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(-) Description

Title :  CRYSTAL STRUCTURE OF PQQC ACTIVE SITE MUTANT Y175F IN COMPLEX WITH PQQ
 
Authors :  S. Puehringer, R. Schwarzenbacher
Date :  28 May 09  (Deposition) - 12 May 10  (Release) - 14 Jul 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A,D
Keywords :  Pqqc, Pqq Biosynthesis, Oxidase, Complex, All Helical, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Puehringer, J. Rosefigura, M. Metlitzky, H. Toyama, J. P. Klinman, R. Schwarzenbacher
Structural Studies Of Mutant Forms Of The Pqq-Forming Enzym Pqqc In The Presence Of Product And Substrate
Proteins V. 78 2554 2010
PubMed-ID: 20602352  |  Reference-DOI: 10.1002/PROT.22769

(-) Compounds

Molecule 1 - PYRROLOQUINOLINE-QUINONE SYNTHASE
    Chains: A, D
    EC Number: 1.3.3.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PQQC
    Mutation: YES
    Organism Scientific: KLEBSIELLA PNEUMONIAE SUBSP. PNEUMONIAE
    Organism Taxid: 272620
    Strain: MGH 78578
    Synonym: PQQC, COENZYME PQQ SYNTHESIS PROTEIN C, PYRROLOQUINOLINE QUINONE BIOSYNTHESIS PROTEIN C

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2GOL4Ligand/IonGLYCEROL
3PQQ2Ligand/IonPYRROLOQUINOLINE QUINONE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:23 , HIS A:24 , ARG A:50 , TYR A:53 , GLN A:54 , LYS A:60 , HIS A:84 , TYR A:128 , SER A:144 , THR A:146 , ILE A:153 , HIS A:154 , ARG A:157 , PHE A:175 , ARG A:179 , LYS A:214 , CL A:261 , HOH A:295BINDING SITE FOR RESIDUE PQQ A 500
2AC2SOFTWARELYS A:76 , TRP A:77 , ARG A:80 , ARG A:185 , ASP A:186 , HIS A:189 , HOH A:390BINDING SITE FOR RESIDUE GOL A 259
3AC3SOFTWAREARG A:233 , HOH A:407 , THR D:226 , ALA D:230BINDING SITE FOR RESIDUE GOL A 260
4AC4SOFTWAREALA A:150 , HIS A:154 , ARG A:179 , PQQ A:500BINDING SITE FOR RESIDUE CL A 261
5AC5SOFTWARETYR D:23 , HIS D:24 , ARG D:50 , TYR D:53 , GLN D:54 , ILE D:57 , LYS D:60 , HIS D:84 , TYR D:128 , SER D:144 , THR D:146 , ILE D:153 , HIS D:154 , ARG D:157 , PHE D:175 , ARG D:179 , LYS D:214 , CL D:261 , HOH D:273BINDING SITE FOR RESIDUE PQQ D 500
6AC6SOFTWARELYS D:76 , TRP D:77 , ARG D:80 , ARG D:185 , ASP D:186 , HIS D:189BINDING SITE FOR RESIDUE GOL D 259
7AC7SOFTWARETYR A:29 , ALA A:32 , THR A:226 , ALA A:230 , ARG D:233 , HOH D:403BINDING SITE FOR RESIDUE GOL D 260
8AC8SOFTWAREALA D:150 , HIS D:154 , ARG D:179 , PQQ D:500BINDING SITE FOR RESIDUE CL D 261

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3HLX)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser A:87 -His A:88

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3HLX)

(-) Exons   (0, 0)

(no "Exon" information available for 3HLX)

(-) 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:254
 aligned with PQQC_KLEP7 | A6T9H1 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:254
                                                                                                                                                                                                                                                                                   251    
                                    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    
           PQQC_KLEP7     2 LITDTLSPQAFEEALRAKGDFYHIHHPYHIAMHNGNATREQIQGWVANRFYYQTTIPLKDAAIMANCPDAQTRRKWVQRILDHDGSHGEDGGIEAWLRLGEAVGLSRDDLLSERHVLPGVRFAVDAYLNFARRACWQEAACSSLTELFAPQIHQSRLDSWPQHYPWIKEEGYFYFRSRLSQANRDVEHGLALAKAYCDSAEKQNRMLEILQFKLDILWSMLDAMTMAYALQRPPYHTVTDKAAWHTTRLV----   -
               SCOP domains d3hlxa_ A: Coenzyme PQQ synthesis protein C, PqqC                                                                                                                                                                                                              SCOP domains
               CATH domains 3hlxA00 A:2-255 Heme Oxygenase; Chain A                                                                                                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hlx A   2 LITDTLSPQAFEEALRAKGDFYHIHHPYHIAMHNGNATREQIQGWVANRFYYQTTIPLKDAAIMANCPDAQTRRKWVQRILDHDGSHGEDGGIEAWLRLGEAVGLSRDDLLSERHVLPGVRFAVDAYLNFARRACWQEAACSSLTELFAPQIHQSRLDSWPQHYPWIKEEGYFFFRSRLSQANRDVEHGLALAKAYCDSAEKQNRMLEILQFKLDILWSMLDAMTMAYALQRPPYHTVTDKAAWHTTRLVLEHH 255
                                    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    


Chain D from PDB  Type:PROTEIN  Length:254
 aligned with PQQC_KLEP7 | A6T9H1 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:254
                                                                                                                                                                                                                                                                                   251    
                                    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    
           PQQC_KLEP7     2 LITDTLSPQAFEEALRAKGDFYHIHHPYHIAMHNGNATREQIQGWVANRFYYQTTIPLKDAAIMANCPDAQTRRKWVQRILDHDGSHGEDGGIEAWLRLGEAVGLSRDDLLSERHVLPGVRFAVDAYLNFARRACWQEAACSSLTELFAPQIHQSRLDSWPQHYPWIKEEGYFYFRSRLSQANRDVEHGLALAKAYCDSAEKQNRMLEILQFKLDILWSMLDAMTMAYALQRPPYHTVTDKAAWHTTRLV----   -
               SCOP domains d3hlxd_ D: Coenzyme PQQ synthesis protein C, PqqC                                                                                                                                                                                                              SCOP domains
               CATH domains 3hlxD00 D:2-255 Heme Oxygenase; Chain A                                                                                                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh..hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hlx D   2 LITDTLSPQAFEEALRAKGDFYHIHHPYHIAMHNGNATREQIQGWVANRFYYQTTIPLKDAAIMANCPDAQTRRKWVQRILDHDGSHGEDGGIEAWLRLGEAVGLSRDDLLSERHVLPGVRFAVDAYLNFARRACWQEAACSSLTELFAPQIHQSRLDSWPQHYPWIKEEGYFFFRSRLSQANRDVEHGLALAKAYCDSAEKQNRMLEILQFKLDILWSMLDAMTMAYALQRPPYHTVTDKAAWHTTRLVLEHH 255
                                    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
   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  (1, 2)

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

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HLX)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,D   (PQQC_KLEP7 | A6T9H1)
molecular function
    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:0033732    pyrroloquinoline-quinone synthase activity    Catalysis of the reaction: 6-(2-amino-2-carboxyethyl)-7,8-dioxo-1,2,3,4,7,8-hexahydroquinoline-2,4-dicarboxylate + 3 O(2) = 2 H(2)O + 2 H(2)O(2) + H(+) + pyrroloquinoline quinone.
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.
    GO:0018189    pyrroloquinoline quinone biosynthetic process    The chemical reactions and pathways resulting in the formation of the cofactor pyrroloquinoline quinone (PQQ); it is synthesized from a small peptide containing tyrosine and glutamic acid; these amino acids in the peptide are multiply cross-linked and the rest of the peptide is removed.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PQQC_KLEP7 | A6T9H1: 3hml 3hnh 4ny7

(-) Related Entries Specified in the PDB File

1otv PQQC
1otw PQQC IN COMPLEX WITH PQQ
3hml PQQC H154S MUTANT IN COMPLEX WITH PQQ
3hnh PQQC Y175S,R179S MUTANT IN COMPLEX WITH A REACTION INTERMEDIATE