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(-) Description

Title :  HYPOTHETICAL PROTEIN YFDW FROM E. COLI BOUND TO COENZYME A
 
Authors :  A. Gogos, J. Gorman, L. Shapiro, S. K. Burley, New York Sgx Research For Structural Genomics (Nysgxrc)
Date :  14 Aug 03  (Deposition) - 30 Sep 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Intertwined Dimer, Structural Genomics, Coenzyme A, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Gogos, J. Gorman, L. Shapiro
Structure Of Escherichia Coli Yfdw, A Type Iii Coa Transferase.
Acta Crystallogr. , Sect. D V. 60 507 2004
PubMed-ID: 14993676  |  Reference-DOI: 10.1107/S0907444904000034

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN YFDW
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSMT3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YFDW
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1COA1Ligand/IonCOENZYME A
2MPD7Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 1 (2, 16)
No.NameCountTypeFull Name
1COA2Ligand/IonCOENZYME A
2MPD14Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:15 , VAL A:18 , GLN A:19 , SER A:20 , ARG A:40 , LEU A:74 , ASN A:75 , THR A:76 , LYS A:77 , ASN A:98 , PHE A:99 , HIS A:100 , ALA A:103 , MET A:107 , ILE A:126 , LYS A:139 , ALA A:140 , ASP A:171 , MET A:202 , GLN A:275 , GLN A:277 , HOH A:1211 , HOH A:1302 , HOH A:1307 , HOH A:1329 , HOH A:1330 , HOH A:1339 , HOH A:1451 , HOH A:1453 , HOH A:1455BINDING SITE FOR RESIDUE COA A 500
2AC2SOFTWAREGLY A:160 , ARG A:243 , TRP A:262 , GLU A:263 , PRO A:266 , TYR A:269BINDING SITE FOR RESIDUE MPD A 600
3AC3SOFTWARETYR A:317BINDING SITE FOR RESIDUE MPD A 700
4AC4SOFTWAREPRO A:134 , THR A:331BINDING SITE FOR RESIDUE MPD A 800
5AC5SOFTWARETHR A:5 , ALA A:29 , TRP A:30 , GLY A:32 , ASN A:68 , PRO A:383 , ASP A:384 , LYS A:386BINDING SITE FOR RESIDUE MPD A 900
6AC6SOFTWAREGLN A:218 , ASP A:221 , LEU A:370 , HOH A:1257BINDING SITE FOR RESIDUE MPD A 1000
7AC7SOFTWARETRP A:158 , PRO A:230 , GLY A:235 , HOH A:1243 , HOH A:1244BINDING SITE FOR RESIDUE MPD A 1100
8AC8SOFTWAREGLU A:73 , THR A:395 , MET A:412 , LYS A:413 , HOH A:1272BINDING SITE FOR RESIDUE MPD A 1200

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Q6Y)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Tyr A:232 -Pro A:233

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Q6Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Q6Y)

(-) Exons   (0, 0)

(no "Exon" information available for 1Q6Y)

(-) 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:417
 aligned with FCTA_ECOLI | P69902 from UniProtKB/Swiss-Prot  Length:416

    Alignment length:417
                                                                                                                                                                                                                                                                                                                                                                                                                                                         416 
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410     | 
           FCTA_ECOLI     1 MSTPLQGIKVLDFTGVQSGPSCTQMLAWFGADVIKIERPGVGDVTRHQLRDIPDIDALYFTMLNSNKRSIELNTKTAEGKEVMEKLIREADILVENFHPGAIDHMGFTWEHIQEINPRLIFGSIKGFDECSPYVNVKAYENVAQAAGGAASTTGFWDGPPLVSAAALGDSNTGMHLLIGLLAALLHREKTGRGQRVTMSMQDAVLNLCRVKLRDQQRLDKLGYLEEYPQYPNGTFGDAVPRGGNAGGGGQPGWILKCKGWETDPNAYIYFTIQEQNWENTCKAIGKPEWITDPAYSTAHARQPHIFDIFAEIEKYTVTIDKHEAVAYLTQFDIPCAPVLSMKEISLDPSLRQSGSVVEVEQPLRGKYLTVGCPMKFSAFTPDIKAAPLLGEHTAAVLQELGYSDDEIAAMKQNHAI-   -
               SCOP domains d1q6ya_ A: Hypothetical protein YfdW                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1q6yA01 A:3-244,A:342-419 Crotonobetainyl-coa:carnitine coa-transferase; domain 1                                                                                                                                                                 1q6yA02 A:245-341 formyl-coa transferase, domain 3                                               1q6yA01 A:3-244,A:342-419                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------CoA_transf_3-1q6yA01 A:72-246                                                                                                                                                  ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee...hhhhhhhhhhhhh..eeeeee.....hhhhh.........hhhhhh.....eeee....hhhhhhhhhhhhhhh.eeee....hhhhhh..hhhhhhhhh...eeeeee.............hhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhhhhhh.............................eeeee..........eeeee.hhhhhhhhhhhhhhhhhhh.....hhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhh..eee..hhhhhhhhhhhhhh..eeeeee...eeeeee.....................hhhhhhhhh..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1q6y A   3 LSTPLQGIKVLDFTGVQSGPSCTQMLAWFGADVIKIERPGVGDVTRHQLRDIPDIDALYFTMLNSNKRSIELNTKTAEGKEVMEKLIREADILVENFHPGAIDHMGFTWEHIQEINPRLIFGSIKGFDECSPYVNVKAYENVAQAAGGAASTTGFWDGPPLVSAAALGDSNTGMHLLIGLLAALLHREKTGRGQRVTMSMQDAVLNLCRVKLRDQQRLDKLGYLEEYPQYPNGTFGDAVPRGGNAGGGGQPGWILKCKGWETDPNAYIYFTIQEQNWENTCKAIGKPEWITDPAYSTAHARQPHIFDIFAEIEKYTVTIDKHEAVAYLTQFDIPCAPVLSMKEISLDPSLRQSGSVVEVEQPLRGKYLTVGCPMKFSAFTPDIKAAPLLGEHTAAVLQELGYSDDEIAAMKQNHAIE 419
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412
   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: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (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

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UniProtKB/Swiss-Prot
        FCTA_ECOLI | P69902: 1pqy 1pt5 1pt7 1pt8 1q7e

(-) Related Entries Specified in the PDB File

1pqy HYPOTHETICAL PROTEIN YFDW FROM E. COLI RELATED ID: NYSGXRC-T783 RELATED DB: TARGETDB