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(-) Description

Title :  CRYSTAL STRUCTURE OF PQQC ACTIVE SITE MUTANT Y175S,R179S IN COMPLEX WITH A REACTION INTERMEDIATE
 
Authors :  S. Puehringer, R. Schwarzenbacher
Date :  31 May 09  (Deposition) - 12 May 10  (Release) - 14 Jul 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
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
    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

  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
1AHQ1Ligand/Ion(2S,7R,9R)-4,5-DIHYDROXY-2,3,6,7,8,9-HEXAHYDRO-1H-PYRROLO[2,3-F]QUINOLINE-2,7,9-TRICARBOXYLIC ACID
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1AHQ2Ligand/Ion(2S,7R,9R)-4,5-DIHYDROXY-2,3,6,7,8,9-HEXAHYDRO-1H-PYRROLO[2,3-F]QUINOLINE-2,7,9-TRICARBOXYLIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:23 , HIS A:24 , ARG A:50 , TYR A:53 , ILE A:57 , LYS A:60 , HIS A:84 , TYR A:128 , THR A:146 , GLU A:147 , ARG A:185 , LYS A:214 , HOH A:347BINDING SITE FOR RESIDUE AHQ A 259

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Pro A:162 -Gln A:163
2Gln A:163 -His A:164

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3HNH)

(-) 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:238
 aligned with PQQC_KLEP7 | A6T9H1 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:252
                                                                                                                                                                                                                                                                                   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 d3hnha_ A: Coenzyme PQQ synthesis protein C, PqqC                                                                                                                                                                                                            SCOP domains
               CATH domains 3hnhA00 A:2-253 Heme Oxygenase; Chain A                                                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.---.hhhhhhhhhhhhh..hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh-----------.......hhhhhhhhhhhhhhh....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3hnh A   2 LITDTLSPQAFEEALRAKGDFYHIHHPYHIAMHNGNATREQIQGWVANRFYYQTTIPLKDAAIMANCPDAQTRRKWVQRILDHDGS---DGGIEAWLRLGEAVGLSRDDLLSERHVLPGVRFAVDAYLNFARRACWQEAACSSLTELFA-----------PQHYPWIKEEGYFSFRSSLSQANRDVEHGLALAKAYCDSAEKQNRMLEILQFKLDILWSMLDAMTMAYALQRPPYHTVTDKAAWHTTRLVLE 253
                                    11        21        31        41        51        61        71        81     |  91       101       111       121       131       141        |-         -|      171       181       191       201       211       221       231       241       251  
                                                                                                                87  91                                                        150         162
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (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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  1.3.3.11
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

1otv PQQC
1otw PQQC IN COMPLEX WITH PQQ
3hlx PQQC Y175F MUTANT IN COMPLEX WITH PQQ
3hml PQQC H154S MUTANT IN COMPLEX WITH PQQ