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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PRS1 D52H MUTANT
 
Authors :  P. Chen, M. Teng, X. Li
Date :  17 May 12  (Deposition) - 22 May 13  (Release) - 12 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.27
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Prpp Synthesis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Chen, J. Li, J. Ma, M. Teng, X. Li
A Small Disturbance, But A Serious Disease: The Possible Mechanism Of D52H-Mutant Of Human Prs1 That Causes Gout
Iubmb Life V. 65 518 2013
PubMed-ID: 23509005  |  Reference-DOI: 10.1002/IUB.1154

(-) Compounds

Molecule 1 - RIBOSE-PHOSPHATE PYROPHOSPHOKINASE 1
    Chains: A, B
    EC Number: 2.7.6.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PRPS1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PPRIBP, PHOSPHORIBOSYL PYROPHOSPHATE SYNTHASE I, PRS-I

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2SO46Ligand/IonSULFATE ION
Biological Unit 1 (1, 18)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2SO418Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:224 , THR A:225 , CYS A:226 , GLY A:227 , THR A:228 , HOH A:516BINDING SITE FOR RESIDUE SO4 A 401
2AC2SOFTWARESER A:47 , ARG A:49 , SER A:308 , VAL A:309 , SER A:310 , HOH A:511 , HOH A:529 , ARG B:104BINDING SITE FOR RESIDUE SO4 A 402
3AC3SOFTWARESER A:132 , GLN A:135 , ASN A:144 , TYR A:146 , HOH A:501 , LYS B:100 , ASP B:101 , LYS B:102BINDING SITE FOR RESIDUE SO4 A 403
4AC4SOFTWAREHIS A:52 , TYR A:54BINDING SITE FOR RESIDUE MG A 404
5AC5SOFTWAREASP B:224 , THR B:225 , CYS B:226 , GLY B:227 , THR B:228BINDING SITE FOR RESIDUE SO4 B 1001
6AC6SOFTWAREARG A:104 , SER B:47 , ARG B:49 , SER B:308 , VAL B:309 , SER B:310 , HOH B:1121BINDING SITE FOR RESIDUE SO4 B 1002
7AC7SOFTWAREASP A:101 , LYS A:102 , SER B:132 , GLN B:135 , ASN B:144 , TYR B:146 , HOH B:1103BINDING SITE FOR RESIDUE SO4 B 1003
8AC8SOFTWAREHIS B:52 , TYR B:54BINDING SITE FOR RESIDUE MG B 1004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4F8E)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4F8E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4F8E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4F8E)

(-) Exons   (0, 0)

(no "Exon" information available for 4F8E)

(-) 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:308
                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4f8ea1 A:2-160 automated matches                                                                                                                              d4f8ea2 A:161-316 automated matches                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....hhhhhhhhhhhh.....ee...........ee.......eeeee.....hhhhhhhhhhhhhhhhhh....eeeeee.................hhhhhhhhhhhhhh..eeeee...hhhhhhhh...eeee.hhhhhhhhhhh.hhhhhh.eeee.hhhhhhhhhhhhhhhh.eeeeeee...eeee.......eeeeeeee..hhhhhhhhhhhhhh....eeeeeeee....hhhhhhhh..eeeeeee....hhhhhhh...eeee.hhhhhhhhhhhhhhh.hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f8e A   2 PNIKIFSGSSHQDLSQKIADRLGLELGKVVTKKFSNQETCVEIGESVRGEHVYIVQSGCGEINDNLMELLIMINACKIASASRVTAVIPCFPYARQDKKDKSRAPISAKLVANMLSVAGADHIITMDLHASQIQGFFDIPVDNLYAEPAVLKWIRENISEWRNCTIVSPDAGGAKRVTSIADRLNVDFALIHKERRMVLVGDVKDRVAILVDDMADTCGTICHAADKLLSAGATRVYAILTHGIFSGPAISRINNACFEAVVVTNTIPQEDKMKHCSKIQVIDISMILAEAIRRTHNGESVSYLFSHV 316
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191    || 208       218       228       238       248       258       268       278       288       298       308        
                                                                                                                                                                                                                            196|                                                                                                                
                                                                                                                                                                                                                             204                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:308
                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4f8eb1 B:3-160 automated matches                                                                                                                             d4f8eb2 B:161-317 automated matches                                                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhh......eeeee.....eeeee.......eeeee.....hhhhhhhhhhhhhhhhhhh...eeeeee.................hhhhhhhhhhhhhh..eeeee...hhhhhhhh...eeee.hhhhhhhhhhhhh.hhhh.eeee.hhhhhhhhhhhhhhhh.eeeeeee...eeeee.....eeeeeeeee..hhhhhhhhhhhhhh...eeeeeeeee....hhhhhhhh....eeeee....hhhhhhh...eeee.hhhhhhhhhhhhhh....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f8e B   3 NIKIFSGSSHQDLSQKIADRLGLELGKVVTKKFSNQETCVEIGESVRGEHVYIVQSGCGEINDNLMELLIMINACKIASASRVTAVIPCFPYARQDKKDKSRAPISAKLVANMLSVAGADHIITMDLHASQIQGFFDIPVDNLYAEPAVLKWIRENISEWRNCTIVSPDAGGAKRVTSIADRLNVDFALIHKEDRMVLVGDVKDRVAILVDDMADTCGTICHAADKLLSAGATRVYAILTHGIFSGPAISRINNACFEAVVVTNTIPQEDKMKHCSKIQVIDISMILAEAIRRTHNGESVSYLFSHVP 317
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192  ||   209       219       229       239       249       259       269       279       289       299       309        
                                                                                                                                                                                                                          195|                                                                                                                  
                                                                                                                                                                                                                           203
   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  (1, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4F8E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4F8E)

(-) Gene Ontology  (30, 30)

Asymmetric Unit(hide GO term definitions)

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  4f8e
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  PRPS1_HUMAN | P60891
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  2.7.6.1
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 Related Entries

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

UniProtKB/Swiss-Prot
        PRPS1_HUMAN | P60891: 2h06 2h07 2h08 2hcr 3efh 3s5j 4lyg 4lzn 4lzo 4m0p 4m0u

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4F8E)