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(-) Description

Title :  STRUCTURAL INSIGHT INTO DGTP-DEPENDENT ACTIVATION OF TETRAMERIC SAMHD1 DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE
 
Authors :  C. Zhu, W. Gao, K. Zhao, X. Qin, Y. Zhang, X. Peng, L. Zhang, Y. Dong, W. Zha W. Wei, Y. Gong, X. F. Yu
Date :  29 Sep 13  (Deposition) - 20 Nov 13  (Release) - 29 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Hd-Domain, Hydrolase, Dntp Binding, Phosphorylation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Zhu, W. Gao, K. Zhao, X. Qin, Y. Zhang, X. Peng, L. Zhang, Y. Dong, W. Zhang, P. Li, W. Wei, Y. Gong, X. F. Yu
Structural Insight Into Dgtp-Dependent Activation Of Tetrameric Samhd1 Deoxynucleoside Triphosphate Triphosphohydrolase
Nat Commun V. 4 2722 2013
PubMed-ID: 24217394  |  Reference-DOI: 10.1038/NCOMMS3722

(-) Compounds

Molecule 1 - DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1
    Chains: A, B
    EC Number: 3.1.5.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 109-626
    Gene: SAMHD1, MOP5
    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

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
1DGT5Ligand/Ion2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
2DTP1Ligand/Ion2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
3MG2Ligand/IonMAGNESIUM ION
4ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1DGT10Ligand/Ion2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
2DTP2Ligand/Ion2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:167 , HIS A:206 , ASP A:207 , ASP A:311BINDING SITE FOR RESIDUE ZN A 701
02AC2SOFTWAREGLN A:149 , LEU A:150 , ARG A:164 , HIS A:215 , ASP A:309 , ASP A:311 , LYS A:312 , TYR A:315 , ASP A:319 , ARG A:366 , HIS A:370 , TYR A:374 , GLN A:375 , HOH A:923 , HOH A:1008 , HOH A:1043 , HOH A:1044 , HOH A:1073BINDING SITE FOR RESIDUE DGT A 702
03AC3SOFTWAREVAL A:156 , PHE A:157 , ILE A:325 , ARG A:372 , HIS A:376 , LYS A:377 , VAL A:378 , HOH A:830 , HOH A:832 , HOH A:859 , HOH A:889 , HOH A:900 , HOH A:912 , HOH A:974 , HOH A:1025 , VAL B:117 , ASN B:119 , HIS B:125 , DGT B:801 , MG B:802 , HOH B:1241BINDING SITE FOR RESIDUE DGT A 703
04AC4SOFTWARELYS A:116 , VAL A:117 , ILE A:118 , ASP A:137 , GLN A:142 , ARG A:145 , PHE A:165 , MG A:705 , HOH A:804 , HOH A:826 , HOH A:843 , HOH A:854 , HOH A:871 , HOH A:886 , HOH A:936 , HOH A:1038 , HOH A:1049 , HOH A:1130 , TYR B:155 , VAL B:156 , VAL B:378 , ARG B:451 , LYS B:455 , DTP B:805BINDING SITE FOR RESIDUE DGT A 704
05AC5SOFTWAREDGT A:704 , HOH A:1038 , DTP B:805BINDING SITE FOR RESIDUE MG A 705
06AC6SOFTWARETYR A:155 , VAL A:156 , VAL A:378 , ARG A:451 , LYS A:455 , DGT A:703 , HOH A:1059 , LYS B:116 , VAL B:117 , ILE B:118 , ASP B:137 , GLN B:142 , ARG B:145 , PHE B:165 , MG B:802 , HOH B:916 , HOH B:978 , HOH B:1033 , HOH B:1061 , HOH B:1118 , HOH B:1141 , HOH B:1150 , HOH B:1241 , HOH B:1258BINDING SITE FOR RESIDUE DGT B 801
07AC7SOFTWAREDGT A:703 , DGT B:801 , HOH B:1241BINDING SITE FOR RESIDUE MG B 802
08AC8SOFTWAREHIS B:167 , HIS B:206 , ASP B:207 , ASP B:311BINDING SITE FOR RESIDUE ZN B 803
09AC9SOFTWAREGLN B:149 , LEU B:150 , ARG B:164 , HIS B:215 , ASP B:309 , ASP B:311 , LYS B:312 , TYR B:315 , ASP B:319 , ARG B:366 , HIS B:370 , TYR B:374 , GLN B:375 , HOH B:944 , HOH B:1048 , HOH B:1070 , HOH B:1081 , HOH B:1137 , HOH B:1216 , HOH B:1249 , HOH B:1333BINDING SITE FOR RESIDUE DGT B 804
10BC1SOFTWAREVAL A:117 , ASN A:119 , DGT A:704 , MG A:705 , HOH A:1038 , VAL B:156 , PHE B:157 , ARG B:372 , HIS B:376 , LYS B:377 , VAL B:378 , HOH B:923 , HOH B:942 , HOH B:1071 , HOH B:1206 , HOH B:1254BINDING SITE FOR RESIDUE DTP B 805

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:341 -A:350
2B:341 -B:350

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4MZ7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4MZ7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4MZ7)

(-) Exons   (0, 0)

(no "Exon" information available for 4MZ7)

(-) Sequences/Alignments

Asymmetric 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:481
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               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..eeeeeee..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....ee.hhh.ee...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh....eeeeee........hhhhhhhhhhhhhhh..........hhh.eeeeeeeee......hhhhhheeee..eeeeee..hhhhh........eeeeeeeee...hhhhhhhhhhhhhhhhhhhh.....hhhhhh..hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mz7 A 113 DTMKVINDPIHGHIELHPLLVRIIDTPQFQRLRYIKQLGGGYYVFPGASHNRFEHSLGVGYLAGCLVHALGEKQPELQISERDVLCVQIAGLCHDLGHGPFSHMFDGRFIPLARPEVKWTHEQGSVMMFEHLINSNGIKPVMEQYGLIPEEDIYFIKEQIVGPLELWPYKGRPENKSFLYEIVSNKRNGIDVDKWDYFARDCHHLGIQNNFDYKRFIKFARVCEVDNELRICARDKEVGNLYDMFHTRNSLHRRAYQHKVGNIIDTMITDAFLKADDYIEITGAGGKKYRISTAIDDMEAYTKLTDNIFLEILYSTDPKLKDAREILKQIEYRNLFKYVGETQPTGQIKIKREDYESLPKEVASAKPKVLLDVKLKAEDFIVDVINMDYGMQEKNPIDHVSFYCKTAPNRAIRITKNQVSQLLPEKFAEQLIRVYCKKVDRKSLYAARQYFVQWCADRNFTKPQDGDVIAPLITPQKKEWN 599
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272    || 288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598 
                                                                                                                                                                                              277|                                                                                                                                                                                                                                                                                                                           
                                                                                                                                                                                               284                                                                                                                                                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:493
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..ee......eeeee...eeeeehhhhhhhhhhhhhhhhhhh..hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...........hhhhhhhhhh........hhhhhhhhhhhhhhhh.....hhhhhhhheeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....ee.hhh.ee...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh....eeeeee........hhhhhhhhhhhhhh...........hhh.eeeeeeeee......hhhhhheeee..eeeeee..hhhhh........eeeeeeeee...hhhhhhhhhhhhhhhhhhh......hhhhhh..hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mz7 B 102 NLYFQGSQIHVDTMKVINDPIHGHIELHPLLVRIIDTPQFQRLRYIKQLGGGYYVFPGASHNRFEHSLGVGYLAGCLVHALGEKQPELQISERDVLCVQIAGLCHDLGHGPFSHMFDGRFIPLARPEVKWTHEQGSVMMFEHLINSNGIKPVMEQYGLIPEEDIYFIKEQIVGPLESLWPYKGRPENKSFLYEIVSNKRNGIDVDKWDYFARDCHHLGIQNNFDYKRFIKFARVCEVDNELRICARDKEVGNLYDMFHTRNSLHRRAYQHKVGNIIDTMITDAFLKADDYIEITGAGGKKYRISTAIDDMEAYTKLTDNIFLEILYSTDPKLKDAREILKQIEYRNLFKYVGETQPTGQIKIKREDYESLPKEVASAKPKVLLDVKLKAEDFIVDVINMDYGMQEKNPIDHVSFYCKTAPNRAIRITKNQVSQLLPEKFAEQLIRVYCKKVDRKSLYAARQYFVQWCADRNFTKPQDGDVIAPLITPQKKEWN 599
                                   111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271      |286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596   
                                                                                                                                                                                                          278|                                                                                                                                                                                                                                                                                                                           
                                                                                                                                                                                                           284
   Legend:   → Mismatch (orange background)
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    → 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 4MZ7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4MZ7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4MZ7)

(-) Gene Ontology  (23, 23)

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 Related Entries

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UniProtKB/Swiss-Prot
        SAMH1_HUMAN | Q9Y3Z3: 2e8o 3u1n 4bzb 4bzc 4cc9 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 5ao4

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