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(-) Description

Title :  REFINED CRYSTAL STRUCTURE OF LIPOAMIDE DEHYDROGENASE FROM AZOTOBACTER VINELANDII AT 2.2 ANGSTROMS RESOLUTION. A COMPARISON WITH THE STRUCTURE OF GLUTATHIONE REDUCTASE
 
Authors :  A. Mattevi, A. J. Schierbeek, W. G. J. Hol
Date :  11 Dec 91  (Deposition) - 31 Jan 94  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Mattevi, A. J. Schierbeek, W. G. Hol
Refined Crystal Structure Of Lipoamide Dehydrogenase From Azotobacter Vinelandii At 2. 2 A Resolution. A Comparison With The Structure Of Glutathione Reductase.
J. Mol. Biol. V. 220 975 1991
PubMed-ID: 1880807  |  Reference-DOI: 10.1016/0022-2836(91)90367-F
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DIHYDROLIPOAMIDE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.8.1.4
    Engineered: YES
    Organism Scientific: AZOTOBACTER VINELANDII
    Organism Taxid: 354

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:10 , GLY A:12 , PRO A:13 , GLY A:14 , ILE A:32 , GLU A:33 , LYS A:34 , TYR A:35 , GLY A:46 , THR A:47 , CYS A:48 , GLY A:52 , CYS A:53 , SER A:56 , LYS A:57 , GLY A:119 , HIS A:120 , GLY A:121 , ALA A:149 , SER A:150 , GLY A:151 , ILE A:191 , ARG A:278 , LEU A:285 , GLY A:317 , ASP A:318 , LEU A:325 , ALA A:326 , HIS A:327 , TYR A:357 , HOH A:582 , HIS B:450BINDING SITE FOR RESIDUE FAD A 480
2AC2SOFTWAREHIS A:450 , PRO A:451 , ILE B:9 , GLY B:10 , GLY B:12 , PRO B:13 , GLY B:14 , ILE B:32 , GLU B:33 , LYS B:34 , TYR B:35 , GLY B:46 , THR B:47 , CYS B:48 , GLY B:52 , CYS B:53 , LYS B:57 , GLY B:119 , HIS B:120 , GLY B:121 , ALA B:149 , SER B:150 , GLY B:151 , SER B:152 , ILE B:191 , ARG B:278 , GLY B:317 , ASP B:318 , MET B:324 , LEU B:325 , ALA B:326 , HIS B:327 , HOH B:704BINDING SITE FOR RESIDUE FAD B 480

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:48 -A:53
2B:48 -B:53

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1His A:450 -Pro A:451
2His B:450 -Pro B:451

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PYRIDINE_REDOX_1PS00076 Pyridine nucleotide-disulphide oxidoreductases class-I active site.DLDH_AZOVI46-56
 		  2A:45-55
B:45-55

(-) Exons   (0, 0)

(no "Exon" information available for 3LAD)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:472
 aligned with DLDH_AZOVI | P18925 from UniProtKB/Swiss-Prot  Length:477

    Alignment length:472
                                    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       371       381       391       401       411       421       431       441       451       461       471  
           DLDH_AZOVI     2 SQKFDVIVIGAGPGGYVAAIKSAQLGLKTALIEKYKGKEGKTALGGTCLNVGCIPSKALLDSSYKFHEAHESFKLHGISTGEVAIDVPTMIARKDQIVRNLTGGVASLIKANGVTLFEGHGKLLAGKKVEVTAADGSSQVLDTENVILASGSKPVEIPPAPVDQDVIVDSTGALDFQNVPGKLGVIGAGVIGLELGSVWARLGAEVTVLEAMDKFLPAVDEQVAKEAQKILTKQGLKILLGARVTGTEVKNKQVTVKFVDAEGEKSQAFDKLIVAVGRRPVTTDLLAADSGVTLDERGFIYVDDYCATSVPGVYAIGDVVRGAMLAHKASEEGVVVAERIAGHKAQMNYDLIPAVIYTHPEIAGVGKTEQALKAEGVAINVGVFPFAASGRAMAANDTAGFVKVIADAKTDRVLGVHVIGPSAAELVQQGAIAMEFGTSAEDLGMMVFAHPALSEALHEAALAVSGHAIHVA 473
               SCOP domains d3lada1 A:1-158,A:278-348 Dihydrolipoamide dehydrogenase                                                                                                      d3lada2 A:159-277 Dihydrolipoamide dehydrogenase                                                                       d3lada1 A:1-158,A:278-348 Dihydrolipoamide dehydrogenase               d3lada3 A:349-472 Dihydrolipoamide dehydrogenase                                                                             SCOP domains
               CATH domains 3ladA01 A:1-154,A:277-350  [code=3.50.50.60, no name defined]                                                                                             3ladA02 A:155-276  [code=3.50.50.60, no name defined]                                                                     3ladA01 A:1-154,A:277-350  [code=3.50.50.60, no name defined]             3ladA03 A:351-472  [code=3.30.390.30, no name defined]                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.hhhhhhhhhhhhhh..eeeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee.....eeeee....eee...eeeee.eeeee.............hhhhhhhh....eeeeeee.hhhhhhhhhhhhhhh.eeeeee.........hhhhhhhhhhhhhh...eee...eeeeee....eeeeeee....eeeeeeeeeeee.eeeee........................eee...eeeee........hhhhhhhhhhhhhhhh.............eee....eeeeeeehhhhh.........eeeeeee...........eeeeeee.....eeeeeeeee.hhhhhhhhhhhhhh....hhhhhh........hhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------PYRIDINE_RE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lad A   1 SQKFDVIVIGAGPGGYVAAIKSAQLGLKTALIEKYKGKEGKTALGGTCLNVGCIPSKALLDSSYKFHEAHESFKLHGISTGEVAIDVPTMIARKDQIVRNLTGGVASLIKANGVTLFEGHGKLLAGKKVEVTAADGSSQVLDTENVILASGSKPVEIPPAPVDQDVIVDSTGALDFQNVPGKLGVIGAGVIGLELGSVWARLGAEVTVLEAMDKFLPAVDEQVAKEAQKILTKQGLKILLGARVTGTEVKNKQVTVKFVDAEGEKSQAFDKLIVAVGRRPVTTDLLAADSGVTLDERGFIYVDDYCATSVPGVYAIGDVVRGAMLAHKASEEGVVVAERIAGHKAQMNYDLIPAVIYTHPEIAGVGKTEQALKAEGVAINVGVFPFAASGRAMAANDTAGFVKVIADAKTDRVLGVHVIGPSAAELVQQGAIAMEFGTSAEDLGMMVFAHPALSEALHEAALAVSGHAIHVA 472
                                    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:472
 aligned with DLDH_AZOVI | P18925 from UniProtKB/Swiss-Prot  Length:477

    Alignment length:472
                                    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       371       381       391       401       411       421       431       441       451       461       471  
           DLDH_AZOVI     2 SQKFDVIVIGAGPGGYVAAIKSAQLGLKTALIEKYKGKEGKTALGGTCLNVGCIPSKALLDSSYKFHEAHESFKLHGISTGEVAIDVPTMIARKDQIVRNLTGGVASLIKANGVTLFEGHGKLLAGKKVEVTAADGSSQVLDTENVILASGSKPVEIPPAPVDQDVIVDSTGALDFQNVPGKLGVIGAGVIGLELGSVWARLGAEVTVLEAMDKFLPAVDEQVAKEAQKILTKQGLKILLGARVTGTEVKNKQVTVKFVDAEGEKSQAFDKLIVAVGRRPVTTDLLAADSGVTLDERGFIYVDDYCATSVPGVYAIGDVVRGAMLAHKASEEGVVVAERIAGHKAQMNYDLIPAVIYTHPEIAGVGKTEQALKAEGVAINVGVFPFAASGRAMAANDTAGFVKVIADAKTDRVLGVHVIGPSAAELVQQGAIAMEFGTSAEDLGMMVFAHPALSEALHEAALAVSGHAIHVA 473
               SCOP domains d3ladb1 B:1-158,B:278-348 Dihydrolipoamide dehydrogenase                                                                                                      d3ladb2 B:159-277 Dihydrolipoamide dehydrogenase                                                                       d3ladb1 B:1-158,B:278-348 Dihydrolipoamide dehydrogenase               d3ladb3 B:349-472 Dihydrolipoamide dehydrogenase                                                                             SCOP domains
               CATH domains 3ladB01 B:1-154,B:277-350  [code=3.50.50.60, no name defined]                                                                                             3ladB02 B:155-276  [code=3.50.50.60, no name defined]                                                                     3ladB01 B:1-154,B:277-350  [code=3.50.50.60, no name defined]             3ladB03 B:351-472  [code=3.30.390.30, no name defined]                                                                     CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Pyr_redox-3ladB01 B:182-265                                                         -----------------Pyr_redox_2-3ladB03 B:283-324             ---------------------------Pyr_redox_dim-3ladB09 B:352-461                                                                               ----------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Pyr_redox-3ladB02 B:182-265                                                         -----------------Pyr_redox_2-3ladB04 B:283-324             ---------------------------Pyr_redox_dim-3ladB10 B:352-461                                                                               ----------- Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Pyr_redox_2-3ladB05 B:283-324             ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Pyr_redox_2-3ladB06 B:283-324             ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (4)
           Pfam domains (5) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Pyr_redox_2-3ladB07 B:283-324             ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (5)
           Pfam domains (6) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Pyr_redox_2-3ladB08 B:283-324             ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (6)
         Sec.struct. author .....eeeee.hhhhhhhhhhhhhh..eeeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee.....eeeee....eee...eeeee.eeeee.............hhhhhhhh....eeeeeee.hhhhhhhhhhhhhhh.eeeeee.........hhhhhhhhhhhhhh...eee...eeeeee....eeeeeee....eeeeeeeeeeee.eeeee........................eee...eeeee........hhhhhhhhhhhhhhhh.............eee....eeeeeeehhhhh.........eeeeeee...........eeeeeee.....eeeeeeeee.hhhhhhhhhhhhhh....hhhhhh........hhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------PYRIDINE_RE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lad B   1 SQKFDVIVIGAGPGGYVAAIKSAQLGLKTALIEKYKGKEGKTALGGTCLNVGCIPSKALLDSSYKFHEAHESFKLHGISTGEVAIDVPTMIARKDQIVRNLTGGVASLIKANGVTLFEGHGKLLAGKKVEVTAADGSSQVLDTENVILASGSKPVEIPPAPVDQDVIVDSTGALDFQNVPGKLGVIGAGVIGLELGSVWARLGAEVTVLEAMDKFLPAVDEQVAKEAQKILTKQGLKILLGARVTGTEVKNKQVTVKFVDAEGEKSQAFDKLIVAVGRRPVTTDLLAADSGVTLDERGFIYVDDYCATSVPGVYAIGDVVRGAMLAHKASEEGVVVAERIAGHKAQMNYDLIPAVIYTHPEIAGVGKTEQALKAEGVAINVGVFPFAASGRAMAANDTAGFVKVIADAKTDRVLGVHVIGPSAAELVQQGAIAMEFGTSAEDLGMMVFAHPALSEALHEAALAVSGHAIHVA 472
                                    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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 6)

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

(-) Pfam Domains  (3, 10)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)
(-)
Clan: no clan defined [family: Pyr_redox_dim] (44)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DLDH_AZOVI | P18925)
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: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.
biological process
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    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: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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  3lad
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