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(-) Description

Title :  CRYSTAL STRUCTURE OF YFDW PROTEIN FROM E. COLI
 
Authors :  A. Gogos, J. Gorman, L. Shapiro, S. K. Burley, New York Sgx Research For Structural Genomics (Nysgxrc)
Date :  18 Aug 03  (Deposition) - 30 Sep 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Structural Genomics, Intertwined Dimer, 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 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  (3, 18)

Asymmetric Unit (3, 18)
No.NameCountTypeFull Name
1MET2Mod. Amino AcidMETHIONINE
2MPD7Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3MSE9Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (3, 36)
No.NameCountTypeFull Name
1MET4Mod. Amino AcidMETHIONINE
2MPD14Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3MSE18Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:98 , PHE A:99 , HIS A:100 , PRO A:101 , ILE A:126 , LYS A:127 , GLY A:128 , LYS A:139 , ALA A:140 , HOH A:1625 , HOH A:1662BINDING SITE FOR RESIDUE MET A 500
2AC2SOFTWARETRP A:255 , PHE A:308 , ALA A:312 , GLU A:315 , HOH A:1395 , HOH A:1527BINDING SITE FOR RESIDUE MET A 600
3AC3SOFTWAREGLY A:160 , ARG A:243 , TRP A:262 , GLU A:263 , ASP A:265 , PRO A:266 , TYR A:269 , HOH A:1460BINDING SITE FOR RESIDUE MPD A 700
4AC4SOFTWAREGLU A:73 , LEU A:74 , ASN A:75 , THR A:395 , MSE A:412 , HIS A:416 , HOH A:1530 , HOH A:1536BINDING SITE FOR RESIDUE MPD A 800
5AC5SOFTWARETRP A:158 , PRO A:230 , GLN A:231 , GLY A:235 , HOH A:1387 , HOH A:1425BINDING SITE FOR RESIDUE MPD A 900
6AC6SOFTWAREALA A:285 , HOH A:1634BINDING SITE FOR RESIDUE MPD A 1000
7AC7SOFTWAREPRO A:134 , ALA A:328 , THR A:331 , HOH A:1493BINDING SITE FOR RESIDUE MPD A 1100
8AC8SOFTWARETHR A:5 , TRP A:30 , GLY A:32 , PRO A:383 , ASP A:384BINDING SITE FOR RESIDUE MPD A 1200
9AC9SOFTWARELYS A:11 , LEU A:13 , LEU A:88 , GLU A:91 , GLU A:401 , HOH A:1430 , HOH A:1558BINDING SITE FOR RESIDUE MPD A 1300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Q7E)

(-) 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 1Q7E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Q7E)

(-) Exons   (0, 0)

(no "Exon" information available for 1Q7E)

(-) 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:412
 aligned with FCTA_ECOLI | P69902 from UniProtKB/Swiss-Prot  Length:416

    Alignment length:419
                                                                                                                                                                                                                                                                                                                                                                                                                                                         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 d1q7ea_ A: Hypothetical protein YfdW                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1q7eA01 A:3-244,A:342-419 Crotonobetainyl-coa:carnitine coa-transferase; domain 1                                                                                                                                                                 1q7eA02 A:245-341 formyl-coa transferase, domain 3                                               1q7eA01 A:3-244,A:342-419                                                     -- CATH domains
               Pfam domains ---------------------------------------------------------------------CoA_transf_3-1q7eA01 A:72-246                                                                                                                                                  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee....hhhhhhhhhhhhh..eeeeee.....hhhhh.........hhhhhh.....eeee....hhhhhhhhhhhhhhh.eeee....-------.hhhhhhhhh...eeeeee.............hhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhhhhhh.............................eeeee..........eeeee.hhhhhhhhhhhh.hhhhhh.....hhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhh..eee..hhhhhhhhhhhhhh..eeeeee...eeeeee.....................hhhhhhhhh..hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1q7e A   3 LSTPLQGIKVLDFTGVQSGPSCTQmLAWFGADVIKIERPGVGDVTRHQLRDIPDIDALYFTmLNSNKRSIELNTKTAEGKEVmEKLIREADILVENFHP-------FTWEHIQEINPRLIFGSIKGFDECSPYVNVKAYENVAQAAGGAASTTGFWDGPPLVSAAALGDSNTGmHLLIGLLAALLHREKTGRGQRVTmSmQDAVLNLCRVKLRDQQRLDKLGYLEEYPQYPNGTFGDAVPRGGNAGGGGQPGWILKCKGWETDPNAYIYFTIQEQNWENTCKAIGKPEWITDPAYSTAHARQPHIFDIFAEIEKYTVTIDKHEAVAYLTQFDIPCAPVLSmKEISLDPSLRQSGSVVEVEQPLRGKYLTVGCPmKFSAFTPDIKAAPLLGEHTAAVLQELGYSDDEIAAmKQNHAIEMM 600
                                    12        22    |   32        42        52        62 |      72        82  |     92        |-      |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      |||
                                                   27-MSE                               64-MSE               85-MSE         101     109                                                                176-MSE                 200-MSE                                                                                                                                        343-MSE                          376-MSE                             412-MSE419||
                                                                                                                                                                                                                                 202-MSE                                                                                                                                                                                                                   500|
                                                                                                                                                                                                                                                                                                                                                                                                                                                            600
   Legend:   → Mismatch (orange background)
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    → 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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        FCTA_ECOLI | P69902: 1pqy 1pt5 1pt7 1pt8 1q6y

(-) Related Entries Specified in the PDB File

1pqy
1q6y RELATED ID: NYSGXRC-T783 RELATED DB: TARGETDB