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(-) Description

Title :  FORMYL-COA TRANSFERASE WITH ASPARTYL-FORMYL ANHYDIDE INTERMEDIATE
 
Authors :  C. L. Berthold, C. G. Toyota, N. G. J. Richards, Y. Lindqvist
Date :  11 Dec 07  (Deposition) - 25 Dec 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.89
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cytoplasm, Transferase, Class Iii Coa Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. L. Berthold, C. G. Toyota, N. G. J. Richards, Y. Lindqvist
Reinvestigation Of The Catalytic Mechanism Of Formyl-Coa Transferase, A Class Iii Coa- Transferase.
J. Biol. Chem. V. 283 6519 2008
PubMed-ID: 18162462  |  Reference-DOI: 10.1074/JBC.M709353200

(-) Compounds

Molecule 1 - FORMYL-COENZYME A TRANSFERASE
    Chains: A
    EC Number: 2.8.3.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-9A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: OXALOBACTER FORMIGENES
    Organism Taxid: 847
    Synonym: FORMYL-COA TRANSFERASE
 
Molecule 2 - FORMYL-COENZYME A TRANSFERASE
    Chains: B
    EC Number: 2.8.3.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-9A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: OXALOBACTER FORMIGENES
    Organism Taxid: 847
    Synonym: FORMYL-COA TRANSFERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
1A0A1Mod. Amino Acid(2S)-2-AMINO-4-(FORMYLOXY)-4-OXOBUTANOIC ACID
2COA2Ligand/IonCOENZYME A
3EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
4NA1Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:15 , ALA A:18 , ARG A:38 , LEU A:72 , MET A:74 , LYS A:75 , ASN A:96 , PHE A:97 , GLY A:98 , ARG A:104 , MET A:105 , VAL A:124 , LYS A:137 , VAL A:138 , ASP A:169 , MET A:200 , HOH A:2170 , HOH A:2171 , HOH A:2172 , HOH A:2174BINDING SITE FOR RESIDUE COA A1169
2AC2SOFTWAREASP A:294 , ASP A:297 , HOH A:2287 , HOH A:2418 , HOH A:2419BINDING SITE FOR RESIDUE NA A1429
3AC3SOFTWARELYS A:52 , HIS B:15 , VAL B:16 , GLN B:17 , ALA B:18 , ARG B:38 , LEU B:72 , MET B:74 , LYS B:75 , ASN B:96 , PHE B:97 , GLY B:98 , ALA B:101 , ARG B:104 , MET B:105 , LYS B:137 , VAL B:138 , A0A B:169 , MET B:200 , HOH B:2138 , HOH B:2315 , HOH B:2316 , HOH B:2317 , HOH B:2318 , HOH B:2319BINDING SITE FOR RESIDUE COA B1429
4AC4SOFTWARETRP A:272 , GLU A:273 , THR A:274 , ASP A:275 , ALA A:276 , HOH A:2271 , TRP B:156 , ASP B:157 , GLY B:158 , ARG B:238 , HOH B:2158 , HOH B:2320 , HOH B:2321 , HOH B:2322 , HOH B:2323 , HOH B:2324BINDING SITE FOR RESIDUE EPE B1430

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VJM)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2VJM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VJM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VJM)

(-) Exons   (0, 0)

(no "Exon" information available for 2VJM)

(-) 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:427
 aligned with FCTA_OXAFO | O06644 from UniProtKB/Swiss-Prot  Length:428

    Alignment length:427
                                    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       421       
           FCTA_OXAFO     2 TKPLDGINVLDFTHVQAGPACTQMMGFLGANVIKIERRGSGDMTRGWLQDKPNVDSLYFTMFNCNKRSIELDMKTPEGKELLEQMIKKADVMVENFGPGALDRMGFTWEYIQELNPRVILASVKGYAEGHANEHLKVYENVAQCSGGAAATTGFWDGPPTVSGAALGDSNSGMHLMIGILAALEMRHKTGRGQKVAVAMQDAVLNLVRIKLRDQQRLERTGILAEYPQAQPNFAFDRDGNPLSFDNITSVPRGGNAGGGGQPGWMLKCKGWETDADSYVYFTIAANMWPQICDMIDKPEWKDDPAYNTFEGRVDKLMDIFSFIETKFADKDKFEVTEWAAQYGIPCGPVMSMKELAHDPSLQKVGTVVEVVDEIRGNHLTVGAPFKFSGFQPEITRAPLLGEHTDEVLKELGLDDAKIKELHAKQVV 428
               SCOP domains d2vjma_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2vjmA01 A:2-254,A:352-428 Crotonobetainyl-coa:carnitine coa-transferase; domain 1                                                                                                                                                                            2vjmA02 A:255-351 formyl-coa transferase, domain 3                                               2vjmA01 A:2-254,A:352-428                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee....hhhhhhhhhhhhh..eeeeee.....hhhhhh........hhhhhh.....eeee....hhhhhhhhhhhhhhh.eeee....hhhhhh..hhhhhhhhh...eeeeee.............hhhhhhhhh......................hhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhhhhhh....hhhhh............hhhhh...............eeeee..........eeeee.hhhhhhhhhhhh.hhhhh......hhhhhh.hhhhhhhhhhhh....hhhhhhhhhhhh...eee..hhhhhhhhhhhhhh..eeee.......eeee...eee...............hhhhhhhhh..hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vjm A   2 TKPLDGINVLDFTHVQAGPACTQMMGFLGANVIKIERRGSGDMTRGWLQDKPNVDSLYFTMFNCNKRSIELDMKTPEGKELLEQMIKKADVMVENFGPGALDRMGFTWEYIQELNPRVILASVKGYAEGHANEHLKVYENVAQCSGGAAATTGFWDGPPTVSGAALGDSNSGMHLMIGILAALEIRHKTGRGQKVAVAMQDAVLNLVRIKLRDQQRLERTGILAEYPQAQPNFAFDRDGNPLSFDNITSVPRGGNAGGGGQPGWMLKCKGWETDADSYVYFTIAANMWPQICDMIDKPEWKDDPAYNTFEGRVDKLMDIFSFIETKFADKDKFEVTEWAAQYGIPCGPVMSMKELAHDPSLQKVGTVVEVVDEIRGNHLTVGAPFKFSGFQPEITRAPLLGEHTDEVLKELGLDDAKIKELHAKQVV 428
                                    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       421       


Chain B from PDB  Type:PROTEIN  Length:427
 aligned with FCTA_OXAFO | O06644 from UniProtKB/Swiss-Prot  Length:428

    Alignment length:427
                                    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       421       
           FCTA_OXAFO     2 TKPLDGINVLDFTHVQAGPACTQMMGFLGANVIKIERRGSGDMTRGWLQDKPNVDSLYFTMFNCNKRSIELDMKTPEGKELLEQMIKKADVMVENFGPGALDRMGFTWEYIQELNPRVILASVKGYAEGHANEHLKVYENVAQCSGGAAATTGFWDGPPTVSGAALGDSNSGMHLMIGILAALEMRHKTGRGQKVAVAMQDAVLNLVRIKLRDQQRLERTGILAEYPQAQPNFAFDRDGNPLSFDNITSVPRGGNAGGGGQPGWMLKCKGWETDADSYVYFTIAANMWPQICDMIDKPEWKDDPAYNTFEGRVDKLMDIFSFIETKFADKDKFEVTEWAAQYGIPCGPVMSMKELAHDPSLQKVGTVVEVVDEIRGNHLTVGAPFKFSGFQPEITRAPLLGEHTDEVLKELGLDDAKIKELHAKQVV 428
               SCOP domains d2vjmb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2vjmB01 B:2-254,B:352-428 Crotonobetainyl-coa:carnitine coa-transferase; domain 1                                                                                                                                                                            2vjmB02 B:255-351 formyl-coa transferase, domain 3                                               2vjmB01 B:2-254,B:352-428                                                     CATH domains
           Pfam domains (1) --------------------------------------------------------------------CoA_transf_3-2vjmB01 B:70-241                                                                                                                                               ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------CoA_transf_3-2vjmB02 B:70-241                                                                                                                                               ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .......eeee....hhhhhhhhhhhhh..eeeeee.....hhhhhh........hhhhhh.....eeee....hhhhhhhhhhhhhh..eeee....hhhhhh..hhhhhhhhh...eeeeee.............hhhhhhhhh.hhhhh................hhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhhhhhh....hhhhh............hhhhh...............eeeee..........eeeee....hhhhhhhhhh.hhhhhh....hhhhhh.hhhhhhhhhhhhh...hhhhhhhhhhh....eee..hhhhhhhhhhhhhh..eeee.......eeee...eee...............hhhhhhhhh..hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vjm B   2 TKPLDGINVLDFTHVQAGPACTQMMGFLGANVIKIERRGSGDMTRGWLQDKPNVDSLYFTMFNCNKRSIELDMKTPEGKELLEQMIKKADVMVENFGPGALDRMGFTWEYIQELNPRVILASVKGYAEGHANEHLKVYENVAQCSGGAAATTGFWDGPPTVSGAALGdSNSGMHLMIGILAALEIRHKTGRGQKVAVAMQDAVLNLVRIKLRDQQRLERTGILAEYPQAQPNFAFDRDGNPLSFDNITSVPRGGNAGGGGQPGWMLKCKGWETDADSYVYFTIAANMWPQICDMIDKPEWKDDPAYNTFEGRVDKLMDIFSFIETKFADKDKFEVTEWAAQYGIPCGPVMSMKELAHDPSLQKVGTVVEVVDEIRGNHLTVGAPFKFSGFQPEITRAPLLGEHTDEVLKELGLDDAKIKELHAKQVV 428
                                    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       421       
                                                                                                                                                                                                 169-A0A
   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_OXAFO | O06644)
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: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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  2vjm
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  2.8.3.16
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 Related Entries

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

UniProtKB/Swiss-Prot
        FCTA_OXAFO | O06644: 1p5h 1p5r 1t3z 1t4c 1vgq 1vgr 2vjk 2vjl 2vjn 2vjo 2vjp 2vjq

(-) Related Entries Specified in the PDB File

1p5h CRYSTAL STRUCTURE OF FORMYL-COA TRANSFERASE ( APOENZYME)FROM OXALOBACTER FORMIGENES
1p5r FORMYL-COA TRANSFERASE IN COMPLEX WITH COENZYME A
1t3z FORMYL-COA TRANFERASE MUTANT ASP169 TO SER
1t4c FORMYL-COA TRANSFERASE IN COMPLEX WITH OXALYL-COA
1vgq FORMYL-COA TRANSFERASE MUTANT ASP169 TO ALA
1vgr FORMYL-COA TRANSFERASE MUTANT ASP169 TO GLU
2vjk FORMYL-COA TRANSFERASE WITH ASPARTYL-COA THIOESTER INTERMEDIATE DERIVED FROM OXALYL-COA
2vjl FORMYL-COA TRANSFERASE WITH ASPARTYL-COA THIOESTER INTERMEDIATE DERIVED FROM FORMYL-COA
2vjn FORMYL-COA TRANSFERASE MUTANT VARIANT G260A
2vjo FORMYL-COA TRANSFERASE MUTANT VARIANT Q17A WITH ASPARTYL-COA THIOESTER INTERMEDIATES AND OXALATE
2vjp FORMYL-COA TRANSFERASE MUTANT VARIANT W48F
2vjq FORMYL-COA TRANSFERASE MUTANT VARIANT W48Q