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(-) Description

Title :  HUMAN ADENINE PHOSPHORIBOSYLTRANSFERASE COMPLEXED WITH PRPP, ADE AND R5P
 
Authors :  J. Iulek, M. Silva, C. H. T. P. Tomich, O. H. Thiemann
Date :  11 May 05  (Deposition) - 25 Apr 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.83
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase, Glycosyltransferase, Purine Salvage (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. H. Silva, M. Silva, J. Iulek, O. H. Thiemann
Structural Complexes Of Human Adenine Phosphoribosyltransferase Reveal Novel Features Of The Aprt Catalytic Mechanism
J. Biomol. Struct. Dyn. V. 25 589 2008
PubMed-ID: 18399692

(-) Compounds

Molecule 1 - ADENINE PHOSPHORIBOSYLTRANSFERASE
    ChainsA, B
    EC Number2.4.2.7
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET29A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneAPRT
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymAPRT

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric/Biological Unit (5, 10)
No.NameCountTypeFull Name
1ADE2Ligand/IonADENINE
2HSX2Ligand/Ion5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE
3MG2Ligand/IonMAGNESIUM ION
4PO42Ligand/IonPHOSPHATE ION
5PRP2Ligand/IonALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRP A:502 , PO4 A:504 , HSX A:506 , HOH A:662 , HOH A:663BINDING SITE FOR RESIDUE MG A 500
02AC2SOFTWARESER A:66 , ARG A:67 , LYS A:88 , MG A:500 , HSX A:506 , HOH A:663 , ARG B:87 , LYS B:91BINDING SITE FOR RESIDUE PO4 A 504
03AC3SOFTWAREARG A:87 , LYS A:91 , SER B:66 , ARG B:67 , LYS B:88 , MG B:501 , HSX B:507 , HOH B:663 , HOH B:664BINDING SITE FOR RESIDUE PO4 A 505
04AC4SOFTWARESER A:66 , ARG A:67 , LYS A:88 , ASP A:127 , ASP A:128 , LEU A:129 , ALA A:131 , THR A:132 , GLY A:133 , GLY A:134 , THR A:135 , MG A:500 , ADE A:655 , HOH A:658 , HOH A:662 , HOH A:663 , HOH A:687 , HOH A:729 , HOH A:745 , HOH A:819 , HOH A:829 , ARG B:87 , LYS B:91BINDING SITE FOR RESIDUE PRP A 502
05AC5SOFTWAREARG A:67 , ASP A:127 , ASP A:128 , LEU A:129 , ALA A:131 , THR A:132 , GLY A:133 , GLY A:134 , THR A:135 , MG A:500 , PO4 A:504 , HOH A:658 , HOH A:659 , HOH A:687 , HOH A:745 , HOH A:819 , HOH A:829BINDING SITE FOR RESIDUE HSX A 506
06AC6SOFTWAREVAL A:25 , PHE A:26 , ARG A:27 , ARG A:67 , LEU A:129 , ALA A:131 , LEU A:159 , PRP A:502 , HOH A:656 , HOH A:657 , HOH A:658 , HOH A:659 , HOH A:660 , HOH A:661 , HOH A:809BINDING SITE FOR RESIDUE ADE A 655
07AC7SOFTWAREPO4 A:505 , PRP B:503 , HSX B:507 , HOH B:663 , HOH B:664BINDING SITE FOR RESIDUE MG B 501
08AC8SOFTWAREARG A:87 , LYS A:91 , SER B:66 , ARG B:67 , LYS B:88 , ASP B:127 , ASP B:128 , LEU B:129 , ALA B:131 , THR B:132 , GLY B:133 , GLY B:134 , THR B:135 , MG B:501 , ADE B:656 , HOH B:657 , HOH B:663 , HOH B:664 , HOH B:701 , HOH B:717 , HOH B:794 , HOH B:796 , HOH B:836 , HOH B:846BINDING SITE FOR RESIDUE PRP B 503
09AC9SOFTWAREPO4 A:505 , ARG B:67 , ASP B:127 , ASP B:128 , LEU B:129 , ALA B:131 , THR B:132 , GLY B:133 , GLY B:134 , THR B:135 , MG B:501 , HOH B:657 , HOH B:701 , HOH B:717 , HOH B:796 , HOH B:836BINDING SITE FOR RESIDUE HSX B 507
10BC1SOFTWAREVAL B:25 , PHE B:26 , ARG B:27 , ARG B:67 , LEU B:129 , ALA B:131 , LEU B:159 , PRP B:503 , HOH B:657 , HOH B:659 , HOH B:660 , HOH B:661 , HOH B:662 , HOH B:819 , HOH B:838BINDING SITE FOR RESIDUE ADE B 656

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ZN7)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Phe A:19 -Pro A:20
2Asp A:65 -Ser A:66
3Ala A:169 -Pro A:170
4Phe B:19 -Pro B:20
5Asp B:65 -Ser B:66
6Ala B:169 -Pro B:170

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (9, 18)

Asymmetric/Biological Unit (9, 18)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_069049L33PAPT_HUMANDisease (APRTD)  ---A/BL33P
2UniProtVAR_006747D65VAPT_HUMANDisease (APRTD)104894506A/BD65V
3UniProtVAR_069050V84MAPT_HUMANDisease (APRTD)200392753A/BV84M
4UniProtVAR_006748L110PAPT_HUMANDisease (APRTD)104894508A/BL110P
5UniProtVAR_019055Q121RAPT_HUMANPolymorphism8191494A/BQ121R
6UniProtVAR_069051G133DAPT_HUMANDisease (APRTD)  ---A/BG133D
7UniProtVAR_006749M136TAPT_HUMANDisease (APRTD)28999113A/BM136T
8UniProtVAR_022608V150FAPT_HUMANDisease (APRTD)281860266A/BV150F
9UniProtVAR_022609C153RAPT_HUMANDisease (APRTD)  ---A/BC153R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUR_PYR_PR_TRANSFERPS00103 Purine/pyrimidine phosphoribosyl transferases signature.APT_HUMAN123-135
 
  2A:123-135
B:123-135

(-) Exons   (5, 10)

Asymmetric/Biological Unit (5, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003783641ENSE00001436135chr16:88878342-88878228115APT_HUMAN1-27272A:3-27
B:3-27
25
25
1.2ENST000003783642ENSE00001503918chr16:88878064-88877958107APT_HUMAN27-63372A:27-63
B:27-63
37
37
1.3ENST000003783643ENSE00001503917chr16:88876964-88876831134APT_HUMAN63-107452A:63-107
B:63-107
45
45
1.4ENST000003783644ENSE00001436356chr16:88876556-8887647879APT_HUMAN108-134272A:108-134
B:108-134
27
27
1.5aENST000003783645aENSE00001436502chr16:88876248-88875877372APT_HUMAN134-180472A:134-180
B:134-180
47
47

(-) 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:178
 aligned with APT_HUMAN | P07741 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:178
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172        
            APT_HUMAN     3 DSELQLVEQRIRSFPDFPTPGVVFRDISPVLKDPASFRAAIGLLARHLKATHGGRIDYIAGLDSRGFLFGPSLAQELGLGCVLIRKRGKLPGPTLWASYSLEYGKAELEIQKDALEPGQRVVVVDDLLATGGTMNAACELLGRLQAEVLECVSLVELTSLKGREKLAPVPFFSLLQYE 180
               SCOP domains d1zn7a_ A: Adenine PRTase                                                                                                                                                          SCOP domains
               CATH domains 1zn7A00 A:3-180  [code=3.40.50.2020, no name defined]                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh..eeee.......eeeehhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhh.eeeeeee.......eeeeeeee..eeeeeeee........eeeeeeeee..hhhhhhhhhhhhhh..eeeeeeeeeee...hhhhhhh...eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------P-------------------------------V------------------M-------------------------P----------R-----------D--T-------------F--R--------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------PUR_PYR_PR_TR--------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:3-27    -----------------------------------Exon 1.3  PDB: A:63-107 UniProt: 63-107      Exon 1.4  PDB: A:108-134   ---------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------Exon 1.2  PDB: A:27-63 UniProt: 27-63----------------------------------------------------------------------Exon 1.5a  PDB: A:134-180 UniProt: 134-180      Transcript 1 (2)
                 1zn7 A   3 DSELQLVEQRIRSFPDFPTPGVVFRDISPVLKDPASFRAAIGLLARHLKATHGGRIDYIAGLDSRGFLFGPSLAQELGLGCVLIRKRGKLPGPTLWASYSLEYGKAELEIQKDALEPGQRVVVVDDLLATGGTMNAACELLGRLQAEVLECVSLVELTSLKGREKLAPVPFFSLLQYE 180
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172        

Chain B from PDB  Type:PROTEIN  Length:178
 aligned with APT_HUMAN | P07741 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:178
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172        
            APT_HUMAN     3 DSELQLVEQRIRSFPDFPTPGVVFRDISPVLKDPASFRAAIGLLARHLKATHGGRIDYIAGLDSRGFLFGPSLAQELGLGCVLIRKRGKLPGPTLWASYSLEYGKAELEIQKDALEPGQRVVVVDDLLATGGTMNAACELLGRLQAEVLECVSLVELTSLKGREKLAPVPFFSLLQYE 180
               SCOP domains d1zn7b_ B: Adenine PRTase                                                                                                                                                          SCOP domains
               CATH domains 1zn7B00 B:3-180  [code=3.40.50.2020, no name defined]                                                                                                                              CATH domains
           Pfam domains (1) ---------------------------Pribosyltran-1zn7B01 B:30-157                                                                                                   ----------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------Pribosyltran-1zn7B02 B:30-157                                                                                                   ----------------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhh..eeee.......eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhhhh.eeeeeee.......eeeeeeee..eeeeeeee........eeeeeeeee..hhhhhhhhhhhhhh..eeeeeeeeeee...hhhhhhh...eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------P-------------------------------V------------------M-------------------------P----------R-----------D--T-------------F--R--------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------PUR_PYR_PR_TR--------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: B:3-27    -----------------------------------Exon 1.3  PDB: B:63-107 UniProt: 63-107      Exon 1.4  PDB: B:108-134   ---------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------Exon 1.2  PDB: B:27-63 UniProt: 27-63----------------------------------------------------------------------Exon 1.5a  PDB: B:134-180 UniProt: 134-180      Transcript 1 (2)
                 1zn7 B   3 DSELQLVEQRIRSFPDFPTPGVVFRDISPVLKDPASFRAAIGLLARHLKATHGGRIDYIAGLDSRGFLFGPSLAQELGLGCVLIRKRGKLPGPTLWASYSLEYGKAELEIQKDALEPGQRVVVVDDLLATGGTMNAACELLGRLQAEVLECVSLVELTSLKGREKLAPVPFFSLLQYE 180
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172        

   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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (APT_HUMAN | P07741)
molecular function
    GO:0016208    AMP binding    Interacting selectively and non-covalently with AMP, adenosine monophosphate.
    GO:0002055    adenine binding    Interacting selectively and non-covalently with adenine, a purine base.
    GO:0003999    adenine phosphoribosyltransferase activity    Catalysis of the reaction: AMP + diphosphate = adenine + 5-phospho-alpha-D-ribose 1-diphosphate.
    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.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
biological process
    GO:0044209    AMP salvage    The chemical reactions and pathways resulting in the formation of adenosine monophosphate (AMP) from derivatives of it (either adenine, ADP or adenosine 3',5'-bisphosphate) without de novo synthesis.
    GO:0046083    adenine metabolic process    The chemical reactions and pathways involving adenine, 6-aminopurine, one of the five main bases found in nucleic acids and a component of numerous important derivatives of its corresponding ribonucleoside, adenosine.
    GO:0006168    adenine salvage    Any process that generates adenine, 6-aminopurine, from derivatives of it without de novo synthesis.
    GO:0032869    cellular response to insulin stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
    GO:0007625    grooming behavior    The specific behavior of an organism relating to grooming, cleaning and brushing to remove dirt and parasites.
    GO:0007595    lactation    The regulated release of milk from the mammary glands and the period of time that a mother lactates to feed her young.
    GO:0009116    nucleoside metabolic process    The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine).
    GO:0006166    purine ribonucleoside salvage    Any process which produces a purine nucleoside from derivatives of it, without de novo synthesis.
    GO:0043101    purine-containing compound salvage    Any process that generates a purine-containing compound, any nucleobase, nucleoside, nucleotide or nucleic acid that contains a purine base, from derivatives of them without de novo synthesis.
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.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.

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 Related Entries

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

UniProtKB/Swiss-Prot
        APT_HUMAN | P077411opu 1ore 1zn8 1zn9 4x44 4x45

(-) Related Entries Specified in the PDB File

1ore STRUCTURE OF HUMAN ADENINE PHOSPHORIBOSYLTRANSFERASE
1zn8 SAME PROTEIN COMPLEXED WITH AMP, IN SPACE GROUP P1 AT 1.76 A RESOLUTION
1zn9 SAME PROTEIN IN APO AND AMP COMPLEXED FORMS