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(-) Description

Title :  CRYSTAL STRUCTURE OF THE GLUTATHIONE-DEPENDENT FORMALDEHYDE-ACTIVATING ENZYME (GFA)
 
Authors :  A. M. Neculai, D. Neculai, J. A. Vorholt, S. Becker
Date :  11 Aug 04  (Deposition) - 23 Nov 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Zn-Enzyme, Formaldehyde, 3_10 Helix, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. M. Neculai, D. Neculai, C. Griesinger, J. A. Vorholt, S. Becker
A Dynamic Zinc Redox Switch
J. Biol. Chem. V. 280 2826 2005
PubMed-ID: 15548539  |  Reference-DOI: 10.1074/JBC.C400517200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLUTATHIONE-DEPENDENT FORMALDEHYDE-ACTIVATING ENZYME
    Chains: A, B, C, D
    EC Number: 4.4.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET16B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: GFA
    Organism Scientific: PARACOCCUS DENITRIFICANS
    Organism Taxid: 266
    Synonym: GFA

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 20)

Asymmetric Unit (3, 20)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
2SO47Ligand/IonSULFATE ION
3ZN8Ligand/IonZINC ION
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO44Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 7)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2SO43Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:33 , CYS A:35 , CYS A:101 , CYS A:104BINDING SITE FOR RESIDUE ZN A 200
02AC2SOFTWARECYS A:54 , CYS A:56 , CYS A:59BINDING SITE FOR RESIDUE ZN A 201
03AC3SOFTWARECYS B:33 , CYS B:35 , CYS B:101 , CYS B:104BINDING SITE FOR RESIDUE ZN B 200
04AC4SOFTWARECYS B:54 , CYS B:56 , CYS B:59BINDING SITE FOR RESIDUE ZN B 201
05AC5SOFTWARECYS C:33 , CYS C:35 , CYS C:101 , CYS C:104BINDING SITE FOR RESIDUE ZN C 200
06AC6SOFTWARECYS C:54 , CYS C:56 , CYS C:59BINDING SITE FOR RESIDUE ZN C 201
07AC7SOFTWARECYS D:33 , CYS D:35 , CYS D:101 , CYS D:104BINDING SITE FOR RESIDUE ZN D 200
08AC8SOFTWARECYS D:54 , CYS D:56 , CYS D:59BINDING SITE FOR RESIDUE ZN D 201
09AC9SOFTWAREALA A:94 , PRO A:95 , ILE A:96 , ARG A:98 , HOH A:583BINDING SITE FOR RESIDUE SO4 A 501
10BC1SOFTWARELYS B:58 , ALA B:94 , PRO B:95 , ILE B:96 , ARG B:98 , GOL B:601 , HOH B:662BINDING SITE FOR RESIDUE SO4 B 502
11BC2SOFTWARELYS C:58 , PRO C:95 , ILE C:96 , ARG C:98BINDING SITE FOR RESIDUE SO4 C 503
12BC3SOFTWAREALA C:14 , LYS C:20 , GLN C:69 , GLU C:128 , HOH C:640BINDING SITE FOR RESIDUE SO4 C 504
13BC4SOFTWARELYS D:58 , ALA D:94 , PRO D:95 , ILE D:96 , ARG D:98BINDING SITE FOR RESIDUE SO4 D 505
14BC5SOFTWAREALA D:14 , LYS D:20 , GLN D:69 , GLU D:128 , HOH D:619 , HOH D:635BINDING SITE FOR RESIDUE SO4 D 506
15BC6SOFTWAREPRO A:177 , ARG D:161 , ARG D:165 , HOH D:636BINDING SITE FOR RESIDUE SO4 D 507
16BC7SOFTWARELYS B:58 , VAL B:90 , ASN B:91 , ALA B:94 , ILE B:96 , ARG B:98 , SO4 B:502 , HOH B:610 , HOH B:631BINDING SITE FOR RESIDUE GOL B 601
17BC8SOFTWAREALA B:14 , GLN B:69 , GLU B:128 , HOH B:625 , HOH B:646BINDING SITE FOR RESIDUE GOL B 602
18BC9SOFTWAREGLN B:47 , VAL B:73 , GLY B:74 , HOH B:638BINDING SITE FOR RESIDUE GOL B 603
19CC1SOFTWARELEU C:179 , ALA C:182 , HOH C:605 , HOH C:635 , HOH C:641BINDING SITE FOR RESIDUE GOL C 604
20CC2SOFTWAREPRO D:118 , LEU D:122 , LEU D:179 , ALA D:182BINDING SITE FOR RESIDUE GOL D 605

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X6M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1X6M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1X6M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1X6M)

(-) Exons   (0, 0)

(no "Exon" information available for 1X6M)

(-) 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:196
 aligned with GFA_PARDE | Q51669 from UniProtKB/Swiss-Prot  Length:194

    Alignment length:196
                              1                                                                                                                                                                                                 
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188      
            GFA_PARDE     - --MVDTSGVKIHPAVDNGIKPAQPGFAGGTLHCKCSTNPVRVAVRAQTAHNHVCGCTKCWKPEGAIFSQVAVVGRDALEVLEGAEKLEIVNAEAPIQRHRCRDCGVHMYGRIENRDHPFYGLDFVHTELSDEDGWSAPEFAAFVSSIIESGVDPSRMEAIRARLRELGLEPYDALSPPLMDAIATHIAKRSGALAA 194
               SCOP domains d1x6ma_ A: Glutathione-dependent formaldehyde-activating enzyme, Gfa                                                                                                                                 SCOP domains
               CATH domains 1x6mA00 A:1-196 glutathione-dependent formaldehyde- activating enzyme (gfa)                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhh............eeee........eeee....eeeeee.............eeeeeeehhheeeee.hhheee......eeeeee.....eeeeee.........eeee.hhh..........eee.hhhhhhh...hhhhhhhhhhhhhh..ee.....hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1x6m A   1 GHMVDTSGVKIHPAVDNGIKPAQPGFAGGTLHCKCSTNPVRVAVRAQTAHNHVCGCTKCWKPEGAIFSQVAVVGRDALEVLEGAEKLEIVNAEAPIQRHRCRDCGVHMYGRIENRDHPFYGLDFVHTELSDEDGWSAPEFAAFVSSIIESGVDPSRMEAIRARLRELGLEPYDALSPPLMDAIATHIAKRSGALAA 196
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190      


Chain B from PDB  Type:PROTEIN  Length:196
 aligned with GFA_PARDE | Q51669 from UniProtKB/Swiss-Prot  Length:194

    Alignment length:196
                              1                                                                                                                                                                                                 
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188      
            GFA_PARDE     - --MVDTSGVKIHPAVDNGIKPAQPGFAGGTLHCKCSTNPVRVAVRAQTAHNHVCGCTKCWKPEGAIFSQVAVVGRDALEVLEGAEKLEIVNAEAPIQRHRCRDCGVHMYGRIENRDHPFYGLDFVHTELSDEDGWSAPEFAAFVSSIIESGVDPSRMEAIRARLRELGLEPYDALSPPLMDAIATHIAKRSGALAA 194
               SCOP domains d1x6mb_ B: Glutathione-dependent formaldehyde-activating enzyme, Gfa                                                                                                                                 SCOP domains
               CATH domains 1x6mB00 B:1-196 glutathione-dependent formaldehyde- activating enzyme (gfa)                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhh............eeee........eeee....eeeeee.............eeeeeeehhheeeee.hhheee.......eeeee.....eeeee..........eeee.hhh..........eee.hhhhhhh...hhhhhhhhhhhhhh..ee.....hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1x6m B   1 GHMVDTSGVKIHPAVDNGIKPAQPGFAGGTLHCKCSTNPVRVAVRAQTAHNHVCGCTKCWKPEGAIFSQVAVVGRDALEVLEGAEKLEIVNAEAPIQRHRCRDCGVHMYGRIENRDHPFYGLDFVHTELSDEDGWSAPEFAAFVSSIIESGVDPSRMEAIRARLRELGLEPYDALSPPLMDAIATHIAKRSGALAA 196
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190      


Chain C from PDB  Type:PROTEIN  Length:194
 aligned with GFA_PARDE | Q51669 from UniProtKB/Swiss-Prot  Length:194

    Alignment length:194
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190    
            GFA_PARDE     1 MVDTSGVKIHPAVDNGIKPAQPGFAGGTLHCKCSTNPVRVAVRAQTAHNHVCGCTKCWKPEGAIFSQVAVVGRDALEVLEGAEKLEIVNAEAPIQRHRCRDCGVHMYGRIENRDHPFYGLDFVHTELSDEDGWSAPEFAAFVSSIIESGVDPSRMEAIRARLRELGLEPYDALSPPLMDAIATHIAKRSGALAA 194
               SCOP domains d1x6mc_ C: Glutathione-dependent formaldehyde-activating enzyme, Gfa                                                                                                                               SCOP domains
               CATH domains 1x6mC00 C:3-196 glutathione-dependent formaldehyde- activating enzyme (gfa)                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh............eeee........eeee....eeeeee.............eeeeeeehhheeeee.hhheee......eeeeee.....eeeeee.........eeee.hhh........eeeee.hhhhhhh...hhhhhhhhhhhhhh..ee.....hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1x6m C   3 MVDTSGVKIHPAVDNGIKPAQPGFAGGTLHCKCSTNPVRVAVRAQTAHNHVCGCTKCWKPEGAIFSQVAVVGRDALEVLEGAEKLEIVNAEAPIQRHRCRDCGVHMYGRIENRDHPFYGLDFVHTELSDEDGWSAPEFAAFVSSIIESGVDPSRMEAIRARLRELGLEPYDALSPPLMDAIATHIAKRSGALAA 196
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192    


Chain D from PDB  Type:PROTEIN  Length:194
 aligned with GFA_PARDE | Q51669 from UniProtKB/Swiss-Prot  Length:194

    Alignment length:194
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190    
            GFA_PARDE     1 MVDTSGVKIHPAVDNGIKPAQPGFAGGTLHCKCSTNPVRVAVRAQTAHNHVCGCTKCWKPEGAIFSQVAVVGRDALEVLEGAEKLEIVNAEAPIQRHRCRDCGVHMYGRIENRDHPFYGLDFVHTELSDEDGWSAPEFAAFVSSIIESGVDPSRMEAIRARLRELGLEPYDALSPPLMDAIATHIAKRSGALAA 194
               SCOP domains d1x6md_ D: Glutathione-dependent formaldehyde-activating enzyme, Gfa                                                                                                                               SCOP domains
               CATH domains 1x6mD00 D:3-196 glutathione-dependent formaldehyde- activating enzyme (gfa)                                                                                                                        CATH domains
           Pfam domains (1) -------------------------------------------------GFA-1x6mD01 D:52-146                                                                           -------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------GFA-1x6mD02 D:52-146                                                                           -------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -------------------------------------------------GFA-1x6mD03 D:52-146                                                                           -------------------------------------------------- Pfam domains (3)
           Pfam domains (4) -------------------------------------------------GFA-1x6mD04 D:52-146                                                                           -------------------------------------------------- Pfam domains (4)
         Sec.struct. author .........hhhhh............eeee........eeee....eeeeee.............eeeeeeehhheeeee.hhheee......eeeeee.....eeeeee.........eeee.hhh..........eee.hhhhhhh...hhhhhhhhhhhhhh..ee.....hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1x6m D   3 MVDTSGVKIHPAVDNGIKPAQPGFAGGTLHCKCSTNPVRVAVRAQTAHNHVCGCTKCWKPEGAIFSQVAVVGRDALEVLEGAEKLEIVNAEAPIQRHRCRDCGVHMYGRIENRDHPFYGLDFVHTELSDEDGWSAPEFAAFVSSIIESGVDPSRMEAIRARLRELGLEPYDALSPPLMDAIATHIAKRSGALAA 196
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192
   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, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: GFA] (2)
(-)
Family: GFA (2)
(-)
Paracoccus denitrificans (2)
1aGFA-1x6mD01D:52-146
1bGFA-1x6mD02D:52-146
1cGFA-1x6mD03D:52-146
1dGFA-1x6mD04D:52-146

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (GFA_PARDE | Q51669)
molecular function
    GO:0051907    S-(hydroxymethyl)glutathione synthase activity    Catalysis of the reaction: S-(hydroxymethyl)glutathione = formaldehyde + glutathione.
    GO:0016846    carbon-sulfur lyase activity    Catalysis of the elimination of hydrogen sulfide or substituted H2S.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0046294    formaldehyde catabolic process    The chemical reactions and pathways resulting in the breakdown of formaldehyde (methanal, H2C=O), the simplest aldehyde.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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  1x6m
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 Related Entries

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

UniProtKB/Swiss-Prot
        GFA_PARDE | Q51669: 1xa8

(-) Related Entries Specified in the PDB File

1xa8 THE SAME PROTEIN COMPLEXED WITH GLUTATHIONE