE | P21873 from UniProtKB/Swiss-Prot  Length:369

    Alignment length:365
                                    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     
           ODPA_GEOSE     5 TFQFPFAEQLEKVAEQFPTFQILNEEGEVVNEEAMPELSDEQLKELMRRMVYTRILDQRSISLNRQGRLGFYAPTAGQEASQIASHFALEKEDFILPGYRDVPQIIWHGLPLYQAFLFSRGHFHGNQIPEGVNVLPPQIIIGAQYIQAAGVALGLKMRGKKAVAITYTGDGGTSQGDFYEGINFAGAFKAPAIFVVQNNRFAISTPVEKQTVAKTLAQKAVAAGIPGIQVDGMDPLAVYAAVKAARERAINGEGPTLIETLCFRYGPHTMSGDDPTRYRSKELENEWAKKDPLVRFRKFLEAKGLWSEEEENNVIEQAKEEIKEAIKKADETPKQKVTDLISIMFEELPFNLKEQYEIYKEKESK 369
               SCOP domains d3dufc_ C: automated matches                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 3dufC00 C:4-368  [code=3.40.50.970, no name defined]                                                                                                                                                                                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh......................hhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhh.....eee....hhhhhhhh..hhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhh...eeeeeee..ee..ee.hhh.....hhhhhhh....eeeee..hhhhhhhhhhhhhhhhhh....eeeeee............hhhhh............hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh.....hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3duf C   4 TFQFPFAEQLEKVAEQFPTFQILNEEGEVVNEEAMPELSDEQLKELMRRMVYTRILDQRSISLNRQGRLGFYAPTAGQEASQIASHFALEKEDFILPGYRDVPQIIWHGLPLYQAFLFSRGHFHGNQIPEGVNVLPPQIIIGAQYIQAAGVALGLKMRGKKAVAITYTGDGGTSQGDFYEGINFAGAFKAPAIFVVQNNRFAISTPVEKQTVAKTLAQKAVAAGIPGIQVDGMDPLAVYAAVKAARERAINGEGPTLIETLCFRYGPHTMSGDDPTRYRSKELENEWAKKDPLVRFRKFLEAKGLWSEEEENNVIEQAKEEIKEAIKKADETPKQKVTDLISIMFEELPFNLKEQYEIYKEKESK 368
                                    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     


Chain D from PDB  Type:PROTEIN  Length:324
 aligned with ODPB_GEOSE | P21874 from UniProtKB/Swiss-Prot  Length:325

    Alignment length:324
                                    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    
           ODPB_GEOSE     2 AQMTMVQAITDALRIELKNDPNVLIFGEDVGVNGGVFRATEGLQAEFGEDRVFDTPLAESGIGGLAIGLALQGFRPVPEIQFFGFVYEVMDSICGQMARIRYRTGGRYHMPITIRSPFGGGVHTPELHSDSLEGLVAQQPGLKVVIPSTPYDAKGLLISAIRDNDPVIFLEHLKLYRSFRQEVPEGEYTIPIGKADIKREGKDITIIAYGAMVHESLKAAAELEKEGISAEVVDLRTVQPLDIETIIGSVEKTGRAIVVQEAQRQAGIAANVVAEINERAILSLEAPVLRVAAPDTVYPFAQAESVWLPNFKDVIETAKKVMNF 325
               SCOP domains d3dufd1 D:1-186 automated matches                                                                                                                                                         d3dufd2 D:187-324 automated matches                                                                                                        SCOP domains
               CATH domains 3dufD01 D:1-191  [code=3.40.50.970, no name defined]                                                                                                                                           3dufD02 D:192-324  [code=3.40.50.920, no name defined]                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eehhhhhhhhhhhhhhhhh..eeeee..............hhhhhhh...eee...hhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh..hhhhhh........eeeeee.............hhhhhh.....eee...hhhhhhhhhhhhhhh...eeeeee........ee.............eeee....eeeee..hhhhhhhhhhhhhhh....eeeee..eee..hhhhhhhhhhhhh.eeeeeeee....hhhhhhhhhhhhhhhhh....eeeee......hhhhhhhhh.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3duf D   1 AQMTMVQAITDALRIELKNDPNVLIFGEDVGVNGGVFRATEGLQAEFGEDRVFDTPLAESGIGGLAIGLALQGFRPVPEIQFFGFVYEVMDSICGQMARIRYRTGGRYHMPITIRSPFGGGVHTPELHSDSLEGLVAQQPGLKVVIPSTPYDAKGLLISAIRDNDPVIFLEHLKLYRSFRQEVPEGEYTIPIGKADIKREGKDITIIAYGAMVHESLKAAAELEKEGISAEVVDLRTVQPLDIETIIGSVEKTGRAIVVQEAQRQAGIAANVVAEINERAILSLEAPVLRVAAPDTVYPFAQAESVWLPNFKDVIETAKKVMNF 324
                                    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    


Chain E from PDB  Type:PROTEIN  Length:365
 aligned with ODPA_GEOSE | P21873 from UniProtKB/Swiss-Prot  Length:369

    Alignment length:365
                                    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     
           ODPA_GEOSE     5 TFQFPFAEQLEKVAEQFPTFQILNEEGEVVNEEAMPELSDEQLKELMRRMVYTRILDQRSISLNRQGRLGFYAPTAGQEASQIASHFALEKEDFILPGYRDVPQIIWHGLPLYQAFLFSRGHFHGNQIPEGVNVLPPQIIIGAQYIQAAGVALGLKMRGKKAVAITYTGDGGTSQGDFYEGINFAGAFKAPAIFVVQNNRFAISTPVEKQTVAKTLAQKAVAAGIPGIQVDGMDPLAVYAAVKAARERAINGEGPTLIETLCFRYGPHTMSGDDPTRYRSKELENEWAKKDPLVRFRKFLEAKGLWSEEEENNVIEQAKEEIKEAIKKADETPKQKVTDLISIMFEELPFNLKEQYEIYKEKESK 369
               SCOP domains d3dufe_ E: automated matches                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 3dufE00 E:4-368  [code=3.40.50.970, no name defined]                                                                                                                                                                                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhh...ee..........hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhh.....eee....hhhhhhh...hhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhhh..eeeeeee..ee..ee.hhh.....hhhhhhh....eeeee..hhhhhhhhhhhhhhhhhh....eeeeee...................hhhhhhhhh.hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh.....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3duf E   4 TFQFPFAEQLEKVAEQFPTFQILNEEGEVVNEEAMPELSDEQLKELMRRMVYTRILDQRSISLNRQGRLGFYAPTAGQEASQIASHFALEKEDFILPGYRDVPQIIWHGLPLYQAFLFSRGHFHGNQIPEGVNVLPPQIIIGAQYIQAAGVALGLKMRGKKAVAITYTGDGGTSQGDFYEGINFAGAFKAPAIFVVQNNRFAISTPVEKQTVAKTLAQKAVAAGIPGIQVDGMDPLAVYAAVKAARERAINGEGPTLIETLCFRYGPHTMSGDDPTRYRSKELENEWAKKDPLVRFRKFLEAKGLWSEEEENNVIEQAKEEIKEAIKKADETPKQKVTDLISIMFEELPFNLKEQYEIYKEKESK 368
                                    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     


Chain F from PDB  Type:PROTEIN  Length:324
 aligned with ODPB_GEOSE | P21874 from UniProtKB/Swiss-Prot  Length:325

    Alignment length:324
                                    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    
           ODPB_GEOSE     2 AQMTMVQAITDALRIELKNDPNVLIFGEDVGVNGGVFRATEGLQAEFGEDRVFDTPLAESGIGGLAIGLALQGFRPVPEIQFFGFVYEVMDSICGQMARIRYRTGGRYHMPITIRSPFGGGVHTPELHSDSLEGLVAQQPGLKVVIPSTPYDAKGLLISAIRDNDPVIFLEHLKLYRSFRQEVPEGEYTIPIGKADIKREGKDITIIAYGAMVHESLKAAAELEKEGISAEVVDLRTVQPLDIETIIGSVEKTGRAIVVQEAQRQAGIAANVVAEINERAILSLEAPVLRVAAPDTVYPFAQAESVWLPNFKDVIETAKKVMNF 325
               SCOP domains d3duff1 F:1-186 automated matches                                                                                                                                                         d3duff2 F:187-324 automated matches                                                                                                        SCOP domains
               CATH domains 3dufF01 F:1-191  [code=3.40.50.970, no name defined]                                                                                                                                           3dufF02 F:192-324  [code=3.40.50.920, no name defined]                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eehhhhhhhhhhhhhhhhh..eeeee..............hhhhhhh...eee...hhhhhhhhhhhhhh...ee.....hhhhhhhhhhhhhh...hhhhhh........eeeeee.............hhhhhhh....eee...hhhhhhhhhhhhhhh...eeeeee.hhh....ee.............eeee....eeeee..hhhhhhhhhhhhhhh....eeeee..eee..hhhhhhhhhhhhh.eeeeeeee....hhhhhhhhhhhhh........eeeee......hhhhhhhhh.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3duf F   1 AQMTMVQAITDALRIELKNDPNVLIFGEDVGVNGGVFRATEGLQAEFGEDRVFDTPLAESGIGGLAIGLALQGFRPVPEIQFFGFVYEVMDSICGQMARIRYRTGGRYHMPITIRSPFGGGVHTPELHSDSLEGLVAQQPGLKVVIPSTPYDAKGLLISAIRDNDPVIFLEHLKLYRSFRQEVPEGEYTIPIGKADIKREGKDITIIAYGAMVHESLKAAAELEKEGISAEVVDLRTVQPLDIETIIGSVEKTGRAIVVQEAQRQAGIAANVVAEINERAILSLEAPVLRVAAPDTVYPFAQAESVWLPNFKDVIETAKKVMNF 324
                                    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    


Chain G from PDB  Type:PROTEIN  Length:365
 aligned with ODPA_GEOSE | P21873 from UniProtKB/Swiss-Prot  Length:369

    Alignment length:365
                                    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     
           ODPA_GEOSE     5 TFQFPFAEQLEKVAEQFPTFQILNEEGEVVNEEAMPELSDEQLKELMRRMVYTRILDQRSISLNRQGRLGFYAPTAGQEASQIASHFALEKEDFILPGYRDVPQIIWHGLPLYQAFLFSRGHFHGNQIPEGVNVLPPQIIIGAQYIQAAGVALGLKMRGKKAVAITYTGDGGTSQGDFYEGINFAGAFKAPAIFVVQNNRFAISTPVEKQTVAKTLAQKAVAAGIPGIQVDGMDPLAVYAAVKAARERAINGEGPTLIETLCFRYGPHTMSGDDPTRYRSKELENEWAKKDPLVRFRKFLEAKGLWSEEEENNVIEQAKEEIKEAIKKADETPKQKVTDLISIMFEELPFNLKEQYEIYKEKESK 369
               SCOP domains d3dufg_ G: automated matches                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 3dufG00 G:4-368  [code=3.40.50.970, no name defined]                                                                                                                                                                                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh..ee..................hhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhh......eee....hhhhhhhh..hhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhh...eeeeeee..ee..ee.hhh.....hhhhhh.....eeeee..hhhhhhhhhhhhhhhhh.....eeeeee............hhhhh.hhhhhhhhhh.hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh.....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3duf G   4 TFQFPFAEQLEKVAEQFPTFQILNEEGEVVNEEAMPELSDEQLKELMRRMVYTRILDQRSISLNRQGRLGFYAPTAGQEASQIASHFALEKEDFILPGYRDVPQIIWHGLPLYQAFLFSRGHFHGNQIPEGVNVLPPQIIIGAQYIQAAGVALGLKMRGKKAVAITYTGDGGTSQGDFYEGINFAGAFKAPAIFVVQNNRFAISTPVEKQTVAKTLAQKAVAAGIPGIQVDGMDPLAVYAAVKAARERAINGEGPTLIETLCFRYGPHTMSGDDPTRYRSKELENEWAKKDPLVRFRKFLEAKGLWSEEEENNVIEQAKEEIKEAIKKADETPKQKVTDLISIMFEELPFNLKEQYEIYKEKESK 368
                                    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     


Chain H from PDB  Type:PROTEIN  Length:324
 aligned with ODPB_GEOSE | P21874 from UniProtKB/Swiss-Prot  Length:325

    Alignment length:324
                                    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    
           ODPB_GEOSE     2 AQMTMVQAITDALRIELKNDPNVLIFGEDVGVNGGVFRATEGLQAEFGEDRVFDTPLAESGIGGLAIGLALQGFRPVPEIQFFGFVYEVMDSICGQMARIRYRTGGRYHMPITIRSPFGGGVHTPELHSDSLEGLVAQQPGLKVVIPSTPYDAKGLLISAIRDNDPVIFLEHLKLYRSFRQEVPEGEYTIPIGKADIKREGKDITIIAYGAMVHESLKAAAELEKEGISAEVVDLRTVQPLDIETIIGSVEKTGRAIVVQEAQRQAGIAANVVAEINERAILSLEAPVLRVAAPDTVYPFAQAESVWLPNFKDVIETAKKVMNF 325
               SCOP domains d3dufh1 H:1-186 automated matches                                                                                                                                                         d3dufh2 H:187-324 automated matches                                                                                                        SCOP domains
               CATH domains 3dufH01 H:1-191  [code=3.40.50.970, no name defined]                                                                                                                                           3dufH02 H:192-324  [code=3.40.50.920, no name defined]                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eehhhhhhhhhhhhhhhhh..eeeee..............hhhhhhh...eee...hhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhh...hhhhhh........eeeeee.............hhhhhhh....eee...hhhhhhhhhhhhhhh...eeeeee.hhh....ee.............eeee.....eeee..hhhhhhhhhhhhhhh.....eeee..eee..hhhhhhhhhhhhh.eeeeeeee....hhhhhhhhhhhhhh.......eeeee......hhhhhhhhh.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3duf H   1 AQMTMVQAITDALRIELKNDPNVLIFGEDVGVNGGVFRATEGLQAEFGEDRVFDTPLAESGIGGLAIGLALQGFRPVPEIQFFGFVYEVMDSICGQMARIRYRTGGRYHMPITIRSPFGGGVHTPELHSDSLEGLVAQQPGLKVVIPSTPYDAKGLLISAIRDNDPVIFLEHLKLYRSFRQEVPEGEYTIPIGKADIKREGKDITIIAYGAMVHESLKAAAELEKEGISAEVVDLRTVQPLDIETIIGSVEKTGRAIVVQEAQRQAGIAANVVAEINERAILSLEAPVLRVAAPDTVYPFAQAESVWLPNFKDVIETAKKVMNF 324
                                    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    


Chain I from PDB  Type:PROTEIN  Length:38
 aligned with ODP2_GEOSE | P11961 from UniProtKB/Swiss-Prot  Length:428

    Alignment length:38
                                   137       147       157        
           ODP2_GEOSE   128 RVIAMPSVRKYAREKGVDIRLVQGTGKNGRVLKEDIDA 165
               SCOP domains d3dufi_ I: automated matches           SCOP domains
               CATH domains -------------------------------------- CATH domains
               Pfam domains -------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhh....................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------- SAPs(SNPs)
                    PROSITE --PSBD  PDB: I:130-165                 PROSITE
                 Transcript -------------------------------------- Transcript
                 3duf I 128 RVIAMPSVRKYAREKGVDIRLVQGTGKNGRVLKEDIDA 165
                                   137       147       157        


Chain J from PDB  Type:PROTEIN  Length:36
 aligned with ODP2_GEOSE | P11961 from UniProtKB/Swiss-Prot  Length:428

    Alignment length:36
                                   139       149       159      
           ODP2_GEOSE   130 IAMPSVRKYAREKGVDIRLVQGTGKNGRVLKEDIDA 165
               SCOP domains d3dufj_ J: automated matches         SCOP domains
               CATH domains ------------------------------------ CATH domains
               Pfam domains ------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh...............hhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------ SAPs(SNPs)
                    PROSITE PSBD  PDB: J:130-165                 PROSITE
                 Transcript ------------------------------------ Transcript
                 3duf J 130 IAMPSVRKYAREKGVDIRLVQGTGKNGRVLKEDIDA 165
                                   139       149       159
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (4, 14)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 12)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DUF)

(-) Gene Ontology  (10, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,C,E,G   (ODPA_GEOSE | P21873)
molecular function
    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:0016624    oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide 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 a disulfide.
    GO:0004739    pyruvate dehydrogenase (acetyl-transferring) activity    Catalysis of the reaction: pyruvate + lipoamide = S-acetyldihydrolipoamide + CO2.
biological process
    GO:0006096    glycolytic process    The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
    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.

Chain B,D,F,H   (ODPB_GEOSE | P21874)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0004739    pyruvate dehydrogenase (acetyl-transferring) activity    Catalysis of the reaction: pyruvate + lipoamide = S-acetyldihydrolipoamide + CO2.
biological process
    GO:0006096    glycolytic process    The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
    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.

Chain I,J   (ODP2_GEOSE | P11961)
molecular function
    GO:0004742    dihydrolipoyllysine-residue acetyltransferase activity    Catalysis of the reaction: acetyl-CoA + dihydrolipoamide = CoA + S-acetyldihydrolipoamide.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
biological process
    GO:0006096    glycolytic process    The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
    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.

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  ODPA_GEOSE | P21873
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  ODPB_GEOSE | P21874
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ODP2_GEOSE | P11961: 1b5s 1ebd 1lab 1lac 1w3d 1w4e 1w4f 1w4g 1w4h 1w85 1w88 2pdd 2pde 3dv0 3dva
        ODPA_GEOSE | P21873: 1w85 1w88 3dv0 3dva
        ODPB_GEOSE | P21874: 1w85 1w88 3dv0 3dva

(-) Related Entries Specified in the PDB File

1w85 PROTEIN WITH DIFFERENT CO-FACTOR
1w88 PROTEIN WITH DIFFERENT CO-FACTOR
3dv0
3dva