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(-) Description

Title :  STRUCTURE AT 1.9 A RESOLUTION OF A QUINOHEMOPROTEIN ALCOHOL DEHYDROGENASE FROM PSEUDOMONAS PUTIDA HK5
 
Authors :  Z. -W. Chen, K. Matsushita, T. Yamashita, T. Fujii, H. Toyama, O. Adachi H. D. Bellamy, F. S. Mathews
Date :  25 Jan 02  (Deposition) - 10 Jul 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Quinohemoprotein Alcohol Dehydrogenase, Electron Transfer, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Z. W. Chen, K. Matsushita, T. Yamashita, T. A. Fujii, H. Toyama, O. Adachi, H. D. Bellamy, F. S. Mathews
Structure At 1. 9 A Resolution Of A Quinohemoprotein Alcohol Dehydrogenase From Pseudomonas Putida Hk5.
Structure V. 10 837 2002
PubMed-ID: 12057198  |  Reference-DOI: 10.1016/S0969-2126(02)00774-8
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TYPE II QUINOHEMOPROTEIN ALCOHOL DEHYDROGENASE
    ChainsA
    EC Number1.1.99.-
    Organism ScientificPSEUDOMONAS PUTIDA
    Organism Taxid303

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 6)

Asymmetric/Biological Unit (6, 6)
No.NameCountTypeFull Name
1ACN1Ligand/IonACETONE
2CA1Ligand/IonCALCIUM ION
3EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4GOL1Ligand/IonGLYCEROL
5HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
6PQQ1Ligand/IonPYRROLOQUINOLINE QUINONE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:173 , ASN A:250 , ASP A:295 , PQQ A:801BINDING SITE FOR RESIDUE CA A 802
2AC2SOFTWAREGLU A:59 , CYS A:105 , CYS A:106 , VAL A:109 , ARG A:111 , THR A:155 , GLY A:170 , GLY A:171 , ALA A:172 , GLU A:173 , THR A:230 , TRP A:232 , ASN A:250 , ASP A:295 , LYS A:322 , ASN A:382 , TRP A:383 , TRP A:460 , GLY A:524 , VAL A:525 , CA A:802 , ACN A:803 , HOH A:1114 , HOH A:1210BINDING SITE FOR RESIDUE PQQ A 801
3AC3SOFTWAREALA A:101 , ARG A:102 , PHE A:590 , CYS A:591 , CYS A:594 , HIS A:595 , ILE A:605 , PRO A:606 , LEU A:608 , SER A:611 , PHE A:619 , VAL A:623 , LEU A:631 , MET A:633 , PHE A:636 , LEU A:640 , HOH A:1091 , HOH A:1139 , HOH A:1242 , HOH A:1362 , HOH A:1514BINDING SITE FOR RESIDUE HEM A 901
4AC4SOFTWARETRP A:48 , ALA A:83 , ALA A:84 , SER A:85 , TYR A:515 , HOH A:1178 , HOH A:1528 , HOH A:1614 , HOH A:1683 , HOH A:1687 , HOH A:1735BINDING SITE FOR RESIDUE EPE A 804
5AC5SOFTWAREGLU A:173 , ASP A:295 , LYS A:322 , PRO A:377 , PQQ A:801BINDING SITE FOR RESIDUE ACN A 803
6AC6SOFTWAREASP A:51 , LEU A:52 , SER A:543 , HOH A:1392 , HOH A:1531BINDING SITE FOR RESIDUE GOL A 805

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:105 -A:106

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ser A:252 -Pro A:253
2Leu A:267 -Tyr A:268
3Trp A:374 -Pro A:375

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1KV9)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BACTERIAL_PQQ_2PS00364 Bacterial quinoprotein dehydrogenases signature 2.QHED_PSEPU254-275  1A:232-253
2CYTCPS51007 Cytochrome c family profile.QHED_PSEPU600-678  1A:578-656

(-) Exons   (0, 0)

(no "Exon" information available for 1KV9)

(-) 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:664
 aligned with QHED_PSEPU | Q8GR64 from UniProtKB/Swiss-Prot  Length:690

    Alignment length:664
                                    32        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       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682    
           QHED_PSEPU    23 AGVDEAAIRATEQAGGEWLSHGRTYAEQRFSPLKQIDASNVRSLGLAWYMDLDNTRGLEATPLFHDGVIYTSMSWSRVIAVDAASGKELWRYDPEVAKVKARTSCCDAVNRGVALWGDKVYVGTLDGRLIALDAKTGKAIWSQQTTDPAKPYSITGAPRVVKGKVIIGNGGAEYGVRGFVSAYDADTGKLAWRFYTVPGDPALPYEHPELREAAKTWQGDQYWKLGGGGTVWDSMAYDPELDLLYVGTGNGSPWNREVRSPGGGDNLYLSSILAIRPDTGKLAWHYQVTPGDSWDFTATQQITLAELNIDGKPRKVLMQAPKNGFFYVLDRTNGKLISAEKFGKVTWAEKVDLATGRPVEAPGVRYEKEPIVMWPSPFGAHNWHSMSFNPGTGLVYIPYQEVPGVYRNEGKDFVTRKAFNTAAGFADATDVPAAVVSGALLAWDPVKQKAAWKVPYPTHWNGGTLSTAGNLVFQGTAAGQMHAYSADKGEALWQFEAQSGIVAAPMTFELAGRQYVAIMAGWGGVATLTGGESMNLPGMKNRSRLLVFALDGKAQLPPPAPAPAKVERVPQPVTAAPEQVQAGKQLYGQFCSVCHGMGTISGGLIPDLRQSSDATREHFQQIVLQGALKPLGMPSFDDSLKPEEVEQIKLYVMSREYEDYMARH 686
               SCOP domains d1kv9a2 A:1-560 Quinoprotein alcohol dehydrogenase, N-terminal domain                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           d1kv9a1 A:561-664 Quinoprotein alcohol dehydrogenase, C-terminal domain                                  SCOP domains
               CATH domains 1kv9A01 A:1-561  [code=2.140.10.10, no name defined]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             1kv9A02 A:562-664 Cytochrome c                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh..................ee........hhh.eeeeeeee...........eee..eeeeeehhheeeeee.....eeeee....hhhhhhhh.........eee..eeeee....eeeeee.....eeeeee..............eee..eeee...........eeeeee.....eeeeee...........hhhhhhhhh.....hhhhhhee......eeee....eeeee...ee..hhhhhh..........eeeee......eeeeee..............eeeeeeee..eeeeeeee.....eeeeee.....eeeeee......eeee......eee..........eee.............eee....eeeeeeee..eee..hhhhh..........hhhhh...hhhhheeeeeeee....eeeeeeee.......eeee...eeeee....eeeeee.....eeeeee.........eeeee..eeeeeeee...hhhhhhhhhhhhh.......eeeeeee.........................hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.hhhhh........hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------BACTERIAL_PQQ_2       ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTC  PDB: A:578-656 UniProt: 600-678                                          -------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kv9 A   1 AGVDEAAIRATEQAGGEWLSHGRTYAEQRFSPLKQIDASNVRSLGLAWYMDLDNTRGLEATPLFHDGVIYTSMSWSRVIAVDAASGKELWRYDPEVAKVKARTSCCDAVNRGVALWGDKVYVGTLDGRLIALDAKTGKAIWSQQTTDPAKPYSITGAPRVVKGKVIIGNGGAEYGVRGFVSAYDADTGKLAWRFYTVPGDPALPYEHPELREAAKTWQGDQYWKLGGGGTVWDSMAYDPELDLLYVGTGNGSPWNREVRSPGGGDNLYLSSILAIRPDTGKLAWHYQVTPGDSWDFTATQQITLAELNIDGKPRKVLMQAPKNGFFYVLDRTNGKLISAEKFGKVTWAEKVDLATGRPVEAPGVRYEKEPIVMWPSPFGAHNWHSMSFNPGTGLVYIPYQEVPGVYRNEGKDFVTRKAFNTAAGFADATDVPAAVVSGALLAWDPVKQKAAWKVPYPTHWNGGTLSTAGNLVFQGTAAGQMHAYSADKGEALWQFEAQSGIVAAPMTFELAGRQYVAIMAGWGGVATLTGGESMNLPGMKNRSRLLVFALDGKAQLPPPAPAPAKVERVPQPVTAAPEQVQAGKQLYGQFCSVCHGMGTISGGLIPDLRQSSDATREHFQQIVLQGALKPLGMPSFDDSLKPEEVEQIKLYVMSREYEDYMARH 664
                                    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    

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1KV9)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (QHED_PSEPU | Q8GR64)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    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.
    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.
    GO:0070968    pyrroloquinoline quinone binding    Interacting selectively and non-covalently with pyrroloquinoline quinone, PQQ, the coenzyme or the prosthetic group of certain alcohol dehydrogenases and glucose dehydrogenases.
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.
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).

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 Related Entries

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(-) Related Entries Specified in the PDB File

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