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(-) Description

Title :  CRYSTAL STRUCTURE OF THE APO-FORM OF THE YFDW GENE PRODUCT OF E. COLI
 
Authors :  A. Gruez, V. Roig-Zamboni, C. Valencia, V. Campanacci, C. Cambillau
Date :  23 Jun 03  (Deposition) - 09 Sep 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Coa Transferase, Oxalate, Acetyl-Coa, E. Coli, Structural Genomics, Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Gruez, V. Roig-Zamboni, C. Valencia, V. Campanacci, C. Cambillau
The Crystal Structure Of The Escherichia Coli Yfdw Gene Product Reveals A New Fold Of Two Interlaced Rings Identifying A Wide Family Of Coa Transferases.
J. Biol. Chem. V. 278 34582 2003
PubMed-ID: 12844490  |  Reference-DOI: 10.1074/JBC.C300282200

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN YFDW
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDEST17
    Expression System Strain: TUNER(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMIDE
    Gene: YFDW OR B2374 OR SF2441
    Organism Common: ,
    Organism Scientific: ESCHERICHIA COLI, SHIGELLA FLEXNERI
    Organism Taxid: 562,623
    Strain: K12, K12

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric/Biological Unit (2, 10)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2PO48Ligand/IonPHOSPHATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:139 , GLU A:140 , ASP A:169 , PO4 A:602 , HOH A:712 , HOH A:804 , HOH A:964 , GLY B:248 , HOH B:703 , HOH B:705BINDING SITE FOR RESIDUE PO4 A 601
02AC2SOFTWAREVAL A:16 , GLN A:48 , TYR A:59 , TYR A:139 , PO4 A:601 , PO4 A:605 , GLY B:248 , GLY B:249 , GLN B:250BINDING SITE FOR RESIDUE PO4 A 602
03AC3SOFTWAREGLY A:249 , GLN A:250 , VAL B:16 , GLN B:48 , TYR B:59 , TYR B:139 , PO4 B:604 , PO4 B:606BINDING SITE FOR RESIDUE PO4 B 603
04AC4SOFTWAREGLY A:248 , HOH A:709 , TYR B:139 , GLU B:140 , ASP B:169 , PO4 B:603 , HOH B:720 , HOH B:748 , HOH B:763BINDING SITE FOR RESIDUE PO4 B 604
05AC5SOFTWAREVAL A:44 , GLN A:48 , TYR A:139 , PO4 A:602 , GLN B:250 , GLN B:273BINDING SITE FOR RESIDUE PO4 A 605
06AC6SOFTWAREGLN A:250 , GLN A:273 , GLN B:48 , TYR B:139 , PO4 B:603BINDING SITE FOR RESIDUE PO4 B 606
07AC7SOFTWAREHIS A:322 , LEU A:339 , GLU A:343 , ASP A:347 , HOH A:833 , TYR B:133BINDING SITE FOR RESIDUE PO4 A 607
08AC8SOFTWARETYR A:133 , HIS B:322 , LEU B:339 , GLU B:343 , ASP B:347 , HOH B:800BINDING SITE FOR RESIDUE PO4 B 608
09AC9SOFTWARETRP A:28 , PRO A:381 , ASP A:382BINDING SITE FOR RESIDUE GOL A 701
10BC1SOFTWAREALA B:27 , TRP B:28 , PRO B:381 , ASP B:382BINDING SITE FOR RESIDUE GOL B 702

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PT7)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:230 -Pro A:231
2Tyr B:230 -Pro B:231

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PT7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1PT7)

(-) Exons   (0, 0)

(no "Exon" information available for 1PT7)

(-) 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:415
 aligned with FCTA_ECOLI | P69902 from UniProtKB/Swiss-Prot  Length:416

    Alignment length:415
                                    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       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411     
           FCTA_ECOLI     2 STPLQGIKVLDFTGVQSGPSCTQMLAWFGADVIKIERPGVGDVTRHQLRDIPDIDALYFTMLNSNKRSIELNTKTAEGKEVMEKLIREADILVENFHPGAIDHMGFTWEHIQEINPRLIFGSIKGFDECSPYVNVKAYENVAQAAGGAASTTGFWDGPPLVSAAALGDSNTGMHLLIGLLAALLHREKTGRGQRVTMSMQDAVLNLCRVKLRDQQRLDKLGYLEEYPQYPNGTFGDAVPRGGNAGGGGQPGWILKCKGWETDPNAYIYFTIQEQNWENTCKAIGKPEWITDPAYSTAHARQPHIFDIFAEIEKYTVTIDKHEAVAYLTQFDIPCAPVLSMKEISLDPSLRQSGSVVEVEQPLRGKYLTVGCPMKFSAFTPDIKAAPLLGEHTAAVLQELGYSDDEIAAMKQNHAI 416
               SCOP domains d1pt7a_ A: Hypothetical protein YfdW                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1pt7A01 A:2-242,A:340-416 Crotonobetainyl-coa:carnitine coa-transferase; domain 1                                                                                                                                                                1pt7A02 A:243-339 formyl-coa transferase, domain 3                                               1pt7A01 A:2-242,A:340-416                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee....hhhhhhhhhhhhh..eeeeee.....hhhhh.........hhhhhh.....eeee....hhhhhhhhhhhhhhh.eeee....hhhhhh..hhhhhhhhh...eeeeee.............hhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhhhhhh.............................eeeee..........eeeee.hhhhhhhhhhhhhhhhhh......hhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhh..eee..hhhhhhhhhhhhhh..eeeeee...eeeeee....ee...............hhhhhhhhh..hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pt7 A   2 STPLQGIKVLDFTGVQSGPSCTQMLAWFGADVIKIERPGVGDVTRHQLRDIPDIDALYFTMLNSNKRSIELNTKTAEGKEVMEKLIREADILVENFHPGAIDHMGFTWEHIQEINPRLIFGSIKGFDECSPYVNVKAYENVAQAAGGAASTTGFWDGPPLVSAAALGDSNTGMHLLIGLLAALLHREKTGRGQRVTMSMQDAVLNLCRVKLRDQQRLDKLGYLEEYPQYPNGTFGDAVPRGGNAGGGGQPGWILKCKGWETDPNAYIYFTIQEQNWENTCKAIGKPEWITDPAYSTAHARQPHIFDIFAEIEKYTVTIDKHEAVAYLTQFDIPCAPVLSMKEISLDPSLRQSGSVVEVEQPLRGKYLTVGCPMKFSAFTPDIKAAPLLGEHTAAVLQELGYSDDEIAAMKQNHAI 416
                                    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       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411     


Chain B from PDB  Type:PROTEIN  Length:415
 aligned with FCTA_ECOLI | P69902 from UniProtKB/Swiss-Prot  Length:416

    Alignment length:415
                                    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       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411     
           FCTA_ECOLI     2 STPLQGIKVLDFTGVQSGPSCTQMLAWFGADVIKIERPGVGDVTRHQLRDIPDIDALYFTMLNSNKRSIELNTKTAEGKEVMEKLIREADILVENFHPGAIDHMGFTWEHIQEINPRLIFGSIKGFDECSPYVNVKAYENVAQAAGGAASTTGFWDGPPLVSAAALGDSNTGMHLLIGLLAALLHREKTGRGQRVTMSMQDAVLNLCRVKLRDQQRLDKLGYLEEYPQYPNGTFGDAVPRGGNAGGGGQPGWILKCKGWETDPNAYIYFTIQEQNWENTCKAIGKPEWITDPAYSTAHARQPHIFDIFAEIEKYTVTIDKHEAVAYLTQFDIPCAPVLSMKEISLDPSLRQSGSVVEVEQPLRGKYLTVGCPMKFSAFTPDIKAAPLLGEHTAAVLQELGYSDDEIAAMKQNHAI 416
               SCOP domains d1pt7b_ B: Hypothetical protein YfdW                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1pt7B01 B:2-242,B:340-416 Crotonobetainyl-coa:carnitine coa-transferase; domain 1                                                                                                                                                                1pt7B02 B:243-339 formyl-coa transferase, domain 3                                               1pt7B01 B:2-242,B:340-416                                                     CATH domains
           Pfam domains (1) --------------------------------------------------------------------CoA_transf_3-1pt7B01 B:70-244                                                                                                                                                  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------CoA_transf_3-1pt7B02 B:70-244                                                                                                                                                  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .......eeee....hhhhhhhhhhhhh..eeeeee.....hhhhh.........hhhhhh.....eeee....hhhhhhhhhhhhhhh.eeee....hhhhhh..hhhhhhhhh...eeeeee.............hhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhhhhhh.............................eeeee..........eeeee.hhhhhhhhhhhh.hhhhh......hhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhh....eee..hhhhhhhhhhhhhh..eeeeee...eeeeee....ee...............hhhhhhhhh..hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pt7 B   2 STPLQGIKVLDFTGVQSGPSCTQMLAWFGADVIKIERPGVGDVTRHQLRDIPDIDALYFTMLNSNKRSIELNTKTAEGKEVMEKLIREADILVENFHPGAIDHMGFTWEHIQEINPRLIFGSIKGFDECSPYVNVKAYENVAQAAGGAASTTGFWDGPPLVSAAALGDSNTGMHLLIGLLAALLHREKTGRGQRVTMSMQDAVLNLCRVKLRDQQRLDKLGYLEEYPQYPNGTFGDAVPRGGNAGGGGQPGWILKCKGWETDPNAYIYFTIQEQNWENTCKAIGKPEWITDPAYSTAHARQPHIFDIFAEIEKYTVTIDKHEAVAYLTQFDIPCAPVLSMKEISLDPSLRQSGSVVEVEQPLRGKYLTVGCPMKFSAFTPDIKAAPLLGEHTAAVLQELGYSDDEIAAMKQNHAI 416
                                    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       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411
   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: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: CoA_transf_3] (25)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (FCTA_ECOLI | P69902)
molecular function
    GO:0008410    CoA-transferase activity    Catalysis of the transfer of a coenzyme A (CoA) group from one compound (donor) to another (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:0033608    formyl-CoA transferase activity    Catalysis of the reaction: formyl-CoA + oxalate = formate + oxalyl-CoA.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0071468    cellular response to acidic pH    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pH stimulus with pH < 7. pH is a measure of the acidity or basicity of an aqueous solution.
    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.
    GO:0033611    oxalate catabolic process    The chemical reactions and pathways resulting in the breakdown of oxalate, the organic acid ethanedioate.

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 Related Entries

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

UniProtKB/Swiss-Prot
        FCTA_ECOLI | P69902: 1pqy 1pt5 1pt8 1q6y 1q7e

(-) Related Entries Specified in the PDB File

1pt5 PROTEIN COMPLEX WITH ACETYL-COA