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(-) Description

Title :  THE STRUCTURE OF GTP-DTTP-BOUND SAMHD1
 
Authors :  C. F. Zhu, W. Wei, X. Peng, Y. H. Dong, Y. Gong, X. F. Yu
Date :  11 Dec 14  (Deposition) - 11 Mar 15  (Release) - 25 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Hd-Domain, Hydrolase, Dntp And Gtp Binding, Phosphorylation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. F. Zhu, W. Wei, X. Peng, Y. H. Dong, Y. Gong, X. F. Yu
The Mechanism Of Substrate-Controlled Allosteric Regulation Of Samhd1 Activated By Gtp.
Acta Crystallogr. , Sect. D V. 71 516 2015
PubMed-ID: 25760601  |  Reference-DOI: 10.1107/S1399004714027527

(-) 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
    Gene: SAMHD1, MOP5
    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  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1GTP2Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
3TTP4Ligand/IonTHYMIDINE-5'-TRIPHOSPHATE
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1GTP4Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3TTP8Ligand/IonTHYMIDINE-5'-TRIPHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:155 , VAL A:156 , VAL A:378 , ARG A:451 , LYS A:455 , LYS A:523 , TTP A:803 , HOH A:920 , HOH A:998 , HOH A:1005 , HOH A:1050 , HOH A:1056 , HOH A:1069 , LYS B:116 , VAL B:117 , ILE B:118 , ASP B:137 , GLN B:142 , ARG B:145 , PHE B:165 , MG B:701BINDING SITE FOR RESIDUE GTP A 801
2AC2SOFTWAREGLN A:149 , LEU A:150 , ARG A:164 , HIS A:167 , HIS A:206 , ASP A:207 , HIS A:210 , HIS A:215 , HIS A:233 , ASP A:311 , TYR A:315 , ASP A:319 , TYR A:374 , GLN A:375 , HOH A:970 , HOH A:1014BINDING SITE FOR RESIDUE TTP A 802
3AC3SOFTWAREVAL A:156 , PHE A:157 , ARG A:333 , PHE A:337 , ARG A:352 , LYS A:354 , ASN A:358 , ARG A:372 , HIS A:376 , LYS A:377 , VAL A:378 , LYS A:523 , GTP A:801 , HOH A:920 , HOH A:941 , HOH A:951 , HOH A:997 , HOH A:1026 , VAL B:117 , ASN B:119 , HIS B:125 , MG B:701BINDING SITE FOR RESIDUE TTP A 803
4AC4SOFTWARELYS A:116 , VAL A:117 , ILE A:118 , ASP A:137 , GLN A:142 , ARG A:145 , PHE A:165 , MG A:805 , HOH A:907 , HOH A:912 , HOH A:916 , HOH A:953 , HOH A:1003 , HOH A:1018 , HOH A:1019 , TYR B:155 , VAL B:156 , VAL B:378 , ARG B:451 , LYS B:455 , LYS B:523 , TTP B:703BINDING SITE FOR RESIDUE GTP A 804
5AC5SOFTWAREGTP A:804 , HOH A:907 , TTP B:703BINDING SITE FOR RESIDUE MG A 805
6AC6SOFTWAREGTP A:801 , TTP A:803 , HOH A:920 , LYS B:116BINDING SITE FOR RESIDUE MG B 701
7AC7SOFTWAREGLN B:149 , LEU B:150 , ARG B:164 , HIS B:167 , HIS B:206 , ASP B:207 , HIS B:210 , HIS B:215 , HIS B:233 , ASP B:311 , TYR B:315 , ASP B:319 , TYR B:374 , GLN B:375 , HOH B:856 , HOH B:887BINDING SITE FOR RESIDUE TTP B 702
8AC8SOFTWAREVAL A:117 , ASN A:119 , HIS A:125 , GTP A:804 , MG A:805 , HOH A:907 , VAL B:156 , PHE B:157 , ARG B:333 , PHE B:337 , ARG B:352 , LYS B:354 , ASN B:358 , ARG B:372 , HIS B:376 , LYS B:377 , VAL B:378 , LYS B:523 , HOH B:814 , HOH B:842 , HOH B:860 , HOH B:889BINDING SITE FOR RESIDUE TTP B 703

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4RXS)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RXS)

(-) 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...hhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhh....eeeeee........hhhhhhhhhhhhhhh..........hhh.eeeeeeeee......hhhhhh.ee.......ee..hhhhh........eeeeeeeee...hhhhhhhhhhhhhhhhhhh......hhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rxs 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:492
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               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...hhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhh....eeeeee........hhhhhhhhhhhhhhh..........hhh.eeeeeeeee......hhhhhh.eee..eeeeee..hhhhh........eeeeeeeee...hhhhhhhhhhhhhhhhhhh......hhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4rxs B 102 NLYFQGSQIHVDTMKVINDPIHGHIELHPLLVRIIDTPQFQRLRYIKQLGGGYYVFPGASHNRFEHSLGVGYLAGCLVHALGEKQPELQISERDVLCVQIAGLCHDLGHGPFSHMFDGRFIPLARPEVKWTHEQGSVMMFEHLINSNGIKPVMEQYGLIPEEDIYFIKEQIVGPLELWPYKGRPENKSFLYEIVSNKRNGIDVDKWDYFARDCHHLGIQNNFDYKRFIKFARVCEVDNELRICARDKEVGNLYDMFHTRNSLHRRAYQHKVGNIIDTMITDAFLKADDYIEITGAGGKKYRISTAIDDMEAYTKLTDNIFLEILYSTDPKLKDAREILKQIEYRNLFKYVGETQPTGQIKIKREDYESLPKEVASAKPKVLLDVKLKAEDFIVDVINMDYGMQEKNPIDHVSFYCKTAPNRAIRITKNQVSQLLPEKFAEQLIRVYCKKVDRKSLYAARQYFVQWCADRNFTKPQDGDVIAPLITPQKKEWN 599
                                   111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271     ||287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597  
                                                                                                                                                                                                         277|                                                                                                                                                                                                                                                                                                                           
                                                                                                                                                                                                          284
   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 4RXS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (23, 23)

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UniProtKB/Swiss-Prot
        SAMH1_HUMAN | Q9Y3Z3: 2e8o 3u1n 4bzb 4bzc 4cc9 4mz7 4q7h 4qfx 4qfy 4qfz 4qg0 4qg1 4qg2 4qg4 4rxo 4rxp 4rxq 4rxr 4tnp 4tnq 4tnr 4tnx 4tny 4tnz 4to0 4to1 4to2 4to3 4to4 4to5 4to6 4zwe 4zwg 5ao0 5ao1 5ao2 5ao3 5ao4

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