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(-) Description

Title :  CRYSTAL STRUCTURE OF LEISHMANIA MAJOR ADP RIBOSYLATION FACTOR-LIKE 1.
 
Authors :  J. R. Fleming, A. Dawson, W. N. Hunter
Date :  24 Feb 10  (Deposition) - 02 Mar 10  (Release) - 15 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Gtp-Binding Protein, Small Gtpase, Nucleotide-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. R. Fleming, A. Dawson, W. N. Hunter
Crystal Structure Of Leishmania Major Adp Ribosylation Factor-Like 1 And A Classification Of Related Gtpase Family Members In This Kinetoplastid.
Mol. Biochem. Parasitol. V. 174 141 2010
PubMed-ID: 20801163  |  Reference-DOI: 10.1016/J.MOLBIOPARA.2010.08.002

(-) Compounds

Molecule 1 - ADP-RIBOSYLATION FACTOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15BTEV
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: RIL
    Expression System Vector Type: PLASMID
    Organism Scientific: LEISHMANIA MAJOR
    Organism Taxid: 5664
    Other Details: DISULPHIDE LINK BETWEEN C83A AND C83B
    Strain: FRIEDLIN
    Synonym: ADP RIBOSYLATION FACTOR-LIKE 1

 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
1GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:29 , ASN A:30 , ALA A:31 , GLY A:32 , LYS A:33 , THR A:34 , SER A:35 , LYS A:130 , ASP A:132 , LEU A:133 , MET A:152 , SER A:162 , SER A:163 , LYS A:164 , MG A:189 , HOH A:2045 , HOH A:2049 , HOH A:2050BINDING SITE FOR RESIDUE GDP A 188
2AC2SOFTWARETHR A:34 , GLU A:57 , GDP A:188 , HOH A:2013 , HOH A:2017 , HOH A:2049 , HOH A:2050BINDING SITE FOR RESIDUE MG A 189
3AC3SOFTWAREASP B:29 , ASN B:30 , ALA B:31 , GLY B:32 , LYS B:33 , THR B:34 , SER B:35 , LYS B:130 , ASP B:132 , LEU B:133 , SER B:150 , MET B:152 , SER B:162 , SER B:163 , LYS B:164 , MG B:189 , HOH B:2015 , HOH B:2029 , HOH B:2030 , HOH B:2031BINDING SITE FOR RESIDUE GDP B 188
4AC4SOFTWARETHR B:34 , GLU B:57 , GDP B:188 , HOH B:2010 , HOH B:2015 , HOH B:2029 , HOH B:2030BINDING SITE FOR RESIDUE MG B 189

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:83 -B:83

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2X77)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2X77)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2X77)

(-) Exons   (0, 0)

(no "Exon" information available for 2X77)

(-) 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:181
 aligned with Q4QEJ1_LEIMA | Q4QEJ1 from UniProtKB/TrEMBL  Length:187

    Alignment length:181
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183 
         Q4QEJ1_LEIMA     4 WLASLKQTLGLLPADRKIRVLMLGLDNAGKTSILYRLHLGDVVTTVPTVGVNLETLQYKNISFEVWDLGGQTGVRPYWRCYFSDTDAVIYVVDSTDRDRMGVAKHELYALLDEDELRKSLLLIFANKQDLPDAASEAEIAEQLGVSSIMNRTWTIVKSSSKTGDGLVEGMDWLVERLREQG 184
               SCOP domains d2x77a_ A: automated matches                                                                                                                                                          SCOP domains
               CATH domains 2x77A00 A:4-184 P-loop containing nucleotide triphosphate hydrolases                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh......eeeeeeee...hhhhhhhhh.....eee.......eeeeee..eeeeeeee..................eeeeeee.....hhhhhhhhhhhhhh.......eeeeeee........hhhhhhhhhhhhhh....eeeee.......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x77 A   4 WLASLKQTLGLLPADRKIRVLMLGLDNAGKTSILYRLHLGDVVTTVPTVGVNLETLQYKNISFEVWDLGGQTGVRPYWRCYFSDTDAVIYVVDSTDRDRMGVAKHELYALLDEDELRKSLLLIFANKQDLPDAASEAEIAEQLGVSSIMNRTWTIVKSSSKTGDGLVEGMDWLVERLREQG 184
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183 


Chain B from PDB  Type:PROTEIN  Length:166
 aligned with Q4QEJ1_LEIMA | Q4QEJ1 from UniProtKB/TrEMBL  Length:187

    Alignment length:181
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182 
         Q4QEJ1_LEIMA     3 AWLASLKQTLGLLPADRKIRVLMLGLDNAGKTSILYRLHLGDVVTTVPTVGVNLETLQYKNISFEVWDLGGQTGVRPYWRCYFSDTDAVIYVVDSTDRDRMGVAKHELYALLDEDELRKSLLLIFANKQDLPDAASEAEIAEQLGVSSIMNRTWTIVKSSSKTGDGLVEGMDWLVERLREQ 183
               SCOP domains d2x77b_ B: automated matches                                                                                                                                                          SCOP domains
               CATH domains 2x77B00 B:3-183 P-loop containing nucleotide t      riphosphate hydrola         ses                                                                                                   CATH domains
           Pfam domains (1) ---Arf-2x77B01 B:6-180                                                                                                                                                            --- Pfam domains (1)
           Pfam domains (2) ---Arf-2x77B02 B:6-180                                                                                                                                                            --- Pfam domains (2)
         Sec.struct. author ....hhhhhhhh......eeeeeeee...hhhhhhhhh.....ee.------..eeeee..eeeee.ee..---------.......eeeeeee..hhhhhhhhhhhhhhhhhhhhhh..eeeeeee........hhhhhhhhh.........eeeee.......hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x77 B   3 AWLASLKQTLGLLPADRKIRVLMLGLDNAGKTSILYRLHLGDVVTT------NLETLQYKNISFEVWDLGG---------CYFSDTDAVIYVVDSTDRDRMGVAKHELYALLDEDELRKSLLLIFANKQDLPDAASEAEIAEQLGVSSIMNRTWTIVKSSSKTGDGLVEGMDWLVERLREQ 183
                                    12        22        32        42     |   -  |     62        72|        -|       92       102       112       122       132       142       152       162       172       182 
                                                                        48     55                73        83
   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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: P-loop_NTPase (1112)
(-)
Family: Arf (26)
(-)
Leishmania major (1)
1aArf-2x77B01B:6-180
1bArf-2x77B02B:6-180

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q4QEJ1_LEIMA | Q4QEJ1)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    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.
biological process
    GO:0006622    protein targeting to lysosome    The process of directing proteins towards the lysosome using signals contained within the protein.
    GO:0030100    regulation of endocytosis    Any process that modulates the frequency, rate or extent of endocytosis.
    GO:0007264    small GTPase mediated signal transduction    Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0005802    trans-Golgi network    The network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination.

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