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(-) Description

Title :  STRUCTURE REFINEMENT OF THE ALDEHYDE OXIDOREDUCTASE FROM DESULFOVIBRIO GIGAS AT 1.28 A
 
Authors :  J. M. Rebelo, J. M. Dias, R. Huber, J. J. G. Moura, M. J. Romao
Date :  20 Jul 04  (Deposition) - 27 Jul 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.28
Chains :  Asym./Biol. Unit :  A
Keywords :  Aldehyde Oxidoreductase; Desulfovibrio Gigas; Iron-Sulphur Cluster (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. M. Rebelo, J. M. Dias, R. Huber, J. J. G. Moura, M. J. Romao
Structure Refinement Of The Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop) At 1. 28 A
J. Biol. Inorg. Chem. V. 6 791 2001
PubMed-ID: 11713686  |  Reference-DOI: 10.1007/S007750100255
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALDEHYDE OXIDOREDUCTASE
    ChainsA
    EC Number1.2.3.1
    Organism ScientificDESULFOVIBRIO GIGAS
    Organism Taxid879
    SynonymMOLYBDENUM IRON SULFUR PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric/Biological Unit (5, 10)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2FES2Ligand/IonFE2/S2 (INORGANIC) CLUSTER
3IPA2Ligand/IonISOPROPYL ALCOHOL
4MG2Ligand/IonMAGNESIUM ION
5PCD1Ligand/Ion(MOLYBDOPTERIN-CYTOSINE DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V)

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:460 , TYR A:535 , GLN A:539BINDING SITE FOR RESIDUE CL A 916
02AC2SOFTWAREASP A:263 , GLU A:899 , GLU A:903 , HOH A:4178 , HOH A:4272 , HOH A:4345BINDING SITE FOR RESIDUE MG A 917
03AC3SOFTWARETYR A:892 , ARG A:893 , HOH A:4194 , HOH A:5012BINDING SITE FOR RESIDUE CL A 918
04AC4SOFTWAREHOH A:4217 , HOH A:4424 , HOH A:4801 , HOH A:4802 , HOH A:4950 , HOH A:5038BINDING SITE FOR RESIDUE MG A 919
05AC5SOFTWARELYS A:248 , PRO A:898 , GLU A:899 , HOH A:4410 , HOH A:4546BINDING SITE FOR RESIDUE CL A 920
06AC6SOFTWAREGLN A:99 , CYS A:139 , THR A:420 , PHE A:421 , GLY A:422 , ALA A:531 , PHE A:532 , ARG A:533 , TRP A:650 , HIS A:653 , GLY A:654 , GLN A:655 , GLY A:656 , GLY A:660 , SER A:695 , GLY A:696 , GLY A:697 , SER A:698 , ARG A:699 , GLN A:700 , GLN A:701 , LEU A:795 , SER A:797 , CYS A:799 , ASN A:800 , THR A:804 , GLN A:807 , ALA A:864 , SER A:865 , GLY A:866 , VAL A:867 , GLY A:868 , GLU A:869 , IPA A:914 , HOH A:4127 , HOH A:4395BINDING SITE FOR RESIDUE PCD A 921
07AC7SOFTWAREGLN A:99 , CYS A:100 , GLY A:101 , CYS A:103 , CYS A:137 , ARG A:138 , CYS A:139 , ILE A:368BINDING SITE FOR RESIDUE FES A 908
08AC8SOFTWAREGLY A:39 , CYS A:40 , GLU A:41 , GLY A:43 , GLN A:44 , CYS A:45 , GLY A:46 , CYS A:48 , ARG A:58 , CYS A:60BINDING SITE FOR RESIDUE FES A 909
09AC9SOFTWAREALA A:531 , TYR A:535 , GLY A:697 , PCD A:921 , HOH A:4375BINDING SITE FOR RESIDUE IPA A 914
10BC1SOFTWAREVAL A:5 , GLU A:12 , ASN A:14 , PRO A:416 , TRP A:683 , HOH A:4047BINDING SITE FOR RESIDUE IPA A 915

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:894 -Pro A:895

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
12FE2S_FER_2PS51085 2Fe-2S ferredoxin-type iron-sulfur binding domain profile.MOP_DESGI2-79  1A:2-79
22FE2S_FER_1PS00197 2Fe-2S ferredoxin-type iron-sulfur binding region signature.MOP_DESGI40-48  1A:40-48

(-) Exons   (0, 0)

(no "Exon" information available for 1VLB)

(-) 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:907
 aligned with MOP_DESGI | Q46509 from UniProtKB/Swiss-Prot  Length:907

    Alignment length:907
                                    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       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       
            MOP_DESGI     1 MIQKVITVNGIEQNLFVDAEALLSDVLRQQLGLTGVKVGCEQGQCGACSVILDGKVVRACVTKMKRVADGAQITTIEGVGQPENLHPLQKAWVLHGGAQCGFCSPGFIVSAKGLLDTNADPSREDVRDWFQKHRNACRCTGYKPLVDAVMDAAAVINGKKPETDLEFKMPADGRIWGSKYPRPTAVAKVTGTLDYGADLGLKMPAGTLHLAMVQAKVSHANIKGIDTSEALTMPGVHSVITHKDVKGKNRITGLITFPTNKGDGWDRPILCDEKVFQYGDCIALVCADSEANARAAAEKVKVDLEELPAYMSGPAAAAEDAIEIHPGTPNVYFEQPIVKGEDTGPIFASADVTVEGDFYVGRQPHMPIEPDVAFAYMGDDGKCYIHSKSIGVHLHLYMIAPGVGLEPDQLVLVANPMGGTFGYKFSPTSEALVAVAAMATGRPVHLRYNYQQQQQYTGKRSPWEMNVKFAAKKDGTLLAMESDWLVDHGPYSEFGDLLTLRGAQFIGAGYNIPNIRGLGRTVATNHVWGSAFRGYGAPQSMFASECLMDMLAEKLGMDPLELRYKNAYRPGDTNPTGQEPEVFSLPDMIDQLRPKYQAALEKAQKESTATHKKGVGISIGVYGSGLDGPDASEAWAELNADGTITVHTAWEDHGQGADIGCVGTAHEALRPMGVAPEKIKFTWPNTATTPNSGPSGGSRQQVMTGNAIRVACENLLKACEKPGGGYYTYDELKAADKPTKITGNWTASGATHCDAVTGLGKPFVVYMYGVFMAEVTVDVATGQTTVDGMTLMADLGSLCNQLATDGQIYGGLAQGIGLALSEDFEDIKKHATLVGAGFPFIKQIPDKLDIVYVNHPRPDGPFGASGVGELPLTSPHAAIINAIKSATGVRIYRLPAYPEKVLEALKA 907
               SCOP domains d1vlba2 A:1-80 Aldehyde oxidoreductase, N-terminal domain                       d1vlba1 A:81-193 Aldehyde oxidoreductase, domain 2                                                               d1vlba3 A:194-310 Aldehyde oxidoreductase, domain 3                                                                  d1vlba4 A:311-907 Aldehyde oxidoreductase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1vlbA01 A:1-74  [code=3.10.20.30, no name defined]                        1vlbA02 A:75-193  [code=1.10.150.120, no name defined]                                                                 --------------1vlbA03 A:208-308  [code=3.90.1170.50, no name defined]                                              ----------------------1vlbA04 A:331-364,A:458-580       1vlbA05 A:365-457 Aldehyde Oxidoreductase; domain 4                                          1vlbA04 A:331-364,A:458-580 Aldehyde Oxidoreductase; domain 4                                                              1vlbA07 A:581-624,A:751-907                 1vlbA06 A:625-750 Aldehyde Oxidoreductase; domain 4                                                                           1vlbA07 A:581-624,A:751-907 Aldehyde Oxidoreductase; domain 4                                                                                                 CATH domains
               Pfam domains -----Fer2-1vlbA01 A:6-73                                                 -Fer2_2-1vlbA02 A:75-151                                                      --------------------------------------Ald_Xan_dh_C-1vlbA04 A:190-308                                                                                         ------Ald_Xan_dh_C2-1vlbA03 A:315-845                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    -------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..eeeeeee....hhhhhhhhh..................eeee..eeee.hhh.hhhh....eeehhhhhh.....hhhhhhhhhhh......hhhhhhhhhhhhhh.....hhhhhhhhhhhh........hhhhhhhhhhhhhhhh...hhhhhh.................hhhhhhh....hhhhhhhh.....eeeeeee.....eeeeeeehhhhhh...eeeeehhhhh....ee...............ee.....ee.....eeeeeee.hhhhhhhhhh..eeeeee.....hhhhhhh............eeeeeeeee..hhhhhhhhh.eeeeeeeee...........eeeeee.....eeeee...hhhhhhhhhhhhhh.hhh.eeeee.......hhhhh..hhhhhhhhhhhhh..eeee.hhhhhhhh......eeeeeeeee.....eeeeeeeeeee......hhhhhhhhhhhhh.......eeeeeeeee.............hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeeeeee.......eeeeeeee.....eeee........hhhhhhhhhhhhhhhhhh.hhh.eee.................hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhh....eeeeeee...................eeeeeeeeeeeee.....eeeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhh..................hhhhh...eeeee.......hhhhh....hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -2FE2S_FER_2  PDB: A:2-79 UniProt: 2-79                                        ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (1)
                PROSITE (2) ---------------------------------------2FE2S_FER------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vlb A   1 MIQKVITVNGIEQNLFVDAEALLSDVLRQQLGLTGVKVGCEQGQCGACSVILDGKVVRACVTKMKRVADGAQITTIEGVGQPENLHPLQKAWVLHGGAQCGFCSPGFIVSAKGLLDTNADPSREDVRDWFQKHRNACRCTGYKPLVDAVMDAAAVINGKKPETDLEFKMPADGRIWGSKYPRPTAVAKVTGTLDYGADLGLKMPAGTLHLAMVQAKVSHANIKGIDTSEALTMPGVHSVITHKDVKGKNRITGLITFPTNKGDGWDRPILCDEKVFQYGDCIALVCADSEANARAAAEKVKVDLEELPAYMSGPAAAAEDAIEIHPGTPNVYFEQPIVKGEDTGPIFASADVTVEGDFYVGRQPHMPIEPDVAFAYMGDDGKCYIHSKSIGVHLHLYMIAPGVGLEPDQLVLVANPMGGTFGYKFSPTSEALVAVAAMATGRPVHLRYNYQQQQQYTGKRSPWEMNVKFAAKKDGTLLAMESDWLVDHGPYSEFGDLLTLRGAQFIGAGYNIPNIRGLGRTVATNHVWGSAFRGYGAPQSMFASECLMDMLAEKLGMDPLELRYKNAYRPGDTNPTGQEPEVFSLPDMIDQLRPKYQAALEKAQKESTATHKKGVGISIGVYGSGLDGPDASEAWAELNADGTITVHTAWEDHGQGADIGCVGTAHEALRPMGVAPEKIKFTWPNTATTPNSGPSGGSRQQVMTGNAIRVACENLLKACEKPGGGYYTYDELKAADKPTKITGNWTASGATHCDAVTGLGKPFVVYMYGVFMAEVTVDVATGQTTVDGMTLMADLGSLCNQLATDGQIYGGLAQGIGLALSEDFEDIKKHATLVGAGFPFIKQIPDKLDIVYVNHPRPDGPFGASGVGELPLTSPHAAIINAIKSATGVRIYRLPAYPEKVLEALKA 907
                                    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       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       

   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, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (4, 7)

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

(-) Pfam Domains  (4, 4)

Asymmetric/Biological Unit
(-)
Clan: Fer2 (69)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MOP_DESGI | Q46509)
molecular function
    GO:0051537    2 iron, 2 sulfur cluster binding    Interacting selectively and non-covalently with a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0033727    aldehyde dehydrogenase (FAD-independent) activity    Catalysis of the reaction: an aldehyde + H2O + acceptor = a carboxylate + reduced acceptor.
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MOP_DESGI | Q465091sij 3fah 3fc4 3l4p 4c7y 4c7z 4c80 4us8 4us9 4usa

(-) Related Entries Specified in the PDB File

1dgj A CLOSELY RELATED ENZYME