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(-) Description

Title :  CRYSTAL STRUCTURE OF SAMHD1 CATALYTIC CORE WITH GTP
 
Authors :  Q. Xiaohong, L. Yanhong, K. Jia, Y. Xiaofang
Date :  25 Apr 14  (Deposition) - 27 May 15  (Release) - 27 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.59
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Protein-Gtp Complex, Hydrolase, Hd-Domain, Dntp Binding, Phosphorylation, Gtp (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. Xiaohong, L. Yanhong, K. Jia, Y. Xiaofang
Structural Insight Into Activation Mechanism Of Samhd1
To Be Published
PubMed: search

(-) 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 Taxid: 562
    Fragment: HD-DOMAIN, 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

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1GTP3Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
2ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GTP2Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GTP1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
2ZN-1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:167 , HIS A:206 , ASP A:207 , ASP A:311BINDING SITE FOR RESIDUE ZN A 901
2AC2SOFTWAREVAL A:117 , ILE A:118 , VAL A:133 , 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:451 , HOH B:1002BINDING SITE FOR RESIDUE GTP A 902
3AC3SOFTWAREARG B:164 , HIS B:167 , HIS B:206 , ASP B:207 , ASP B:311BINDING SITE FOR RESIDUE ZN B 901
4AC4SOFTWARETYR A:155 , VAL A:156 , VAL A:378 , ARG A:451 , LEU A:453 , PHE A:454 , LYS A:455 , LYS B:116 , VAL B:117 , ILE B:118 , VAL B:133 , ASP B:137 , GLN B:142 , ARG B:145 , PHE B:165 , HOH B:1012BINDING SITE FOR RESIDUE GTP B 902
5AC5SOFTWAREHIS C:167 , HIS C:206 , ASP C:207 , ASP C:311BINDING SITE FOR RESIDUE ZN C 901
6AC6SOFTWARELYS C:116 , VAL C:117 , ILE C:118 , ILE C:136 , ASP C:137 , GLN C:142 , ARG C:145 , PHE C:165 , TYR D:155 , VAL D:156 , VAL D:378 , ARG D:451 , LEU D:453BINDING SITE FOR RESIDUE GTP C 902
7AC7SOFTWAREHIS D:167 , HIS D:206 , ASP D:207 , ASP D:311BINDING SITE FOR RESIDUE ZN D 901

(-) SS Bonds  (4, 4)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Ser A:278 -Pro A:279
2Ser B:278 -Pro B:279
3Thr B:463 -Gly B:464
4Phe B:545 -Ala B:546
5Lys D:523 -Thr D:524

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Q7H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Q7H)

(-) Exons   (0, 0)

(no "Exon" information available for 4Q7H)

(-) 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:459
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...eeeeehhhhhhhhhhhhhhhhhhh..hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.hhhhhhhhh..hhhhhhhhhhhhhhh..............hhhhhhhhhh........hhhhhhhhhhhhhhhh.....hhhhhhhhheeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....ee.hhh.ee...hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....eeeeee........hhhhhhhhhhhhhh...........hhh.eeeeeee......hhhhhh.ee...................eeeeeee...hhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q7h A 115 MKVINDPIHGHIELHPLLVRIIDTPQFQRLRYIKQLGGGYYVFPGASHNRFEHSLGVGYLAGCLVHALGEKQPELQISERDVLCVQIAGLCHDLGHGPFSHMFDGRFIPLARPEVKWTHEQGSVMMFEHLINSNGIKPVMEQYGLIPEEDIYFIKEQIVGPLESPDSLWPYKGRPENKSFLYEIVSNKRNGIDVDKWDYFARDCHHLGIQNNFDYKRFIKFARVCEVDNELRICARDKEVGNLYDMFHTRNSLHRRAYQHKVGNIIDTMITDAFLKADDYIEITGAGGKKYRISTAIDDMEAYTKLTDNIFLEILYSTDPKLKDAREILKQIEYRNLFKYVGETQPTGQIKIKREDYESLPKEVASAKPKVLLDVKLKAEDFIVDVINMDYQEKNPIDHVSFYCKTAPNRAIRITLPEKFAEQLIRVYCKKVDRKSLYAARQYFVQWCADRNFTKPQDG 584
                                   124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274    || 286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506||     518       528    || 545       555       565       575         
                                                                                                                                                                                              279|                                                                                                                                                                                                                              507|                    533|                                           
                                                                                                                                                                                               282                                                                                                                                                                                                                               510                     541                                           


Chain B from PDB  Type:PROTEIN  Length:449
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               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..hhhhhhhhhhhhhhhhh......ee.hhh.ee...hhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhhh....eeeeee........hhhhhhhhhhhhhh...........hhh.eeeeee........ee................eeeeee...hhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q7h B 115 MKVINDPIHGHIELHPLLVRIIDTPQFQRLRYIKQLGGGYYVFPGASHNRFEHSLGVGYLAGCLVHALGEKQPELQISERDVLCVQIAGLCHDLGHGPFSHMFDGRFIPLARPEVKWTHEQGSVMMFEHLINSNGIKPVMEQYGLIPEEDIYFIKEQIVGPLESPDSLWPYKGRPENKSFLYEIVSNKRNGIDVDKWDYFARDCHHLGIQNNFDYKRFIKFARVCEVDNELRICARDKEVGNLYDMFHTRNSLHRRAYQHKVGNIIDTMITDAFLKADDYIEITGAGGKKYRISTAIDDMEAYTKLTDNIFLEILYSTDPKLKDAREILKQIEYRNLFKYVGETQPTGQIKIKREDYESLPKEVASAKPKVLLDVKLKAEDFIVDVINMPIDHVSFYCKTAPNRAIRIKFAEQLIRVYCKKVDRKSLYAARQYFVQWCADRNFTKPQDG 584
                                   124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274    || 286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       514       524       545       555       565       575         
                                                                                                                                                                                              279|                                                                                                                                                                                                                            505|               532|                                        
                                                                                                                                                                                               282                                                                                                                                                                                                                             514                544                                        


Chain C from PDB  Type:PROTEIN  Length:447
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               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.eeee....eeeeee..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....ee.hhh.ee...hhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeee........hhhhh.hhhhhhh............hhh.eeeeeee......ee................eeeeeee...hhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q7h C 114 TMKVINDPIHGHIELHPLLVRIIDTPQFQRLRYIKQLGGGYYVFPGASHNRFEHSLGVGYLAGCLVHALGEKQPELQISERDVLCVQIAGLCHDLGHGPFSHMFDGRFIPLARPEVKWTHEQGSVMMFEHLINSNGIKPVMEQYGLIPEEDIYFIKEQIVGPLESSLWPYKGRPENKSFLYEIVSNKRNGIDVDKWDYFARDCHHLGIQNNFDYKRFIKFARVCEVDNELRICARDKEVGNLYDMFHTRNSLHRRAYQHKVGNIIDTMITDAFLKADDYIEITGAGGKKYRISTAIDDMEAYTKLTDNIFLEILYSTDPKLKDAREILKQIEYRNLFKYVGETQPTGQIKIKREDYESLPKEVASAKPKVLLDVKLKAEDFIVDVINMDDHVSFYCKTAPNRAIRIEKFAEQLIRVYCKKVDRKSLYAARQYFVQWCADRNFTKPQD 583
                                   123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273    || 287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       516       526     ||546       556       566       576       
                                                                                                                                                                                              278|                                                                                                                                                                                                                            506|             532|                                        
                                                                                                                                                                                               283                                                                                                                                                                                                                             516              543                                        


Chain D from PDB  Type:PROTEIN  Length:439
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeee.hhhhhhhhhhhhhhhhhhh..hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.hhhhhhhhh..hhhhhhhhhhhhhhh..........hhhhhhhhhh.......hhhhhhhhhhhhhhhh.....hhhhhhhheeeee....eeeeee..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....ee.....ee...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh....eeeeee........hhhhhhhhhhhhhhh..........hhh.eeeeeee.hhhhhh.ee...........eeeeeee...hhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q7h D 115 MKVINDPIHGHIELHPLLVRIIDTPQFQRLRYIKQLGGGYYVFPGASHNRFEHSLGVGYLAGCLVHALGEKQPELQISERDVLCVQIAGLCHDLGHGPFSHMFDGRFIPLARPEVKWTHEQGSVMMFEHLINSNGIKPVMEQYGLIPEEDIYFIKEQIVGPLELWPYKGRPENKSFLYEIVSNKNGIDVDKWDYFARDCHHLGIQNNFDYKRFIKFARVCEVDNELRICARDKEVGNLYDMFHTRNSLHRRAYQHKVGNIIDTMITDAFLKADDYIEITGAGGKKYRISTAIDDMEAYTKLTDNIFLEILYSTDPKLKDAREILKQIEYRNLFKYVGETQPTGQIKIKREDYESLPKEVASAKPKVLLDVKLKAEDFIVDVINMNPIDHVSFYCKTAPNRAIAEQLIRVYCKKVDRKSLYAARQYFVQWCADRNFTKPQ 582
                                   124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274  ||   290       300   ||  311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501   ||  518       528 ||    553       563       573         
                                                                                                                                                                                            277|                 304|                                                                                                                                                                                                    505|              530|                                    
                                                                                                                                                                                             284                  306                                                                                                                                                                                                     513               546
   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 4Q7H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Q7H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Q7H)

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)

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  4q7h
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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 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

(-) Related Entries Specified in the PDB File

3u1n 4bzb 4bzc 4mz7