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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN SAMHD1 (AMINO ACID RESIDUES 115-583) R164A VARIANT BOUND TO DGTP
 
Authors :  D. Schwefel, I. A. Taylor
Date :  09 Sep 15  (Deposition) - 14 Oct 15  (Release) - 14 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.97
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Hydrolase, Deoxynucleoside Triphosphate Triphosphohydrolase, Hiv Restriction Factor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. H. Arnold, H. C. T. Groom, S. Kunzelmann, D. Schwefel, S. J. Caswell, P. Ordonez, M. C. Mann, S. Rueschenbaum, D. C. Goldstone, S. Pennell, S. A. Howell, J. P. Stoye, M. Webb, I. A. Taylor, K. N. Bishop
Phospho-Dependent Regulation Of Samhd1 Oligomerisation Couples Catalysis And Restriction.
Plos Pathog. V. 11 5194 2015
PubMed-ID: 26431200  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1005194

(-) Compounds

Molecule 1 - DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1
    Chains: A, B, C, D
    EC Number: 3.1.5.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA2
    Expression System Vector: PET52B
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 115-583
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DNTPASE, DENDRITIC CELL-DERIVED IFNG-INDUCED PROTEIN, DCIP, MONOCYTE PROTEIN 5, MOP-5, SAM DOMAIN AND HD DOMAIN-CONTAINING PROTEIN 1, SAMHD1

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1DGT4Ligand/Ion2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
2FE4Ligand/IonFE (III) ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:167 , HIS A:206 , ASP A:207 , ASP A:311 , HOH A:2001BINDING SITE FOR RESIDUE FE A1001
2AC2SOFTWAREHIS B:167 , HIS B:206 , ASP B:207 , ASP B:311 , HOH B:2001BINDING SITE FOR RESIDUE FE B1001
3AC3SOFTWAREHIS C:167 , HIS C:206 , ASP C:207 , ASP C:311BINDING SITE FOR RESIDUE FE C1001
4AC4SOFTWAREHIS D:167 , HIS D:206 , ASP D:207 , ASP D:311BINDING SITE FOR RESIDUE FE D1001
5AC5SOFTWARELYS A:116 , VAL A:117 , ILE A:118 , ASP A:137 , GLN A:142 , ARG A:145 , PHE A:165 , TYR B:155 , VAL B:156 , VAL B:378 , ARG B:451BINDING SITE FOR RESIDUE DGT B1583
6AC6SOFTWARETYR A:155 , VAL A:156 , VAL A:378 , ARG A:451 , LEU A:453 , LYS B:116 , VAL B:117 , ILE B:118 , ASP B:137 , GLN B:142 , ARG B:145 , PHE B:165BINDING SITE FOR RESIDUE DGT A1583
7AC7SOFTWARELYS C:116 , VAL C:117 , VAL C:133 , ASP C:137 , GLN C:142 , ARG C:145 , PHE C:165 , TYR D:155 , VAL D:156 , VAL D:378 , ARG D:451BINDING SITE FOR RESIDUE DGT C1583
8AC8SOFTWARETYR C:155 , VAL C:156 , VAL C:378 , ARG C:451 , LYS D:116 , VAL D:117 , ASP D:137 , GLN D:142 , ARG D:145 , PHE D:165BINDING SITE FOR RESIDUE DGT C1584

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:341 -A:350
2B:341 -B:350
3C:341 -C:350
4D:341 -D:350

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Lys A:486 -Val A:487
2Lys B:486 -Val B:487
3Thr D:463 -Gly D:464
4Lys D:486 -Val D:487

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5AO2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5AO2)

(-) Exons   (0, 0)

(no "Exon" information available for 5AO2)

(-) 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:436
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...eeeeehhhhhhhhhhhhhhhhhhh..hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.........hhhhhhhhhh........hhhhhhhhhhhhhhhh.....hhhhhhhh.eeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....ee.hhh.ee...hhhhhhhhhh...hhhhhhhhhh....hhhhhhhhhhhhhh...eeeeee........hhhhh.hhhhhhhh...........hhh.eeeeeee......ee..........eeeeeee....hhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ao2 A 115 MKVINDPIHGHIELHPLLVRIIDTPQFQRLRYIKQLGGGYYVFPGASHNAFEHSLGVGYLAGCLVHALGEKQPELQISERDVLCVQIAGLCHDLGHGPFSHMFDGRFIPLARPEVKWTHEQGSVMMFEHLINSNGIKPVMEQYGLIPEEDICFIKEQIVGPLLWPYKGRPENKSFLYEIVSNKRNGIDVDKWDYFARDCHHLGIQNNFDYKRFIKFARVCEVDNELRICARDKEVGNLYDMFHTRNSLHRRAYQHKVGNIIDTMITDAFLKADDYIEITGAGGKKYRISTAIDDMEAYTKLTDNIFLEILYSTDPKLKDAREILKQIEYRNLFKYVGETQPTGQIKIKREDYESLPKEVASAKPKVLLDVKLKAEDFIVDVINMIDHVSFYCKTAPNRAIEQLIRVYCKKVDRKSLYAARQYFVQWCADRNFTKPQ 582
                                   124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274 ||    291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501   ||  520       530|      556       566       576      
                                                                                                                                                                                           276|                                                                                                                                                                                                                          505|            530|                                   
                                                                                                                                                                                            284                                                                                                                                                                                                                           515             547                                   


Chain B from PDB  Type:PROTEIN  Length:419
                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...eeeeehhhhhhhhhhhhhhhhhhh..hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........hhhhhhhhhh........hhhhhhhhhhhhhhhh.....hhhhhhhheeeeee..eeeeee...hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh......ee.hhh.ee...hhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhh...........hhh.eeeeeee..eeeeeee...hhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ao2 B 115 MKVINDPIHGHIELHPLLVRIIDTPQFQRLRYIKQLGGGYYVFPGASHNAFEHSLGVGYLAGCLVHALGEKQPELQISERDVLCVQIAGLCHDLGHGPFSHMFDGRFIPLARPEVKWTHEQGSVMMFEHLINSNGIKPVMEQYGLIPEEDICFIKEQIVGPLWPYKGRPENKSFLYEIVSNKRNGIDVDKWDYFARDCHHLGIQNNFDYKRFIKFARVCEVDNELRICARDKEVGNLYDMFHTRNSLHRRAYQHKVGNIIDTMITDAFLKADDYIEITGAGGKKYRISTAIDDMEAYTKLTDNIFLEILYSTDPKLKDAREILKQIEYRNLFKYVGETQPTGQIKIKREDYESLPKEVASAKPKVLLDVKLKAEDFIVDVINMEQLIRVYCKKVDRKSLYAARQYFVQWCADRNFTKPQ 582
                                   124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274 ||    292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502  ||   553       563       573         
                                                                                                                                                                                           276|                                                                                                                                                                                                                         505|                                   
                                                                                                                                                                                            285                                                                                                                                                                                                                          547                                   


Chain C from PDB  Type:PROTEIN  Length:438
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee...eeeeehhhhhhhhhhhhhhhhhhh..hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..........hhhhhhhhhh........hhhhhhhhhhhhhhhh.....hhhhhhhhheeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...ee.hhh.ee...hhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhh....eeeeee........hhhhh.hhhhhhhh.....hhh.eeeeeee...hhhhh.ee..............eeeeeee...hhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ao2 C 115 MKVINDPIHGHIELHPLLVRIIDTPQFQRLRYIKQLGGGYYVFPGASHNAFEHSLGVGYLAGCLVHALGEKQPELQISERDVLCVQIAGLCHDLGHGPFSHMFDGRFIPLARPEVKWTHEQGSVMMFEHLINSNGIKPVMEQYGLIPEEDICFIKEQIVGPLSLWPYKGRPENKSFLYEIVSNKRNGIDVDKWDYFARDCHHLGIQNNFDYKRFIKFARVCEVDNELRICARDKEVGNLYDMFHTRNSLHRRAYQHKVGNIIDTMITDAFLKADDYIEITGAGGKKYRISTAIDDMEAYTKLTDNIFLEILYSTDPKLKDAREILKQIEYRNLFKYVGETQPTGQIKIKREDYESLPKEVASADVKLKAEDFIVDVINMDYPIDHVSFYCKTAPNRAIQLLPEQLIRVYCKKVDRKSLYAARQYFVQWCADRNFTKPQ 582
                                   124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274 ||    290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480  ||   496       506||     522       540 ||    554       564       574        
                                                                                                                                                                                           276|                                                                                                                                                                                                     483|              507|             530|  ||                                   
                                                                                                                                                                                            283                                                                                                                                                                                                      490               514              539  ||                                   
                                                                                                                                                                                                                                                                                                                                                                                                                                           542|                                   
                                                                                                                                                                                                                                                                                                                                                                                                                                            547                                   


Chain D from PDB  Type:PROTEIN  Length:419
                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...eeeeehhhhhhhhhhhhhhhhhhh..hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........hhhhhhhhhh........hhhhhhhhhhhhhhhh.....hhhhhhhheeeeee..eeeeee...hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh......ee.hhh.ee...hhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhhh....eeeeee........hhhhh.hhhhhhhh...........hhh.eeeeeee..eeeeeee...hhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ao2 D 115 MKVINDPIHGHIELHPLLVRIIDTPQFQRLRYIKQLGGGYYVFPGASHNAFEHSLGVGYLAGCLVHALGEKQPELQISERDVLCVQIAGLCHDLGHGPFSHMFDGRFIPLARPEVKWTHEQGSVMMFEHLINSNGIKPVMEQYGLIPEEDICFIKEQIVGPLWPYKGRPENKSFLYEIVSNKRNGIDVDKWDYFARDCHHLGIQNNFDYKRFIKFARVCEVDNELRICARDKEVGNLYDMFHTRNSLHRRAYQHKVGNIIDTMITDAFLKADDYIEITGAGGKKYRISTAIDDMEAYTKLTDNIFLEILYSTDPKLKDAREILKQIEYRNLFKYVGETQPTGQIKIKREDYESLPKEVASAKPKVLLDVKLKAEDFIVDVINMEQLIRVYCKKVDRKSLYAARQYFVQWCADRNFTKPQ 582
                                   124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274 ||    292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502  ||   553       563       573         
                                                                                                                                                                                           276|                                                                                                                                                                                                                         505|                                   
                                                                                                                                                                                            285                                                                                                                                                                                                                          547
   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 5AO2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5AO2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5AO2)

(-) Gene Ontology  (23, 23)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Lys A:486 - Val A:487   [ RasMol ]  
    Lys B:486 - Val B:487   [ RasMol ]  
    Lys D:486 - Val D:487   [ RasMol ]  
    Thr D:463 - Gly D:464   [ RasMol ]  
 

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  5ao2
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  SAMH1_HUMAN | Q9Y3Z3
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  3.1.5.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        SAMH1_HUMAN | Q9Y3Z3: 2e8o 3u1n 4bzb 4bzc 4cc9 4mz7 4q7h 4qfx 4qfy 4qfz 4qg0 4qg1 4qg2 4qg4 4rxo 4rxp 4rxq 4rxr 4rxs 4tnp 4tnq 4tnr 4tnx 4tny 4tnz 4to0 4to1 4to2 4to3 4to4 4to5 4to6 4zwe 4zwg 5ao0 5ao1 5ao3 5ao4

(-) Related Entries Specified in the PDB File

5ao0 CRYSTAL STRUCTURE OF HUMAN SAMHD1 (AMINO ACID RESIDUES 41-583) BOUND TO DDGTP
5ao1 CRYSTAL STRUCTURE OF HUMAN SAMHD1 (AMINO ACID RESIDUES 115-583) BOUND TO DDGTP
5ao3 CRYSTAL STRUCTURE OF HUMAN SAMHD1 (AMINO ACID RESIDUES 115-626) BOUND TO GTP
5ao4 CRYSTAL STRUCTURE OF IN VITRO PHOSPHORYLATED HUMAN SAMHD1 (AMINO ACID RESIDUES 115-626) BOUND TO GTP