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(-) Description

Title :  CRYSTAL STRUCTURE OF A FORMYLTETRAHYDROFOLATE DEFORMYLASE (PP_0327) FROM PSEUDOMONAS PUTIDA KT2440 AT 2.25 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  14 May 10  (Deposition) - 16 Jun 10  (Release) - 16 Jun 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Formyl Transferase, Act Domain, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of A Formyltetrahydrofolate Deformylase (Pp_0327) From Pseudomonas Putida Kt2440 At 2. 25 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - FORMYLTETRAHYDROFOLATE DEFORMYLASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PURU-1, PP0327, PP_0327
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 160488
    Strain: KT2440

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 24)

Asymmetric/Biological Unit (1, 24)
No.NameCountTypeFull Name
1MSE24Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3N0V)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3N0V)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3N0V)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3N0V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3N0V)

(-) Exons   (0, 0)

(no "Exon" information available for 3N0V)

(-) 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:280
 aligned with Q88R07_PSEPK | Q88R07 from UniProtKB/TrEMBL  Length:285

    Alignment length:280
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285
         Q88R07_PSEPK     6 DTWILTADCPSMLGTVDVVTRYLFEQRCYVTEHHSFDDRQSGRFFIRVEFRQPDDFDEAGFRAGLAERSEAFGMAFELTAPNHRPKVVIMVSKADHCLNDLLYRQRIGQLGMDVVAVVSNHPDLEPLAHWHKIPYYHFALDPKDKPGQERKVLQVIEETGAELVILARYMQVLSPELCRRLDGWAINIHHSLLPGFKGAKPYHQAYNKGVKMVGATAHYINNDLDEGPIIAQGVEVVDHSHYPEDLIAKGRDIECLTLARAVGYHIERRVFLNANRTVVL 285
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee...hhhhhhhhhhhhh..eeeeeeeeee....eeeeeeeee.....hhhhhhhhhhhhhh....eeeee......eeeeee...hhhhhhhhhhhhh.....eeeeeee....hhhhhhhh...eee......hhhhhhhhhhhhhhhhh..eeee.......hhhhhhhh...eeeeee.........hhhhhhhhhh..eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n0v A   6 DTWILTADCPSmLGTVDVVTRYLFEQRCYVTEHHSFDDRQSGRFFIRVEFRQPDDFDEAGFRAGLAERSEAFGmAFELTAPNHRPKVVImVSKADHCLNDLLYRQRIGQLGmDVVAVVSNHPDLEPLAHWHKIPYYHFALDPKDKPGQERKVLQVIEETGAELVILARYmQVLSPELCRRLDGWAINIHHSLLPGFKGAKPYHQAYNKGVKmVGATAHYINNDLDEGPIIAQGVEVVDHSHYPEDLIAKGRDIECLTLARAVGYHIERRVFLNANRTVVL 285
                                    15 |      25        35        45        55        65        75   |    85        95       105       115 |     125       135       145       155       165       175       185       195       205       215 |     225       235       245       255       265       275       285
                                      17-MSE                                                        79-MSE          95-MSE               117-MSE                                                   175-MSE                                   217-MSE                                                                


Chain B from PDB  Type:PROTEIN  Length:278
 aligned with Q88R07_PSEPK | Q88R07 from UniProtKB/TrEMBL  Length:285

    Alignment length:280
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285
         Q88R07_PSEPK     6 DTWILTADCPSMLGTVDVVTRYLFEQRCYVTEHHSFDDRQSGRFFIRVEFRQPDDFDEAGFRAGLAERSEAFGMAFELTAPNHRPKVVIMVSKADHCLNDLLYRQRIGQLGMDVVAVVSNHPDLEPLAHWHKIPYYHFALDPKDKPGQERKVLQVIEETGAELVILARYMQVLSPELCRRLDGWAINIHHSLLPGFKGAKPYHQAYNKGVKMVGATAHYINNDLDEGPIIAQGVEVVDHSHYPEDLIAKGRDIECLTLARAVGYHIERRVFLNANRTVVL 285
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee...hhhhhhhhhhhhh..eeeeeeeeee....eeeeeeeee.....hhhhhhhhhhhhhhh...eeeee......eeeeee...hhhhhhhhhhhhh.....eeeeeee....hhhhhhhh...eee......hhhhhhhhhhhhhhhh...eeee.......hhhhhhhhh..eeeeeee..--....hhhhhhhhhh..eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n0v B   6 DTWILTADCPSmLGTVDVVTRYLFEQRCYVTEHHSFDDRQSGRFFIRVEFRQPDDFDEAGFRAGLAERSEAFGmAFELTAPNHRPKVVImVSKADHCLNDLLYRQRIGQLGmDVVAVVSNHPDLEPLAHWHKIPYYHFALDPKDKPGQERKVLQVIEETGAELVILARYmQVLSPELCRRLDGWAINIHHSLL--FKGAKPYHQAYNKGVKmVGATAHYINNDLDEGPIIAQGVEVVDHSHYPEDLIAKGRDIECLTLARAVGYHIERRVFLNANRTVVL 285
                                    15 |      25        35        45        55        65        75   |    85        95       105       115 |     125       135       145       155       165       175       185       195  |  | 205       215 |     225       235       245       255       265       275       285
                                      17-MSE                                                        79-MSE          95-MSE               117-MSE                                                   175-MSE                198  |             217-MSE                                                                
                                                                                                                                                                                                                             201                                                                                    


Chain C from PDB  Type:PROTEIN  Length:279
 aligned with Q88R07_PSEPK | Q88R07 from UniProtKB/TrEMBL  Length:285

    Alignment length:280
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285
         Q88R07_PSEPK     6 DTWILTADCPSMLGTVDVVTRYLFEQRCYVTEHHSFDDRQSGRFFIRVEFRQPDDFDEAGFRAGLAERSEAFGMAFELTAPNHRPKVVIMVSKADHCLNDLLYRQRIGQLGMDVVAVVSNHPDLEPLAHWHKIPYYHFALDPKDKPGQERKVLQVIEETGAELVILARYMQVLSPELCRRLDGWAINIHHSLLPGFKGAKPYHQAYNKGVKMVGATAHYINNDLDEGPIIAQGVEVVDHSHYPEDLIAKGRDIECLTLARAVGYHIERRVFLNANRTVVL 285
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee...hhhhhhhhhhhhh..eeeeeeeeee....eeeeeeeee.....hhhhhhhhhhhhhhh...eeeee......eeeeee...hhhhhhhhhhhhh.....eeeeeee....hhhhhhhh...eee......hhhhhhhhhhhhhhhh...eeee.......hhhhhhhh...eeeeeee..-.....hhhhhhhhhh..eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n0v C   6 DTWILTADCPSmLGTVDVVTRYLFEQRCYVTEHHSFDDRQSGRFFIRVEFRQPDDFDEAGFRAGLAERSEAFGmAFELTAPNHRPKVVImVSKADHCLNDLLYRQRIGQLGmDVVAVVSNHPDLEPLAHWHKIPYYHFALDPKDKPGQERKVLQVIEETGAELVILARYmQVLSPELCRRLDGWAINIHHSLL-GFKGAKPYHQAYNKGVKmVGATAHYINNDLDEGPIIAQGVEVVDHSHYPEDLIAKGRDIECLTLARAVGYHIERRVFLNANRTVVL 285
                                    15 |      25        35        45        55        65        75   |    85        95       105       115 |     125       135       145       155       165       175       185       195  | |  205       215 |     225       235       245       255       265       275       285
                                      17-MSE                                                        79-MSE          95-MSE               117-MSE                                                   175-MSE                198 |              217-MSE                                                                
                                                                                                                                                                                                                            200                                                                                     


Chain D from PDB  Type:PROTEIN  Length:280
 aligned with Q88R07_PSEPK | Q88R07 from UniProtKB/TrEMBL  Length:285

    Alignment length:280
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285
         Q88R07_PSEPK     6 DTWILTADCPSMLGTVDVVTRYLFEQRCYVTEHHSFDDRQSGRFFIRVEFRQPDDFDEAGFRAGLAERSEAFGMAFELTAPNHRPKVVIMVSKADHCLNDLLYRQRIGQLGMDVVAVVSNHPDLEPLAHWHKIPYYHFALDPKDKPGQERKVLQVIEETGAELVILARYMQVLSPELCRRLDGWAINIHHSLLPGFKGAKPYHQAYNKGVKMVGATAHYINNDLDEGPIIAQGVEVVDHSHYPEDLIAKGRDIECLTLARAVGYHIERRVFLNANRTVVL 285
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------Formyl_trans_N-3n0vD01 D:90-267                                                                                                                                                   ------------------ Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------Formyl_trans_N-3n0vD02 D:90-267                                                                                                                                                   ------------------ Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------------------------------Formyl_trans_N-3n0vD03 D:90-267                                                                                                                                                   ------------------ Pfam domains (3)
           Pfam domains (4) ------------------------------------------------------------------------------------Formyl_trans_N-3n0vD04 D:90-267                                                                                                                                                   ------------------ Pfam domains (4)
         Sec.struct. author ..eeeeeeee...hhhhhhhhhhhhh..eeeeeeeeee....eeeeeeeee.....hhhhhhhhhhhhhh....eeeee......eeeeee...hhhhhhhhhhhhh.....eeeeeee....hhhhhhhh...eee......hhhhhhhhhhhhhhhh...eeee.......hhhhhhhh...eeeeee.........hhhhhhhhhh..eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n0v D   6 DTWILTADCPSmLGTVDVVTRYLFEQRCYVTEHHSFDDRQSGRFFIRVEFRQPDDFDEAGFRAGLAERSEAFGmAFELTAPNHRPKVVImVSKADHCLNDLLYRQRIGQLGmDVVAVVSNHPDLEPLAHWHKIPYYHFALDPKDKPGQERKVLQVIEETGAELVILARYmQVLSPELCRRLDGWAINIHHSLLPGFKGAKPYHQAYNKGVKmVGATAHYINNDLDEGPIIAQGVEVVDHSHYPEDLIAKGRDIECLTLARAVGYHIERRVFLNANRTVVL 285
                                    15 |      25        35        45        55        65        75   |    85        95       105       115 |     125       135       145       155       165       175       185       195       205       215 |     225       235       245       255       265       275       285
                                      17-MSE                                                        79-MSE          95-MSE               117-MSE                                                   175-MSE                                   217-MSE
   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  (0, 0)

(no "SCOP Domain" information available for 3N0V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3N0V)

(-) Pfam Domains  (1, 4)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q88R07_PSEPK | Q88R07)
molecular function
    GO:0008864    formyltetrahydrofolate deformylase activity    Catalysis of the reaction: 10-formyltetrahydrofolate + H(2)O = (6S)-5,6,7,8-tetrahydrofolate + formate + H(+).
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016742    hydroxymethyl-, formyl- and related transferase activity    Catalysis of the transfer of a hydroxymethyl- or formyl group from one compound (donor) to another (acceptor).
biological process
    GO:0006189    'de novo' IMP biosynthetic process    The chemical reactions and pathways resulting in the formation of IMP, inosine monophosphate, by the stepwise assembly of a purine ring on ribose 5-phosphate.
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    GO:0006730    one-carbon metabolic process    The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
    GO:0006164    purine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.

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