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(-) Description

Title :  STRUCTURE OF DIHYDROLIPOAMIDE DEHYDROGENASE
 
Authors :  I. Li De La Sierra, T. Prange, L. Pernot
Date :  06 Sep 96  (Deposition) - 15 Oct 97  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Redox-Active Center, Glycolysis, Oxidoreductase, Nad, Flavoprotein, Fad, P64K (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Li De La Sierra, L. Pernot, T. Prange, P. Saludjian, M. Schiltz, R. Fourme, G. Padron
Molecular Structure Of The Lipoamide Dehydrogenase Domain O A Surface Antigen From Neisseria Meningitidis.
J. Mol. Biol. V. 269 129 1997
PubMed-ID: 9193005  |  Reference-DOI: 10.1006/JMBI.1997.1009
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SURFACE PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: M-6 OBTAINED FROM A GENOMIC
    Expression System Strain: HB101
    Expression System Taxid: 562
    Fragment: DIHYDROLIPOAMIDE DEHYDROGENASE DOMAIN
    Gene: M-6 OBTAINED FROM A GENOMIC
    Organism Scientific: NEISSERIA MENINGITIDIS
    Organism Taxid: 487

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:128 , GLY A:129 , GLY A:130 , GLY A:131 , PRO A:132 , GLY A:133 , VAL A:151 , GLU A:152 , ARG A:153 , TYR A:154 , GLY A:159 , VAL A:160 , CYS A:161 , VAL A:164 , GLY A:165 , CYS A:166 , LYS A:170 , GLY A:231 , ASP A:232 , GLY A:233 , TYR A:251 , ALA A:271 , ALA A:272 , GLY A:273 , ILE A:312 , ARG A:400 , GLY A:439 , ASP A:440 , MET A:446 , LEU A:447 , ALA A:448 , HIS A:449 , TYR A:479 , HIS A:572 , PRO A:573 , HOH A:712 , HOH A:730 , HOH A:731 , HOH A:763 , HOH A:790 , HOH A:791BINDING SITE FOR RESIDUE FAD A 600

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:161 -A:166

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gln A:444 -Pro A:445
2Ser A:481 -Pro A:482
3His A:572 -Pro A:573

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1OJT)

(-) Exons   (0, 0)

(no "Exon" information available for 1OJT)

(-) 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:482
 aligned with Q51225_NEIME | Q51225 from UniProtKB/TrEMBL  Length:594

    Alignment length:482
                                   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       501       511       521       531       541       551       561       571       581       591  
         Q51225_NEIME   112 GSADAEYDVVVLGGGPGGYSAAFAAADEGLKVAIVERYKTLGGVCLNVGCIPSKALLHNAAVIDEVRHLAANGIKYPEPELDIDMLRAYKDGVVSRLTGGLAGMAKSRKVDVIQGDGQFLDPHHLEVSLTAGDAYEQAAPTGEKKIVAFKNCIIAAGSRVTKLPFIPEDPRIIDSSGALALKEVPGKLLIIGGGIIGLEMGTVYSTLGSRLDVVEMMDGLMQGADRDLVKVWQKQNEYRFDNIMVNTKTVAVEPKEDGVYVTFEGANAPKEPQRYDAVLVAAGRAPNGKLISAEKAGVAVTDRGFIEVDKQMRTNVPHIYAIGDIVGQPMLAHKAVHEGHVAAENCAGHKAYFDARVIPGVAYTSPEVAWVGETELSAKASGRKITKANFPWAASGRAIANGCDKPFTKLIFDAETGRIIGGGIVGPNGGDMIGEVCLAIEMGCDAADIGKTIHPHPTLGESIGMAAEVALGTCTDLPPQKK 593
               SCOP domains d1ojta1 A:117-275,A:401-470 Dihydrolipoamide dehydrogenase                                                                                                     d1ojta2 A:276-400 Dihydrolipoamide dehydrogenase                                                                             d1ojta1 A:117-275,A:401-470 Dihydrolipoamide dehydrogenase            d1ojta3 A:471-598 Dihydrolipoamide dehydrogenase                                                                                 SCOP domains
               CATH domains ---1ojtA01 A:120-276,A:399-472  [code=3.50.50.60, no name defined]                                                                                              1ojtA02 A:277-398  [code=3.50.50.60, no name defined]                                                                     1ojtA01 A:120-276,A:399-472  [code=3.50.50.60, no name defined]           1ojtA03 A:473-594  [code=3.30.390.30, no name defined]                                                                    ---- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Pyr_redox-1ojtA01 A:303-386                                                         ---------------------------------------------------------------------------------------Pyr_redox_dim-1ojtA03 A:474-583                                                                               --------------- Pfam domains (1)
           Pfam domains (2) -------Pyr_redox_2-1ojtA02 A:124-446                                                                                                                                                                                                                                                                                                      -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...eeee.eeee...hhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeeee..eeeeeeeeeee..eeeeeeeeeeeeeeeeee...eee..............hhhh........eeeee...hhhhhhhhhhhhh..eeeee...........hhhhhhhhhhhhhh..eee...eeeeeeee..eeeeeee........eee..eee...eee.........................eee....eee..........hhhhhhhhhhhhhhh............eeee.....eeeee..hhhhhhh...eeeeeee....hhhhhh.....eeeeeee.......eeeee...hhhhhhhhhhhhhh...hhhhh.........hhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ojt A 117 GSADAEYDVVVLGGGPGGYSAAFAAADEGLKVAIVERYKTLGGVCLNVGCIPSKALLHNAAVIDEVRHLAANGIKYPEPELDIDMLRAYKDGVVSRLTGGLAGMAKSRKVDVIQGDGQFLDPHHLEVSLTAGDAYEQAAPTGEKKIVAFKNCIIAAGSRVTKLPFIPEDPRIIDSSGALALKEVPGKLLIIGGGIIGLEMGTVYSTLGSRLDVVEMMDGLMQGADRDLVKVWQKQNEYRFDNIMVNTKTVAVEPKEDGVYVTFEGANAPKEPQRYDAVLVAAGRAPNGKLISAEKAGVAVTDRGFIEVDKQMRTNVPHIYAIGDIVGQPMLAHKAVHEGHVAAENCAGHKAYFDARVIPGVAYTSPEVAWVGETELSAKASARKITKANFPWAASGRAIANGCDKPFTKLIFDAETGRIIGGGIVGPNGGDMIGEVCLAIEMGCDAADIGKTIHPHPTLGESIGMAAEVALGTCTDLPPQKK 598
                                   126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596
   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, 3)

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

(-) CATH Domains  (2, 3)

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

(-) Pfam Domains  (3, 3)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q51225_NEIME | Q51225)
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:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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: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:0005623    cell    The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

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        Q51225_NEIME | Q51225: 1bhy

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