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(-) Description

Title :  CRYSTAL STRUCTURE OF METHANOL DEHYDROGENASE FROM P. DENITRIFICANS
 
Authors :  Z. -X. Xia, W. -W. Dai, Y. -N. He, S. A. White, F. S. Mathews, V. L. Davidson
Date :  16 May 02  (Deposition) - 12 Aug 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Heavy Subunits: 8-Fold Beta-Propeller Superbarrel, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. -X. Xia, W. -W. Dai, Y. -N. He, S. A. White, F. S. Mathews, V. L. Davidson
X-Ray Structure Of Methanol Dehydrogenase From Paracoccus Denitrificans And Molecular Modeling Of Its Interactions With Cytochrome C-551I
J. Biol. Inorg. Chem. V. 8 843 2003
PubMed-ID: 14505072  |  Reference-DOI: 10.1007/S00775-003-0485-0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - METHANOL DEHYDROGENASE SUBUNIT 1
    Chains: A, C
    EC Number: 1.1.99.8
    Organism Scientific: PARACOCCUS DENITRIFICANS
    Organism Taxid: 266
    Synonym: MDH LARGE ALPHA SUBUNIT, MEDH
 
Molecule 2 - METHANOL DEHYDROGENASE SUBUNIT 2
    Chains: B, D
    EC Number: 1.1.99.8
    Organism Scientific: PARACOCCUS DENITRIFICANS
    Organism Taxid: 266
    Synonym: MDH SMALL BETA SUBUNIT, MEDH

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2PQQ2Ligand/IonPYRROLOQUINOLINE QUINONE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:177 , ASN A:261 , ASP A:303 , PQQ A:701BINDING SITE FOR RESIDUE CA A 702
2AC2SOFTWAREGLU C:177 , ASN C:261 , PQQ C:701BINDING SITE FOR RESIDUE CA C 702
3AC3SOFTWAREGLU A:55 , CYS A:103 , CYS A:104 , VAL A:107 , ARG A:109 , THR A:159 , SER A:174 , GLY A:175 , ALA A:176 , GLU A:177 , THR A:241 , TRP A:243 , ARG A:331 , TRP A:476 , GLY A:539 , TRP A:540 , CA A:702 , HOH A:726 , HOH A:820BINDING SITE FOR RESIDUE PQQ A 701
4AC4SOFTWAREGLU C:55 , CYS C:103 , ARG C:109 , THR C:159 , SER C:174 , GLY C:175 , ALA C:176 , GLU C:177 , THR C:241 , TRP C:243 , ASN C:261 , ARG C:331 , TRP C:476 , GLY C:539 , TRP C:540 , CA C:702 , HOH C:771 , HOH C:772 , HOH C:863BINDING SITE FOR RESIDUE PQQ C 701

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:103 -A:104
2A:386 -A:415
3B:6 -B:12
4C:103 -C:104
5C:386 -C:415
6D:6 -D:12

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Phe A:71 -Pro A:72
2Ala A:263 -Pro A:264
3Lys A:275 -Trp A:276
4Cys A:386 -Pro A:387
5Phe C:71 -Pro C:72
6Ala C:263 -Pro C:264
7Lys C:275 -Trp C:276
8Cys C:386 -Pro C:387

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BACTERIAL_PQQ_1PS00363 Bacterial quinoprotein dehydrogenases signature 1.DHM1_PARDE45-73
 		  2A:13-41
C:13-41
2BACTERIAL_PQQ_2PS00364 Bacterial quinoprotein dehydrogenases signature 2.DHM1_PARDE275-296
 		  2A:243-264
C:243-264

(-) Exons   (0, 0)

(no "Exon" information available for 1LRW)

(-) 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:600
 aligned with DHM1_PARDE | P12293 from UniProtKB/Swiss-Prot  Length:631

    Alignment length:600
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      476                                                                                                                                                           
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    475 |                                                                                                                                                           
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472  | |  481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631
           DHM1_PARDE    33 NDQLVELAKDPANWVMTGRDYNAQNYSEMTDINKENVKQLRPAWSFSTGVLHGHEGTPLVVGDRMFIHTPFPNTTFALDLNEPGKILWQNKPKQNPTARTVACCDVVNRGLAYWPGDDQVKPLIFRTQLDGHIVAMDAETGETRWIMENSDIKVGSTLTIAPYVIKDLVLVGSSGAELGVRGYVTAYDVKSGEMRWRAFATGPDEELLLAEDFNAPNPHYGQKNLGLETWEGDAWKIGGGTNWGWYAYDPEVDLFYYGSGNPAPWNETMRPGDNKWTMAIWGREATTGEAKFAYQKTPHDEWDYAGVNVMMLSEQEDKQGQMRKLLTHPDRNGIVYTLDRTNGDLISADKMDDTVNWVKEVQLDTGLPVRDPEFGTRMDHKARDICPSAMGYHNQGHDSYDPERKVFMLGINHICMDWEPFMLPYRAGQFFVGATLTMYPGPK-ATAERAGAGQIKAYDAISGEMKWEKMERFSVWGGTMATAGGLTFYVTLDGFIKARDSDTGDLLWKFKLPSGVIGHPMTYKHDGRQYVAIMYGVGGWPGVGLVFDLADPTAGLGSVGAFKRLQEFTQMGGGVMVFSLDGESPYSDPNVGEYAPGEPT 631
               SCOP domains d1lrwa_ A: Methanol dehydrogenase, heavy chain                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1lrwA00 A:1-600  [code=2.140.10.10, no name defined]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
     Sec.struct. author (1) hhhhhhhhh..........................hhhhh--------..........eee.eeeeeeee..eeeeeeee......eeee....hhhhhhhh.........eee.......eeeeeee..eeeeeeee..eeeeeeeee.hhhhh.......eee.eeeee...hhhhh..eeeeeeee..eeeeeeeee..hhhhhh........hhhhh..hhhhhh.................eee...eeeeeeee.....hhhhh.......eeeeeeee..eeeeeeeee..............eeeeeee..eeeeeeeeee...eeeeeeee..eeeeeeeee.....eeeeee...-----hhhhh......eeee.............eee....eeeeeeeeeeeeeeee...........eeeeeeeee..........eeeeeeee...eeeeeeeee........eee..eeeeeee..eeeeeee...eeeeeeeee........eeeee..eeeeeeee......hhhhhhh.....hhhhh.....hhhhh....eeeeeeeee................... Sec.struct. author (1)
     Sec.struct. author (2) --------------------------------------eeeeeeeeee-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------eeeeee------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------BACTERIAL_PQQ_1  PDB: A:13-41---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------BACTERIAL_PQQ_2       ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1lrw A   1 NDQLVELAKDPANWVMTGRDYNAQNYSEMTDINKENVKQLRPAWSFSTGVLHGHEGTPLVVGDRMFIHTPFPNTTFALDLNEPGKILWQNKPKQNPTARTVACCDVVNRGLAYWPGDDQVKPLIFRTQLDGHIVAMDAETGETRWIMENSDIKVGSTLTIAPYVIKDLVLVGSSGAELGVRGYVTAYDVKSGEMRWRAFATGPDEELLLAEDFNAPNPHYGQKNLGLETWEGDAWKIGGGTNWGWYAYDPEVDLFYYGSGNPAPWNETMRPGDNKWTMAIWGREATTGEAKFAYQKTPHDEWDYAGVNVMMLSEQEDKQGQMRKLLTHPDRNGIVYTLDRTNGDLISADKMDDTVNWVKEVQLDTGLPVRDPEFGTRMDHKARDICPSAMGYHNQGHDSYDPERKVFMLGINHICMDWEPFMLPYRAGQFFVGATLTMYPGPKGDRGNASGLGQIKAYDAISGEMKWEKMERFSVWGGTMATAGGLTFYATLDGFIKARDSDTGDLLWKFKLPSGVIGHPMTYKHDGRQYVAIMYGVGGWPGVGLVFDLADPTAGLGSVGAFKRLQEFTQMGGGVMVFSLDGESPYSDPNVGEYAPGEPT 600
                                    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


Chain B from PDB  Type:PROTEIN  Length:83
 aligned with DHM2_PARDE | P29898 from UniProtKB/Swiss-Prot  Length:103

    Alignment length:83
                                    30        40        50        60        70        80        90       100   
           DHM2_PARDE    21 YDGTNCKAPGNCWEPKPDYPAKVEGSKYDPQHDPAELSKQGESLAVMDARNEWRVWNMKKTGKFEYDVKKIDGYDETKAPPAE 103
               SCOP domains d1lrwb_ B: Methanol dehydrogenase, light chain                                      SCOP domains
               CATH domains 1lrwB00 B:1-83 Methanol Dehydrogenase, chain B                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                 1lrw B   1 YDGTNCKAPGNCWEPKPDYPAKVEGSKYDPQHDPAELSKQGESLAVMDARNEWRVWNMKKTGKFEYDVKKIDGYDETKAPPAE  83
                                    10        20        30        40        50        60        70        80   


Chain C from PDB  Type:PROTEIN  Length:600
 aligned with DHM1_PARDE | P12293 from UniProtKB/Swiss-Prot  Length:631

    Alignment length:600
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      476                                                                                                                                                           
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    475 |                                                                                                                                                           
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472  | |  481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631
           DHM1_PARDE    33 NDQLVELAKDPANWVMTGRDYNAQNYSEMTDINKENVKQLRPAWSFSTGVLHGHEGTPLVVGDRMFIHTPFPNTTFALDLNEPGKILWQNKPKQNPTARTVACCDVVNRGLAYWPGDDQVKPLIFRTQLDGHIVAMDAETGETRWIMENSDIKVGSTLTIAPYVIKDLVLVGSSGAELGVRGYVTAYDVKSGEMRWRAFATGPDEELLLAEDFNAPNPHYGQKNLGLETWEGDAWKIGGGTNWGWYAYDPEVDLFYYGSGNPAPWNETMRPGDNKWTMAIWGREATTGEAKFAYQKTPHDEWDYAGVNVMMLSEQEDKQGQMRKLLTHPDRNGIVYTLDRTNGDLISADKMDDTVNWVKEVQLDTGLPVRDPEFGTRMDHKARDICPSAMGYHNQGHDSYDPERKVFMLGINHICMDWEPFMLPYRAGQFFVGATLTMYPGPK-ATAERAGAGQIKAYDAISGEMKWEKMERFSVWGGTMATAGGLTFYVTLDGFIKARDSDTGDLLWKFKLPSGVIGHPMTYKHDGRQYVAIMYGVGGWPGVGLVFDLADPTAGLGSVGAFKRLQEFTQMGGGVMVFSLDGESPYSDPNVGEYAPGEPT 631
               SCOP domains d1lrwc_ C: Methanol dehydrogenase, heavy chain                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1lrwC00 C:1-600  [code=2.140.10.10, no name defined]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PQQ-1lrwC01 C:485-522                 ------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PQQ-1lrwC02 C:485-522                 ------------------------------------------------------------------------------ Pfam domains (2)
           Pfam domains (3) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PQQ-1lrwC03 C:485-522                 ------------------------------------------------------------------------------ Pfam domains (3)
           Pfam domains (4) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PQQ-1lrwC04 C:485-522                 ------------------------------------------------------------------------------ Pfam domains (4)
           Pfam domains (5) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PQQ-1lrwC05 C:485-522                 ------------------------------------------------------------------------------ Pfam domains (5)
           Pfam domains (6) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PQQ-1lrwC06 C:485-522                 ------------------------------------------------------------------------------ Pfam domains (6)
           Pfam domains (7) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PQQ-1lrwC07 C:485-522                 ------------------------------------------------------------------------------ Pfam domains (7)
           Pfam domains (8) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PQQ-1lrwC08 C:485-522                 ------------------------------------------------------------------------------ Pfam domains (8)
     Sec.struct. author (1) hhhhhhhhh..........................hhhhh--------..........eee.eeeeeeee..eeeeeeee......eeee....hhhhhhhh.........eee.......eeeeeee..eeeeeeee..eeeeeeeee.hhhhh.......eee.eeeee...hhhhh..eeeeeeee..eeeeeeeee..hhhhhh........hhhhh..hhhhhh.................eee...eeeeeeee.....hhhhh.......eeeeeeee..eeeeeeeee..............eeeeeee..eeeeeeeeee...eeeeeeee..eeeeeeeee.....eeeeee...-----hhhhh......eeee.............eee....eeeeeeeeeeeeeeee...........eeeeeeeee..........eeeeeeee...eeeeeeeee........eee..eeeeeee..eeeeeee...eeeeeeeee........eeeee..eeeeeeee......hhhhhhh.....hhhhh.....hhhhh....eeeeeeeee................... Sec.struct. author (1)
     Sec.struct. author (2) --------------------------------------eeeeeeeeee-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------eeeeee------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------BACTERIAL_PQQ_1  PDB: C:13-41---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------BACTERIAL_PQQ_2       ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1lrw C   1 NDQLVELAKDPANWVMTGRDYNAQNYSEMTDINKENVKQLRPAWSFSTGVLHGHEGTPLVVGDRMFIHTPFPNTTFALDLNEPGKILWQNKPKQNPTARTVACCDVVNRGLAYWPGDDQVKPLIFRTQLDGHIVAMDAETGETRWIMENSDIKVGSTLTIAPYVIKDLVLVGSSGAELGVRGYVTAYDVKSGEMRWRAFATGPDEELLLAEDFNAPNPHYGQKNLGLETWEGDAWKIGGGTNWGWYAYDPEVDLFYYGSGNPAPWNETMRPGDNKWTMAIWGREATTGEAKFAYQKTPHDEWDYAGVNVMMLSEQEDKQGQMRKLLTHPDRNGIVYTLDRTNGDLISADKMDDTVNWVKEVQLDTGLPVRDPEFGTRMDHKARDICPSAMGYHNQGHDSYDPERKVFMLGINHICMDWEPFMLPYRAGQFFVGATLTMYPGPKGDRGNASGLGQIKAYDAISGEMKWEKMERFSVWGGTMATAGGLTFYATLDGFIKARDSDTGDLLWKFKLPSGVIGHPMTYKHDGRQYVAIMYGVGGWPGVGLVFDLADPTAGLGSVGAFKRLQEFTQMGGGVMVFSLDGESPYSDPNVGEYAPGEPT 600
                                    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


Chain D from PDB  Type:PROTEIN  Length:83
 aligned with DHM2_PARDE | P29898 from UniProtKB/Swiss-Prot  Length:103

    Alignment length:83
                                    30        40        50        60        70        80        90       100   
           DHM2_PARDE    21 YDGTNCKAPGNCWEPKPDYPAKVEGSKYDPQHDPAELSKQGESLAVMDARNEWRVWNMKKTGKFEYDVKKIDGYDETKAPPAE 103
               SCOP domains d1lrwd_ D: Methanol dehydrogenase, light chain                                      SCOP domains
               CATH domains 1lrwD00 D:1-83 Methanol Dehydrogenase, chain B                                      CATH domains
           Pfam domains (1) MDH-1lrwD01 D:1-71                                                     ------------ Pfam domains (1)
           Pfam domains (2) MDH-1lrwD02 D:1-71                                                     ------------ Pfam domains (2)
         Sec.struct. author ................................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                 1lrw D   1 YDGTNCKAPGNCWEPKPDYPAKVEGSKYDPQHDPAELSKQGESLAVMDARNEWRVWNMKKTGKFEYDVKKIDGYDETKAPPAE  83
                                    10        20        30        40        50        60        70        80
   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, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Few Secondary Structures (1120)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 10)

Asymmetric/Biological Unit
(-)
Clan: Beta_propeller (192)
(-)
Family: PQQ (3)
(-)
Paracoccus denitrificans (1)
1aPQQ-1lrwC01C:485-522
1bPQQ-1lrwC02C:485-522
1cPQQ-1lrwC03C:485-522
1dPQQ-1lrwC04C:485-522
1ePQQ-1lrwC05C:485-522
1fPQQ-1lrwC06C:485-522
1gPQQ-1lrwC07C:485-522
1hPQQ-1lrwC08C:485-522
(-)
Clan: no clan defined [family: MDH] (2)

(-) Gene Ontology  (15, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,C   (DHM1_PARDE | P12293)
molecular function
    GO:0052932    2-chloroethanol cytochrome-c oxidoreductase activity    Catalysis of the reaction: 2-chloroethanol + 2 cytochrome c(L) = chloroacetaldehyde + 2 reduced cytochrome c(L).
    GO:0052933    alcohol dehydrogenase (cytochrome c(L)) activity    Catalysis of the reaction: primary alcohol + 2 cytochrome c(L) = 2 reduced cytochrome c(L) + an aldehyde + 2 H+.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0052931    ethanol cytochrome-c oxidoreductase activity    Catalysis of the reaction: ethanol + 2 cytochrome c(L) = acetaldehyde + 2 reduced cytochrome c(L) + 2 H+.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0052930    methanol ferricytochrome-c oxidoreductase activity    Catalysis of the reaction: methanol + 2 ferricytochrome c = formaldehyde + 2 ferrocytochrome c + 2 H+.
    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:0016614    oxidoreductase activity, acting on CH-OH group of donors    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group act as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
biological process
    GO:0015945    methanol metabolic process    The chemical reactions and pathways involving methanol, CH3-OH, a colorless, flammable, mobile, poisonous liquid, widely used as a solvent.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Chain B,D   (DHM2_PARDE | P29898)
molecular function
    GO:0052932    2-chloroethanol cytochrome-c oxidoreductase activity    Catalysis of the reaction: 2-chloroethanol + 2 cytochrome c(L) = chloroacetaldehyde + 2 reduced cytochrome c(L).
    GO:0004022    alcohol dehydrogenase (NAD) activity    Catalysis of the reaction: an alcohol + NAD+ = an aldehyde or ketone + NADH + H+.
    GO:0052933    alcohol dehydrogenase (cytochrome c(L)) activity    Catalysis of the reaction: primary alcohol + 2 cytochrome c(L) = 2 reduced cytochrome c(L) + an aldehyde + 2 H+.
    GO:0052931    ethanol cytochrome-c oxidoreductase activity    Catalysis of the reaction: ethanol + 2 cytochrome c(L) = acetaldehyde + 2 reduced cytochrome c(L) + 2 H+.
    GO:0052930    methanol ferricytochrome-c oxidoreductase activity    Catalysis of the reaction: methanol + 2 ferricytochrome c = formaldehyde + 2 ferrocytochrome c + 2 H+.
    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:0015945    methanol metabolic process    The chemical reactions and pathways involving methanol, CH3-OH, a colorless, flammable, mobile, poisonous liquid, widely used as a solvent.
    GO:0015946    methanol oxidation    The chemical reactions and pathways resulting in the conversion of methanol to methyl-Coenzyme M.
    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:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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  Cis Peptide Bonds
    Ala A:263 - Pro A:264   [ RasMol ]  
    Ala C:263 - Pro C:264   [ RasMol ]  
    Cys A:386 - Pro A:387   [ RasMol ]  
    Cys C:386 - Pro C:387   [ RasMol ]  
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