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 STRUCTURE OF HUMAN GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE IN COMPLEX WITH ALPHA,BETA-N-(HYDROXYACETYL)-D-RIBOFURANOSYLAMINE AND 10-FORMYL-5,8, DIDEAZAFOLATE
 
Authors :  T. E. S. Dahms, G. Sainz, E. L. Giroux, C. A. Caperelli, J. L. Smith
Date :  09 May 05  (Deposition) - 23 Aug 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.07
Chains :  Asym./Biol. Unit :  A
Keywords :  Purine Biosynthesis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. E. Dahms, G. Sainz, E. L. Giroux, C. A. Caperelli, J. L. Smith
The Apo And Ternary Complex Structures Of A Chemotherapeutic Target: Human Glycinamide Ribonucleotide Transformylase.
Biochemistry V. 44 9841 2005
PubMed-ID: 16026156  |  Reference-DOI: 10.1021/BI050307G
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE
    ChainsA
    EC Number2.1.2.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET17B
    Expression System StrainBL21(DE3) PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 808-1010, GART
    GeneGART, PRGS
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymGART, GAR TRANSFORMYLASE, 5'- PHOSPHORIBOSYLGLYCINAMIDE TRANSFORMYLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1DQB1Ligand/Ion4-[(4-{[(2-AMINO-4-OXO-3,4-DIHYDROQUINAZOLIN-6-YL)METHYL]AMINO}BENZOYL)AMINO]BUTANOIC ACID
2GRF1Ligand/Ion5-O-PHOSPHONO-BETA-D-RIBOFURANOSYLAMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:11 , SER A:12 , ASN A:13 , ALA A:86 , GLY A:87 , ILE A:107 , PRO A:109 , GLU A:173 , HOH A:1453 , HOH A:1485 , HOH A:1525 , HOH A:1526 , HOH A:1529 , HOH A:1534 , HOH A:1551BINDING SITE FOR RESIDUE GRF A 1300
2AC2SOFTWAREPHE A:88 , ARG A:90 , ILE A:91 , LEU A:92 , VAL A:97 , ASN A:106 , VAL A:139 , ALA A:140 , GLU A:141 , VAL A:143 , ASP A:144 , HOH A:1462 , HOH A:1508 , HOH A:1524 , HOH A:1544BINDING SITE FOR RESIDUE DQB A 1301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GARTPS00373 Phosphoribosylglycinamide formyltransferase active site.PUR2_HUMAN940-963  1A:133-156

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2bENST000003818392bENSE00001490224chr21:34915167-34914966202PUR2_HUMAN-00--
1.4aENST000003818394aENSE00002148759chr21:34911662-34911477186PUR2_HUMAN1-49490--
1.5ENST000003818395ENSE00001043425chr21:34907626-3490753196PUR2_HUMAN49-81330--
1.6bENST000003818396bENSE00002174056chr21:34907059-34906885175PUR2_HUMAN81-139590--
1.7aENST000003818397aENSE00001043434chr21:34904762-34904651112PUR2_HUMAN139-176380--
1.8aENST000003818398aENSE00001043411chr21:34903863-3490379569PUR2_HUMAN177-199230--
1.9cENST000003818399cENSE00002197902chr21:34903190-34903065126PUR2_HUMAN200-241420--
1.11ENST0000038183911ENSE00001751727chr21:34901243-3490115688PUR2_HUMAN242-271300--
1.12cENST0000038183912cENSE00001753916chr21:34900910-3490082586PUR2_HUMAN271-299290--
1.12fENST0000038183912fENSE00001621771chr21:34900641-34900473169PUR2_HUMAN300-356570--
1.13aENST0000038183913aENSE00001777765chr21:34897307-34897076232PUR2_HUMAN356-433780--
1.14bENST0000038183914bENSE00001646436chr21:34894589-3489449595PUR2_HUMAN433-465330--
1.15ENST0000038183915ENSE00001653663chr21:34893322-34893213110PUR2_HUMAN465-501370--
1.16bENST0000038183916bENSE00001638032chr21:34892869-34892671199PUR2_HUMAN502-568670--
1.17ENST0000038183917ENSE00001683013chr21:34889915-34889664252PUR2_HUMAN568-652850--
1.18ENST0000038183918ENSE00001681935chr21:34889448-34889296153PUR2_HUMAN652-703520--
1.19aENST0000038183919aENSE00001696316chr21:34883765-34883559207PUR2_HUMAN703-772700--
1.20bENST0000038183920bENSE00001689617chr21:34882227-34882090138PUR2_HUMAN772-818471A:1-1111
1.21bENST0000038183921bENSE00001632330chr21:34878411-34878281131PUR2_HUMAN818-861441A:11-5444
1.22ENST0000038183922ENSE00001656872chr21:34878009-34877868142PUR2_HUMAN862-909481A:55-10248
1.23ENST0000038183923ENSE00001636975chr21:34876834-34876719116PUR2_HUMAN909-947391A:102-14039
1.24bENST0000038183924bENSE00001736479chr21:34876622-34876238385PUR2_HUMAN948-1010631A:141-20060

(-) 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:200
 aligned with PUR2_HUMAN | P22102 from UniProtKB/Swiss-Prot  Length:1010

    Alignment length:200
                                   817       827       837       847       857       867       877       887       897       907       917       927       937       947       957       967       977       987       997      1007
          PUR2_HUMAN    808 ARVAVLISGTGSNLQALIDSTREPNSSAQIDIVISNKAAVAGLDKAERAGIPTRVINHKLYKNRVEFDSAIDLVLEEFSIDIVCLAGFMRILSGPFVQKWNGKMLNIHPSLLPSFKGSNAHEQALETGVTVTGCTVHFVAEDVDAGQIILQEAVPVKRGDTVATLSERVKLAEHKIFPAALQLVASGTVQLGENGKICWV 1007
               SCOP domains d1zlya_ A: Glycinamide ribonucleotide transformylase, GART                                                                                                                                               SCOP domains
               CATH domains 1zlyA00 A:1-200  [code=3.40.50.170, no name defined]                                                                                                                                                     CATH domains
               Pfam domains Formyl_trans_N-1zlyA01 A:1-181                                                                                                                                                       ------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhh......eeeeeee....hhhhhhhhhh...eee..........hhhhhhhhhhhhh...eeee.......hhhhhhhh...eeeee..........hhhhhhhhhh..eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..ee.......ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------GART  PDB: A:133-156    -------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.20b -------------------------------------------Exon 1.22  PDB: A:55-102 UniProt: 862-909       --------------------------------------Exon 1.24b  PDB: A:141-200 UniProt: 948-1010 [INCOMPLETE]    Transcript 1 (1)
           Transcript 1 (2) ----------Exon 1.21b  PDB: A:11-54 UniProt: 818-861   -----------------------------------------------Exon 1.23  PDB: A:102-140              ------------------------------------------------------------ Transcript 1 (2)
                1zly A    1 ARVAVLISGTGSNLQALIDSTREPNSSAQIDIVISNKAAVAGLDKAERAGIPTRVINHKLYKNRVEFDSAIDLVLEEFSIDIVCLAGFMRILSGPFVQKWNGKMLNIHPSLLPSFKGSNAHEQALETGVTVTGCTVHFVAEDVDAGQIILQEAVPVKRGDTVATLSERVKLAEHKIFPAALQLVASGTVQLGENGKICWV  200
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PUR2_HUMAN | P22102)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0016742    hydroxymethyl-, formyl- and related transferase activity    Catalysis of the transfer of a hydroxymethyl- or formyl group from one compound (donor) to another (acceptor).
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0004637    phosphoribosylamine-glycine ligase activity    Catalysis of the reaction: 5-phospho-D-ribosylamine + ATP + glycine = N(1)-(5-phospho-D-ribosyl)glycinamide + ADP + 2 H(+) + phosphate.
    GO:0004641    phosphoribosylformylglycinamidine cyclo-ligase activity    Catalysis of the reaction: 2-(formamido)-N(1)-(5-phospho-D-ribosyl)acetamidine + ATP = 5-amino-1-(5-phospho-D-ribosyl)imidazole + ADP + 2 H(+) + phosphate.
    GO:0004644    phosphoribosylglycinamide formyltransferase activity    Catalysis of the reaction: 10-formyltetrahydrofolate + N1-(5-phospho-D-ribosyl)glycinamide = tetrahydrofolate + N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide.
    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: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:0003360    brainstem development    The progression of the brainstem from its formation to the mature structure. The brainstem is the part of the brain that connects the brain with the spinal cord.
    GO:0021549    cerebellum development    The process whose specific outcome is the progression of the cerebellum over time, from its formation to the mature structure. The cerebellum is the portion of the brain in the back of the head between the cerebrum and the pons. In mice, the cerebellum controls balance for walking and standing, modulates the force and range of movement and is involved in the learning of motor skills.
    GO:0021987    cerebral cortex development    The progression of the cerebral cortex over time from its initial formation until its mature state. The cerebral cortex is the outer layered region of the telencephalon.
    GO:0006544    glycine metabolic process    The chemical reactions and pathways involving glycine, aminoethanoic 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:0009113    purine nucleobase biosynthetic process    The chemical reactions and pathways resulting in the formation of purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine.
    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.
    GO:0009168    purine ribonucleoside monophosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of purine ribonucleoside monophosphate, a compound consisting of a purine base linked to a ribose sugar esterified with phosphate on the sugar.
    GO:0010035    response to inorganic substance    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an inorganic substance stimulus.
    GO:0010033    response to organic substance    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus.
    GO:0009156    ribonucleoside monophosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of a ribonucleoside monophosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with phosphate on the sugar.
    GO:0046654    tetrahydrofolate biosynthetic process    The chemical reactions and pathways resulting in the formation of tetrahydrofolate, 5,6,7,8-tetrahydrofolic acid, a folate derivative bearing additional hydrogens on the pterin group.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

 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
    DQB  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GRF  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1zly)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1zly
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PUR2_HUMAN | P22102
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.1.2.2
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  PUR2_HUMAN | P22102
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PUR2_HUMAN | P221021mej 1men 1meo 1njs 1rbm 1rbq 1rby 1rbz 1rc0 1rc1 1zlx 2qk4 2v9y 4ew1 4ew2 4ew3 4zyt 4zyu 4zyv 4zyw 4zyx 4zyy 4zyz 4zz0 4zz1 4zz2 4zz3 5j9f

(-) Related Entries Specified in the PDB File

1mej THE APO STRUCTURE OF HUMAN GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE
1men THE APO STRUCTURE OF HUMAN GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE
1meo THE APO STRUCTURE OF HUMAN GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE
1njs HUMAN GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE COMPLEXED TO 10-TRIFLUORO-5,10-DIDEAZAACYCLIC-5,6,7,8-TETRAHYDROFOLIC ACID AT PH 7
1zlx THE APO STRUCTURE OF HUMAN GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE AT PH 6.3