Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE FORMIMINOTRANSFERASE DOMAIN OF FORMIMINOTRANSFERASE-CYCLODEAMINASE.
 
Authors :  D. Kohls, T. Sulea, E. Purisima, R. E. Mackenzie, A. Vrielink
Date :  08 Jul 99  (Deposition) - 12 Jan 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Functional Dimer, Alpha-Beta-Beta-Alpha Sandwich, Electrostatically Charged Substrate Tunnel, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Kohls, T. Sulea, E. O. Purisima, R. E. Mackenzie, A. Vrielink
The Crystal Structure Of The Formiminotransferase Domain Of Formiminotransferase-Cyclodeaminase: Implications For Substrate Channeling In A Bifunctional Enzyme.
Structure Fold. Des. V. 8 35 2000
PubMed-ID: 10673422  |  Reference-DOI: 10.1016/S0969-2126(00)00078-2

(-) Compounds

Molecule 1 - FORMIMINOTRANSFERASE-CYCLODEAMINASE
    Chains: A, B
    EC Number: 2.1.2.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBKE-CM1
    Expression System Taxid: 562
    Fragment: FORMIMINOTRANSFERASE DOMAIN
    Organ: LIVER
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1FON2Ligand/IonFOLINIC ACID
2GOL2Ligand/IonGLYCEROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:10 , ASP A:39 , SER A:40 , GLY A:41 , THR A:44 , ARG A:46 , VAL A:48 , HIS A:82 , PRO A:92 , TYR A:126 , ARG A:142 , ARG A:179 , ASN A:186 , TRP A:224 , LEU A:226 , GLU A:228 , GLN A:233 , ASN A:237 , GLN A:268 , VAL A:270 , GOL A:480 , HOH A:588 , HOH A:667 , HOH A:807 , HOH A:829BINDING SITE FOR RESIDUE FON A 330
2AC2SOFTWAREHOH B:528 , HOH B:566 , HOH B:618 , HOH B:909 , HOH B:1122 , HOH B:1131 , HOH B:1237 , ASN B:2010 , ASP B:2039 , SER B:2040 , GLY B:2041 , THR B:2044 , ARG B:2046 , VAL B:2048 , HIS B:2082 , TYR B:2126 , LEU B:2138 , ARG B:2142 , ARG B:2179 , LEU B:2182 , ASN B:2186 , TRP B:2224 , LEU B:2226 , GLU B:2228 , ASN B:2237 , GLN B:2268 , VAL B:2270 , GOL B:2480BINDING SITE FOR RESIDUE FON B 2330
3AC3SOFTWAREHIS A:82 , ARG A:142 , GLN A:220 , ALA A:221 , ILE A:222 , SER A:235 , THR A:236 , ASN A:237 , FON A:330 , HOH A:1228BINDING SITE FOR RESIDUE GOL A 480
4AC4SOFTWAREHOH B:902 , HOH B:909 , HIS B:2082 , ARG B:2142 , SER B:2235 , THR B:2236 , ASN B:2237 , FON B:2330BINDING SITE FOR RESIDUE GOL B 2480

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1QD1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1QD1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QD1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1QD1)

(-) Exons   (0, 0)

(no "Exon" information available for 1QD1)

(-) 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:319
 aligned with FTCD_PIG | P53603 from UniProtKB/Swiss-Prot  Length:541

    Alignment length:325
                                    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     
            FTCD_PIG      2 SQLVECVPNFSEGKNQEVIDAISRAVAQTPGCVLLDVDSGPSTNRTVYTFVGRPEDVVEGALNAARAAYQLIDMSRHHGEHPRMGALDVCPFIPVRGVTMDECVRCAQAFGQRLAEELGVPVYLYGEAARTAGRQSLPALRAGEYEALPEKLKQAEWAPDFGPSAFVPSWGATVAGARKFLLAFNINLLSTREQAHRIALDLREQGRGKDQPGRLKKVQAIGWYLDEKNLAQVSTNLLDFEVTGLHTVFEETCREAQELSLPVVGSQLVGLVPLKALLDAAAFYCEKENLFLLQDEHRIRLVVNRLGLDSLAPFKPKERIIEYLV  326
               SCOP domains d1qd1a1 A:2-180 Formiminotransferase domain of formiminotransferase-cyclodeaminase.                                                                                                d1qd1a2 A:181-326 Formimino      transferase domain of formiminotransferase-cyclodeaminase.                                                        SCOP domains
               CATH domains 1qd1A01 A:2-181 Formiminotransferase-cyclodeaminase; Chain B, domain 1                                                                                                              1qd1A02 A:182-326  [code=3      .30.70.670, no name defined]                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee...hhhhhhhhhhhhhh....eeeeeeee....eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.....hhhhhhhhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..............eeeeee...eeeeeee..hhhhhhhhhhhhh...------.....eeeeeeee....eeeeeeee......hhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.......hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1qd1 A    2 SQLVECVPNFSEGKNQEVIDAISRAVAQTPGCVLLDVDSGPSTNRTVYTFVGRPEDVVEGALNAARAAYQLIDMSRHHGEHPRMGALDVCPFIPVRGVTMDECVRCAQAFGQRLAEELGVPVYLYGEAARTAGRQSLPALRAGEYEALPEKLKQAEWAPDFGPSAFVPSWGATVAGARKFLLAFNINLLSTREQAHRIALDLREQG------GRLKKVQAIGWYLDEKNLAQVSTNLLDFEVTGLHTVFEETCREAQELSLPVVGSQLVGLVPLKALLDAAAFYCEKENLFLLQDEHRIRLVVNRLGLDSLAPFKPKERIIEYLV  326
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201     |   -  |    221       231       241       251       261       271       281       291       301       311       321     
                                                                                                                                                                                                                                       207    214                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:325
 aligned with FTCD_PIG | P53603 from UniProtKB/Swiss-Prot  Length:541

    Alignment length:325
                                    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     
            FTCD_PIG      2 SQLVECVPNFSEGKNQEVIDAISRAVAQTPGCVLLDVDSGPSTNRTVYTFVGRPEDVVEGALNAARAAYQLIDMSRHHGEHPRMGALDVCPFIPVRGVTMDECVRCAQAFGQRLAEELGVPVYLYGEAARTAGRQSLPALRAGEYEALPEKLKQAEWAPDFGPSAFVPSWGATVAGARKFLLAFNINLLSTREQAHRIALDLREQGRGKDQPGRLKKVQAIGWYLDEKNLAQVSTNLLDFEVTGLHTVFEETCREAQELSLPVVGSQLVGLVPLKALLDAAAFYCEKENLFLLQDEHRIRLVVNRLGLDSLAPFKPKERIIEYLV  326
               SCOP domains d1qd1b1 B:2002-2180 Formiminotransferase domain of formiminotransferase-cyclodeaminase.                                                                                            d1qd1b2 B:2181-2326 Formiminotransferase domain of formiminotransferase-cyclodeaminase.                                                            SCOP domains
               CATH domains 1qd1B01 B:2002-2181 Formiminotransferase-cyclodeaminase; Chain B, domain 1                                                                                                          1qd1B02 B:2182-2326  [code=3.30.70.670, no name defined]                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee...hhhhhhhhhhhhhh....eeeeeeee....eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.....hhhhhhhhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..............eeeeee...eeeeeee..hhhhhhhhhhhhh..............eeeeeeee....eeeeeeee......hhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.......hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1qd1 B 2002 SQLVECVPNFSEGKNQEVIDAISRAVAQTPGCVLLDVDSGPSTNRTVYTFVGRPEDVVEGALNAARAAYQLIDMSRHHGEHPRMGALDVCPFIPVRGVTMDECVRCAQAFGQRLAEELGVPVYLYGEAARTAGRQSLPALRAGEYEALPEKLKQAEWAPDFGPSAFVPSWGATVAGARKFLLAFNINLLSTREQAHRIALDLREQGRGKDQPGRLKKVQAIGWYLDEKNLAQVSTNLLDFEVTGLHTVFEETCREAQELSLPVVGSQLVGLVPLKALLDAAAFYCEKENLFLLQDEHRIRLVVNRLGLDSLAPFKPKERIIEYLV 2326
                                  2011      2021      2031      2041      2051      2061      2071      2081      2091      2101      2111      2121      2131      2141      2151      2161      2171      2181      2191      2201      2211      2221      2231      2241      2251      2261      2271      2281      2291      2301      2311      2321
   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, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1QD1)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (FTCD_PIG | P53603)
molecular function
    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:0005542    folic acid binding    Interacting selectively and non-covalently with folic acid, pteroylglutamic acid. Folic acid is widely distributed as a member of the vitamin B complex and is essential for the synthesis of purine and pyrimidines.
    GO:0030412    formimidoyltetrahydrofolate cyclodeaminase activity    Catalysis of the reaction: 5-formimidoyltetrahydrofolate + 2 H(+) = 5,10-methenyltetrahydrofolate + NH(4)(+).
    GO:0030409    glutamate formimidoyltransferase activity    Catalysis of the reaction: 5-formimidoyltetrahydrofolate + L-glutamate = tetrahydrofolate + N-formimidoyl-L-glutamate.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    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:0044237    cellular metabolic process    The chemical reactions and pathways by which individual cells transform chemical substances.
    GO:0006548    histidine catabolic process    The chemical reactions and pathways resulting in the breakdown of histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid.
    GO:0019556    histidine catabolic process to glutamate and formamide    The chemical reactions and pathways resulting in the breakdown of histidine into other compounds, including glutamate and formamide.
    GO:0019557    histidine catabolic process to glutamate and formate    The chemical reactions and pathways resulting in the breakdown of histidine into other compounds, including glutamate and formate.
    GO:0006547    histidine metabolic process    The chemical reactions and pathways involving histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid.
    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:0035999    tetrahydrofolate interconversion    The chemical reactions and pathways by which one-carbon (C1) units are transferred between tetrahydrofolate molecules, to synthesise other tetrahydrofolate molecules.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0005814    centriole    A cellular organelle, found close to the nucleus in many eukaryotic cells, consisting of a small cylinder with microtubular walls, 300-500 nm long and 150-250 nm in diameter. It contains nine short, parallel, peripheral microtubular fibrils, each fibril consisting of one complete microtubule fused to two incomplete microtubules. Cells usually have two centrioles, lying at right angles to each other. At division, each pair of centrioles generates another pair and the twin pairs form the pole of the mitotic spindle.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    FON  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1qd1)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1qd1
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  FTCD_PIG | P53603
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.1.2.5
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  FTCD_PIG | P53603
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1QD1)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1QD1)