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(-) Description

Title :  P-CRESOL METHYLHYDROXYLASE: ALTERATION OF THE STRUCTURE OF THE FLAVOPROTEIN SUBUNIT UPON ITS BINDING TO THE CYTOCHROME SUBUNIT
 
Authors :  L. M. Cunane, Z. -W. Chen, W. S. Mcintire, F. S. Mathews
Date :  15 Dec 04  (Deposition) - 08 Mar 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Flavoprotein, Electron-Transfer, Fad, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. M. Cunane, Z. -W. Chen, W. S. Mcintire, F. S. Mathews
P-Cresol Methylhydroxylase: Alteration Of The Structure Of The Flavoprotein Subunit Upon Its Binding To The Cytochrome Subunit
Biochemistry V. 44 2963 2005
PubMed-ID: 15723539  |  Reference-DOI: 10.1021/BI048020R
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 4-CRESOL DEHYDROGENASE [HYDROXYLATING] FLAVOPROTEIN SUBUNIT
    Chains: A
    EC Number: 1.17.99.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: DH5ALPHA
    Expression System Taxid: 562
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 303
    Synonym: P-CRESOL METHYLHYDROXYLASE, PCMH

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric Unit (4, 6)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2CL1Ligand/IonCHLORIDE ION
3FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
4GOL2Ligand/IonGLYCEROL
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1ACY4Ligand/IonACETIC ACID
2CL-1Ligand/IonCHLORIDE ION
3FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
4GOL4Ligand/IonGLYCEROL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:48 , GLY A:94 , GLY A:96 , SER A:97BINDING SITE FOR RESIDUE CL A 1703
2AC2SOFTWARETRP A:85 , THR A:86 , SER A:88 , THR A:89 , GLY A:90 , ARG A:91 , ASN A:92 , PHE A:93 , SER A:153 , ALA A:154 , PRO A:155 , ALA A:159 , GLY A:160 , GLY A:163 , ASN A:164 , GLY A:169 , VAL A:170 , TYR A:172 , CYS A:231 , GLU A:380 , TYR A:384 , TRP A:394 , ARG A:474 , ARG A:512 , ACY A:1701 , HOH A:1709 , HOH A:1713 , HOH A:1720 , HOH A:1755 , HOH A:1857BINDING SITE FOR RESIDUE FAD A 599
3AC3SOFTWARETYR A:95 , TRP A:394 , TYR A:473 , ARG A:474 , FAD A:599 , HOH A:2506BINDING SITE FOR RESIDUE ACY A 1701
4AC4SOFTWAREARG A:91 , SER A:156 , ALA A:157 , ILE A:158 , LEU A:378 , HOH A:2174BINDING SITE FOR RESIDUE ACY A 1702
5AC5SOFTWAREILE A:116 , LYS A:118 , ILE A:119 , HOH A:2034 , HOH A:2076 , HOH A:2142 , HOH A:2182 , HOH A:2240 , HOH A:2391BINDING SITE FOR RESIDUE GOL A 1704
6AC6SOFTWAREVAL A:51 , GLU A:52 , ARG A:445 , HOH A:1864 , HOH A:2146 , HOH A:2328 , HOH A:2404BINDING SITE FOR RESIDUE GOL A 1705

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:154 -Pro A:155
2Gln A:363 -Pro A:364

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FAD_PCMHPS51387 PCMH-type FAD-binding domain profile.DH4C_PSEPU54-268  1A:54-268
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FAD_PCMHPS51387 PCMH-type FAD-binding domain profile.DH4C_PSEPU54-268  2A:54-268

(-) Exons   (0, 0)

(no "Exon" information available for 1WVF)

(-) 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:515
 aligned with DH4C_PSEPU | P09788 from UniProtKB/Swiss-Prot  Length:521

    Alignment length:515
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516     
           DH4C_PSEPU     7 AVLPKGVTQGEFNKAVQKFRALLGDDNVLVESDQLVPYNKIMMPVENAAHAPSAAVTATTVEQVQGVVKICNEHKIPIWTISTGRNFGYGSAAPVQRGQVILDLKKMNKIIKIDPEMCYALVEPGVTFGQMYDYIQENNLPVMLSFSAPSAIAGPVGNTMDRGVGYTPYGEHFMMQCGMEVVLANGDVYRTGMGGVPGSNTWQIFKWGYGPTLDGMFTQANYGICTKMGFWLMPKPPVFKPFEVIFEDEADIVEIVDALRPLRMSNTIPNSVVIASTLWEAGSAHLTRAQYTTEPGHTPDSVIKQMQKDTGMGAWNLYAALYGTQEQVDVNWKIVTDVFKKLGKGRIVTQEEAGDTQPFKYRAQLMSGVPNLQEFGLYNWRGGGGSMWFAPVSEARGSECKKQAAMAKRVLHKYGLDYVAEFIVAPRDMHHVIDVLYDRTNPEETKRADACFNELLDEFEKEGYAVYRVNTRFQDRVAQSYGPVKRKLEHAIKRAVDPNNILAPGRSGIDLNNDF 521
               SCOP domains d1wvfa2 A:7-242 automated matches                                                                                                                                                                                                           d1wvfa1 A:243-521 automated matches                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1wvfA01 A:7-114 Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2                        1wvfA02 A:115-242  [code=3.30.465.10, no name defined]                                                                          1wvfA03 A:243-473 Vanillyl-alcohol Oxidase; Chain A, domain 3                                                                                                                                                                          1wvfA04 A:474-521                                CATH domains
               Pfam domains ---------------------------------------------------FAD_binding_4-1wvfA02 A:58-198                                                                                                               -----------------------------------------------------------------------FAD-oxidase_C-1wvfA01 A:270-513                                                                                                                                                                                                                     -------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhh...ee.hhhhhhhhhh.....hhhhhh..eeee..hhhhhhhhhhhhhhhh..eeee..................eeee......eeeee....eeee....hhhhhhhhhhhh...ee..........hhhhhhhh.........hhhh.eeeeeee.....eee.hhhhh................hhhhhh.....eeeeeeee.ee...eeeeeeeee.hhhhhhhhhhhhhhhhhh......eeeeehhhhhhhh..hhhhh.......hhhhhhhhhhhhh...eeeeeeeeehhhhhhhhhhhhhhhhhhhh..eeeehhhhh...hhhhhhhhhh....hhhhhhhhh...eeeeee..eee.hhhhhhhhhhhhhhhhhhh.....eeeee...eeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------FAD_PCMH  PDB: A:54-268 UniProt: 54-268                                                                                                                                                                                ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wvf A   7 AVLPKGVTQGEFNKAVQKFRALLGDDNVLVESDQLVPYNKIMMPVENAAHAPSAAVTATTVEQVQGVVKICNEHKIPIWTISTGRNFGYGSAAPVQRGQVILDLKKMNKIIKIDPEMCYALVEPGVTFGQMYDYIQENNLPVMLSFSAPSAIAGPVGNTMDRGVGYTPYGEHFMMQCGMEVVLANGDVYRTGMGGVPGSNTWQIFKWGYGPTLDGMFTQANYGICTKMGFWLMPKPPVFKPFEVIFEDEADIVEIVDALRPLRMSNTIPNSVVIASTLWEAGSAHLTRAQYTTEPGHTPDSVIKQMQKDTGMGAWNLYAALYGTQEQVDVNWKIVTDVFKKLGKGRIVTQEEAGDTQPFKYRAQLMSGVPNLQEFGLYNWRGGGGSMWFAPVSEARGSECKKQAAMAKRVLHKYGLDYVAEFIVAPRDMHHVIDVLYDRTNPEETKRADACFNELLDEFEKEGYAVYRVNTRFQDRVAQSYGPVKRKLEHAIKRAVDPNNILAPGRSGIDLNNDF 521
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516
   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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (4, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: FAD-oxidase_C (26)
(-)
Clan: FAD_PCMH (53)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (DH4C_PSEPU | P09788)
molecular function
    GO:0018695    4-cresol dehydrogenase (hydroxylating) activity    Catalysis of the reaction: 4-cresol + acceptor + H2O = 4-hydroxybenzaldehyde + reduced acceptor.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    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: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
        DH4C_PSEPU | P09788: 1dii 1diq 1wve

(-) Related Entries Specified in the PDB File

1dii FLAVOCYTOCHROME P-CRESOL METHYLHYDROXYLASE AND ITS ENZYME- SUBSTRATE COMPLEX
1diq FLAVOCYTOCHROME P-CRESOL METHYLHYDROXYLASE AND ITS ENZYME- SUBSTRATE COMPLEX
1wve THE SAME PROTEIN COMPLEXED WITH FLAVOCYTOCHROME C AND HEME