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(-) Description

Title :  CRYSTAL STRUCTURE OF IN VITRO PHOSPHORYLATED HUMAN SAMHD1 (AMINO ACID RESIDUES 115-626) BOUND TO GTP
 
Authors :  L. H. Arnold, D. Schwefel, I. A. Taylor
Date :  09 Sep 15  (Deposition) - 14 Oct 15  (Release) - 14 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.70
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: ROSETTA PLYSS
    Expression System Vector: PET52B
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 115-626
    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 PR OTEIN 1, DNTPASE, DENDRITIC CELL-DERIVED IFNG-INDUCED PROTEIN, DCI P, MONOCYTE PROTEIN 5, MOP-5, SAM DOMAIN AND HD DOMAIN-CONTAINING PR OTEIN 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
1FE4Ligand/IonFE (III) ION
2GTP4Ligand/IonGUANOSINE-5'-TRIPHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:164 , HIS A:167 , ASP A:207 , ASP A:311BINDING SITE FOR RESIDUE FE A1584
2AC2SOFTWAREHIS B:167 , ASP B:207 , ASP B:311BINDING SITE FOR RESIDUE FE B1582
3AC3SOFTWAREARG C:164 , HIS C:167 , ASP C:207 , ASP C:311BINDING SITE FOR RESIDUE FE C1581
4AC4SOFTWAREHIS D:167 , ASP D:207 , ASP D:311BINDING SITE FOR RESIDUE FE D1582
5AC5SOFTWARELYS A:116 , VAL A:117 , ILE A:136 , 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 GTP A1585
6AC6SOFTWARETYR A:155 , VAL A:156 , VAL A:378 , ARG A:451 , LYS B:116 , VAL B:117 , ILE B:118 , ASP B:137 , GLN B:142 , ARG B:145 , PHE B:165BINDING SITE FOR RESIDUE GTP A1586
7AC7SOFTWARELYS C:116 , VAL C:117 , ASP C:137 , ARG C:145 , PHE C:165 , TYR D:155 , VAL D:156 , ARG D:451BINDING SITE FOR RESIDUE GTP D1583
8AC8SOFTWARETYR C:155 , VAL C:156 , VAL C:378 , ARG C:451 , LEU C:453 , VAL D:117 , ILE D:118 , ILE D:136 , ASP D:137 , GLN D:142 , PHE D:165BINDING SITE FOR RESIDUE GTP C1582

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5AO4)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys C:560 -Ser C:561

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5AO4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5AO4)

(-) Exons   (0, 0)

(no "Exon" information available for 5AO4)

(-) 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:430
                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...eeeeehhhhhhhhh...hhhhhhh..hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.........hhhhhhhhhh........hhhhhhhhhhhhhhhh.....hhhhhhhheeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....ee.hhh.ee.......hhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhh...........hhh.eeeeeee....ee......eeeeeee.....hhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ao4 A 115 MKVINDPIHGHIELHPLLVRIIDTPQFQRLRYIKQLGGGYYVFPGASHNRFEHSLGVGYLAGCLVHALGEKQPELQISERDVLCVQIAGLCHDLGHGPFSHMFDGRFIPLARPEVKWTHEQGSVMMFEHLINSNGIKPVMEQYGLIPEEDICFIKEQIVGPLWPYKGRPENKSFLYEIVSNKRNGIDVDKWDYFARDCHHLGIQNNFDYKRFIKFARVCEVDNELRICARDKEVGNLYDMFHTRNSLHRRAYQHKVGNIIDTMITDAFLKADDYIEITGAGGKKYRISTAIDDMEAYTKLTDNIFLEILYSTDPKLKDAREILKQIEYRNLFKYVGETQPTGQIKIKREDYESLPKEVASAKPKVLLDVKLKAEDFIVDVINMHVSFYCKTAPEQLIRVYCKKVDRKSLYAARQYFVQWCADRNFTKPQD 583
                                   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  ||   523  ||   553       563       573       583
                                                                                                                                                                                           276|                                                                                                                                                                                                                         505|      526|                                    
                                                                                                                                                                                            285                                                                                                                                                                                                                          517       547                                    


Chain B from PDB  Type:PROTEIN  Length:422
                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...eeeeehhhhhhhhh...hhhhhhh..hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh......hhhhh..hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.........hhhhhhhhhh........hhhhhhhhhhhhhhhh.....hhhhhhhh.eeee....eeeeee...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....ee.hhh.ee...hhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhh.....hhh.eeeeeee.....ee.........eeeeeee.....hhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ao4 B 115 MKVINDPIHGHIELHPLLVRIIDTPQFQRLRYIKQLGGGYYVFPGASHNRFEHSLGVGYLAGCLVHALGEKQPELQISERDVLCVQIAGLCHDLGHGPFSHMFDGRFIPLARPEVKWTHEQGSVMMFEHLINSNGIKPVMEQYGLIPEEDICFIKEQIVGPLWPYKGRPENKSFLYEIVSNKRNGIDVDKWDYFARDCHHLGIQNNFDYKRFIKFARVCEVDNELRICARDKEVGNLYDMFHTRNSLHRRAYQHKVGNIIDTMITDAFLKADDYIEITGAGGKKYRISTAIDDMEAYTKLTDNIFLEILYSTDPKLKDAREILKQIEYRNLFKYVGETQPTIKREDYESLPKEVASAKVKLKAEDFIVDVINMDHVSFYCKTAPNRAEQLIRVYCKKVDRKSLYAARQYFVQWCADRNFTKP 581
                                   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||     476       492       502  ||   522      |549       559       569       579  
                                                                                                                                                                                           276|                                                                                                                                                                               463|             484|           505|          529|                                  
                                                                                                                                                                                            285                                                                                                                                                                                468              491            516           547                                  


Chain C from PDB  Type:PROTEIN  Length:389
                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...eeeeehhhhhhhhh...hhhhhhh..hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..........hhhhhhhhhhhh......hhhhhhhhhhhhhhhh.....hhhhhhhheeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh........hhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhhh....eeeeee..hhhhhhh.....eeeeeee...ee..eeeeeee......hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ao4 C 114 PMKVINDPIHGHIELHPLLVRIIDTPQFQRLRYIKQLGGGYYVFPGASHNRFEHSLGVGYLAGCLVHALGEKQPELQISERDVLCVQIAGLCHDLGHGPFSHMFDGRFIPLARPEVKWTHEQGSVMMFEHLINSNGIKPVMEQYGLIPEEDICFIKEQIVGPLLWPYKGRPENKSFLYEIVSNKRNGIDVDKWDYFARDCHHLGIQNNFDYKRFIKFARVCEVDNELRICARDKEVGNLYDMFHTRNSLHRRAYQHKVGNIIDTMITDAFLKADYRISTAIDDMEAYTKLTDNIFLEILYSTDPKLKDAREILKQIEYRNLFKYVGETIKREDYESLPKEEDFIVDVINMVSFYCEQLIRVYCKKVDRKSLYAARQYFVQWCADRNFTK 580
                                   123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273  ||   290       300       310       320       330       340       350       360       370       380       390   ||  412       422       432       442       452       469       479|      505|   || 551       561       571         
                                                                                                                                                                                            276|                                                                                                           394|                                                  460|        479|      505| 522|                                 
                                                                                                                                                                                             284                                                                                                            407                                                   468         496       518  547                                 


Chain D from PDB  Type:PROTEIN  Length:384
                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee...eee..hhhhhhhhh...hhhhhhh..hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhh....hhhhhhhhhhhhhhhh.....hhhhhhhheeeee....eeeeee...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.....ee.hhh.ee..hhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhhh.......ee..hhhhhhhh...ee.....ee.........eee.hhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ao4 D 117 VINDPIHGHIELHPLLVRIIDTPQFQRLRYIKQLGGGYYVFPGASHNRFEHSLGVGYLAGCLVHALGEKQPELQISERDVLCVQIAGLCHDLGHGPFSHMFDGRFIPLARPEVKWTHEQGSVMMFEHLINSNGIKPVMEQYGLIPEEDICFIKEQIVPYKGRPENKSFLYEIVSNIDVDKWDYFARDCHHLGIQNNFDYKRFIKFARVCEVDNELRICARDKEVGNLYDMFHTRNSLHRRAYQHKVGNIIDTMITDAFLKADDYIEITGAGGKKYRISTAIDDMEAYTKLTDNIFLEILYSTDPKLKDAREILKQIEYRNLFKYVGETESLPKEVASAKVDVINMVSFYCKTAPNRALIRVYKSLYAARQYFVQWCADRNFTKP 581
                                   126       136       146       156       166       176       186       196       206       216       226       236       246       256       266      |288       298    || 312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       475       500    || 522      |551 ||    567       577    
                                                                                                                                                                                      273|              303|                                                                                                                                                     460|       484|  505|        529| 553|                     
                                                                                                                                                                                       286               308                                                                                                                                                      474        500   518         549  560
   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 5AO4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5AO4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5AO4)

(-) Gene Ontology  (23, 23)

Asymmetric/Biological Unit(hide GO term definitions)

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  5ao4
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  SAMH1_HUMAN | Q9Y3Z3
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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 5ao2 5ao3

(-) 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
5ao2 CRYSTAL STRUCTURE OF HUMAN SAMHD1 (AMINO ACID RESIDUES 115-583) R164A VARIANT BOUND TO DGTP
5ao3 CRYSTAL STRUCTURE OF HUMAN SAMHD1 (AMINO ACID RESIDUES 115-626) BOUND TO GTP