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(-) Description

Title :  CRYSTAL STRUCTURE OF MEVALONATE-3-KINASE FROM THERMOPLASMA ACIDOPHILUM (APO FORM)
 
Authors :  J. M. Vinokur, D. Cascio, M. R. Sawaya, J. U. Bowie
Date :  13 Oct 14  (Deposition) - 10 Dec 14  (Release) - 11 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Mevalonate, Mevalonate-3-Kinase, Mevalonate Pyrophosphate Decarboxylase, Mevalonate Diphosphate Decarboxylase, Mevalonic Acid, Mevalonate Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Vinokur, T. P. Korman, M. R. Sawaya, M. Collazo, D. Cascio, J. U. Bowie
Structural Analysis Of Mevalonate-3-Kinase Provides Insight Into The Mechanisms Of Isoprenoid Pathway Decarboxylases.
Protein Sci. V. 24 212 2015
PubMed-ID: 25422158  |  Reference-DOI: 10.1002/PRO.2607

(-) Compounds

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN TA1305
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TA1305
    Organism Scientific: THERMOPLASMA ACIDOPHILUM
    Organism Taxid: 273075
    Strain: ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165
    Synonym: MEVALONATE-3-KINASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2SO47Ligand/IonSULFATE ION
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2SO43Ligand/IonSULFATE ION
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2SO44Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:183 , GLN A:184 , ARG A:251BINDING SITE FOR RESIDUE SO4 A 401
02AC2SOFTWARESER A:105 , GLY A:106 , SER A:107 , SER A:108 , ARG A:185 , HOH A:582BINDING SITE FOR RESIDUE SO4 A 402
03AC3SOFTWAREASP A:70 , ASN A:71 , ARG A:72 , SER A:73BINDING SITE FOR RESIDUE SO4 A 403
04AC4SOFTWARELEU A:19 , GLU A:140 , SER A:188 , HIS A:192 , ACT A:405BINDING SITE FOR RESIDUE ACT A 404
05AC5SOFTWAREGLY A:15 , LEU A:18 , LEU A:19 , ARG A:144 , TYR A:238 , THR A:275 , ACT A:404BINDING SITE FOR RESIDUE ACT A 405
06AC6SOFTWARETYR B:183 , GLN B:184 , ARG B:251BINDING SITE FOR RESIDUE SO4 B 401
07AC7SOFTWAREASP B:70 , ASN B:71 , ARG B:72BINDING SITE FOR RESIDUE SO4 B 402
08AC8SOFTWARESER B:105 , GLY B:106 , SER B:107 , SER B:108 , ARG B:185BINDING SITE FOR RESIDUE SO4 B 403
09AC9SOFTWAREPRO B:187 , SER B:188BINDING SITE FOR RESIDUE SO4 B 404
10BC1SOFTWARELEU B:18 , LEU B:19 , ARG B:144 , TYR B:238 , THR B:275BINDING SITE FOR RESIDUE ACT B 405

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:43 -B:43

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RKP)

(-) 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:317
                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..eeeee................eeeeeee......eeeeeeee.....eee..eee...hhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhhhh...hhhhhhhhhh....hhhhhhhh.eeeeee....eeeeeeehhhhhh.eeeeeee......hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh...eeee.....eeeeeee..hhhhhhh.......eeeeeee....ee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rkp A   2 TYRSIGSTAYPTIGVVLLGGIANPVTRTPLHTSAGIAYSDSCGSIRSETRIYADEATHIYFNGTESTDDNRSVRRVLDRYSSVFEEAFGTKTVSYSSQNFGILSGSSDAGAASIGAAILGLKPDLDPHDVENDLRAVSESAGRSLFGGLTITWSDGFHAYTEKILDPEAFSGYSIVAFAFDYQRNPSDVIHQNIVRSDLYPARKKHADEHAHMIKEYAKTNDIKGIFDLAQEDTEEYHSILRGVGVNVIRENMQKLISYLKLIRKDYWNAYIVTGGSNVYVAVESENADRLFSIENTFGSKKKMLRIVGGAWHRRPE 318
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       


Chain B from PDB  Type:PROTEIN  Length:320
                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee..eeeee................eeeeeee......eeeeeeee.....eee..ee....hhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhhhh...hhhhhhhhhh....hhhhhhhh.eeeeee....eeeeeeehhhhhh.eeeeeee......hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh....eeee.....eeeeeee..hhhhhhh.......eeeeeee....ee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rkp B  -1 GSMTYRSIGSTAYPTIGVVLLGGIANPVTRTPLHTSAGIAYSDSCGSIRSETRIYADEATHIYFNGTESTDDNRSVRRVLDRYSSVFEEAFGTKTVSYSSQNFGILSGSSDAGAASIGAAILGLKPDLDPHDVENDLRAVSESAGRSLFGGLTITWSDGFHAYTEKILDPEAFSGYSIVAFAFDYQRNPSDVIHQNIVRSDLYPARKKHADEHAHMIKEYAKTNDIKGIFDLAQEDTEEYHSILRGVGVNVIRENMQKLISYLKLIRKDYWNAYIVTGGSNVYVAVESENADRLFSIENTFGSKKKMLRIVGGAWHRRPE 318
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318
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  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 4RKP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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        MV3K_THEAC | Q9HIN1: 4rks 4rkz

(-) Related Entries Specified in the PDB File

4rks 4rkz