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(-) Description

Title :  CRYSTAL STRUCTURE OF FORMYLTETRAHYDROFOLATE DEFORMYLASE FROM THERMUS THERMOPHILUS HB8
 
Authors :  G. Sampei, Y. Yanagida, N. Ogata, M. Kusano, K. Terao, H. Kawai, Y. Fukai M. Kanagawa, Y. Inoue, S. Baba, G. Kawai
Date :  28 Feb 13  (Deposition) - 08 Jan 14  (Release) - 08 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.71
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Formyltetrahydrofolate Deformylase, Formyltetrahydrofolate, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Sampei, M. Kanagawa, S. Baba, T. Shimasaki, H. Taka, S. Mitsui, S. Fujiwara, Y. Yanagida, M. Kusano, S. Suzuki, K. Terao, H. Kawai, Y. Fukai, N. Nakagawa, A. Ebihara, S. Kuramitsu, S. Yokoyama, G. Kawai
Structures And Reaction Mechanisms Of The Two Related Enzymes, Purn And Puru
J. Biochem. V. 154 569 2013
PubMed-ID: 24108189  |  Reference-DOI: 10.1093/JB/MVT090

(-) Compounds

Molecule 1 - FORMYLTETRAHYDROFOLATE DEFORMYLASE
    Chains: A, B
    EC Number: 3.5.1.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: TTHA1321
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8 / ATCC 27634 / DSM 579

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3W7B)

(-) Sites  (0, 0)

(no "Site" information available for 3W7B)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3W7B)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:197 -Pro A:198
2Leu B:197 -Pro B:198

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3W7B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3W7B)

(-) Exons   (0, 0)

(no "Exon" information available for 3W7B)

(-) 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:285
 aligned with Q5SIP8_THET8 | Q5SIP8 from UniProtKB/TrEMBL  Length:285

    Alignment length:285
                                    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     
         Q5SIP8_THET8     1 MEEARLLVTCPDRPGIVAAVSGFLYAHGANITDLQQHSTDPEGGTFFMRVAFTASHLDLARPALERAFQEVVASRFQMQWRLAYASERKRTAILVSKPAHALLELLWRYRVGELPMELRLVISNHPDHREEVERFGIPYHHVPVEKGRKEEAEERILALLEAEGVELVVLARYMQILSPGFVERFPMRIINIHHSFLPAFAGADPYRQAYERGVKLIGATAHYVTEELDQGPIIEQDVVRVSHRHSVREMKRLGRELERTVLARAVRWHLEDRILVHENRTVVFV 285
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee...hhhhhhhhhhhhh..eeeeeeeee......eeeeeeeee.....hhhhhhhhhhhhhhhhhhh.eeeeee....eeeeeee...hhhhhhhhhhhhh....eeeeeeee....hhhhhhhh...eee......hhhhhhhhhhhhhhhhh..eeee.......hhhhhh.....eeeeeee........hhhhhhhhhh..eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w7b A   1 MEEARLLVTCPDRPGIVAAVSGFLYAHGANITDLQQHSTDPEGGTFFMRVAFTASHLDLARPALERAFQEVVASRFQMQWRLAYASERKRTAILVSKPAHALLELLWRYRVGELPMELRLVISNHPDHREEVERFGIPYHHVPVEKGRKEEAEERILALLEAEGVELVVLARYMQILSPGFVERFPMRIINIHHSFLPAFAGADPYRQAYERGVKLIGATAHYVTEELDQGPIIEQDVVRVSHRHSVREMKRLGRELERTVLARAVRWHLEDRILVHENRTVVFV 285
                                    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     


Chain B from PDB  Type:PROTEIN  Length:285
 aligned with Q5SIP8_THET8 | Q5SIP8 from UniProtKB/TrEMBL  Length:285

    Alignment length:285
                                    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     
         Q5SIP8_THET8     1 MEEARLLVTCPDRPGIVAAVSGFLYAHGANITDLQQHSTDPEGGTFFMRVAFTASHLDLARPALERAFQEVVASRFQMQWRLAYASERKRTAILVSKPAHALLELLWRYRVGELPMELRLVISNHPDHREEVERFGIPYHHVPVEKGRKEEAEERILALLEAEGVELVVLARYMQILSPGFVERFPMRIINIHHSFLPAFAGADPYRQAYERGVKLIGATAHYVTEELDQGPIIEQDVVRVSHRHSVREMKRLGRELERTVLARAVRWHLEDRILVHENRTVVFV 285
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee...hhhhhhhhhhhhh.eeeeeeeeee......eeeeeeeeee....hhhhhhhhhhhhhhhhhhh.eeeeee....eeeeeee...hhhhhhhhhhhhh....eeeeeeee....hhhhhhhh...eee......hhhhhhhhhhhhhhhhh..eeee.......hhhhhh.....eee..ee........hhhhhhhhhh..eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w7b B   1 MEEARLLVTCPDRPGIVAAVSGFLYAHGANITDLQQHSTDPEGGTFFMRVAFTASHLDLARPALERAFQEVVASRFQMQWRLAYASERKRTAILVSKPAHALLELLWRYRVGELPMELRLVISNHPDHREEVERFGIPYHHVPVEKGRKEEAEERILALLEAEGVELVVLARYMQILSPGFVERFPMRIINIHHSFLPAFAGADPYRQAYERGVKLIGATAHYVTEELDQGPIIEQDVVRVSHRHSVREMKRLGRELERTVLARAVRWHLEDRILVHENRTVVFV 285
                                    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
   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 3W7B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3W7B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3W7B)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q5SIP8_THET8 | Q5SIP8)
molecular function
    GO:0016597    amino acid binding    Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents.
    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: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: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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  Cis Peptide Bonds
    Leu A:197 - Pro A:198   [ RasMol ]  
    Leu B:197 - Pro B:198   [ RasMol ]  
 
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