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(-) Description

Title :  CRYSTAL STRUCTURE OF MEVALONATE-3-KINASE FROM THERMOPLASMA ACIDOPHILUM (MEVALONATE 3-PHOSPHATE/ADP BOUND)
 
Authors :  J. M. Vinokur, D. Cascio, M. R. Sawaya, J. U. Bowie
Date :  14 Oct 14  (Deposition) - 10 Dec 14  (Release) - 11 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
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  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
13S42Ligand/Ion(3R)-5-HYDROXY-3-METHYL-3-(PHOSPHONOOXY)PENTANOIC ACID
2ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
3SO44Ligand/IonSULFATE ION
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
13S41Ligand/Ion(3R)-5-HYDROXY-3-METHYL-3-(PHOSPHONOOXY)PENTANOIC ACID
2ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
3SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
13S41Ligand/Ion(3R)-5-HYDROXY-3-METHYL-3-(PHOSPHONOOXY)PENTANOIC ACID
2ADP-1Ligand/IonADENOSINE-5'-DIPHOSPHATE
3SO43Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:48 , PHE A:62 , TYR A:96 , SER A:98 , ASN A:100 , SER A:105 , GLY A:106 , SER A:107 , SER A:108 , GLY A:111 , ARG A:185 , SER A:188 , 3S4 A:402BINDING SITE FOR RESIDUE ADP A 401
2AC2SOFTWAREGLY A:15 , LEU A:18 , LEU A:19 , SER A:105 , GLU A:140 , ARG A:144 , ARG A:185 , HIS A:192 , THR A:275 , GLY A:276 , ADP A:401BINDING SITE FOR RESIDUE 3S4 A 402
3AC3SOFTWARETYR A:183 , GLN A:184 , ARG A:251BINDING SITE FOR RESIDUE SO4 A 403
4AC4SOFTWARELEU B:18 , LEU B:19 , SER B:105 , GLU B:140 , ARG B:144 , ARG B:185 , THR B:275 , GLY B:276 , SO4 B:404BINDING SITE FOR RESIDUE 3S4 B 401
5AC5SOFTWAREARG B:251 , GLU B:252BINDING SITE FOR RESIDUE SO4 B 402
6AC6SOFTWARETYR B:183 , GLN B:184 , ARG B:251BINDING SITE FOR RESIDUE SO4 B 403
7AC7SOFTWARELEU B:104 , SER B:105 , GLY B:106 , SER B:107 , SER B:108 , ARG B:185 , 3S4 B:401BINDING SITE FOR RESIDUE SO4 B 404

(-) SS Bonds  (1, 1)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RKZ)

(-) 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:313
                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..eeeee................eeeeeee......eeeeeeee.....eee..eee..hhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhhhh...hhhhhhhhhh....hhhhhhhh.eeeeee....eeeeeeehhhhhh.eeeeeee......hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh..eee.....eeeeeee..hhhhhhh.......eeeeeee....ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rkz A   2 TYRSIGSTAYPTIGVVLLGGIANPVTRTPLHTSAGIAYSDSCGSIRSETRIYADEATHIYFNGTESTSVRRVLDRYSSVFEEAFGTKTVSYSSQNFGILSGSSDAGAASIGAAILGLKPDLDPHDVENDLRAVSESAGRSLFGGLTITWSDGFHAYTEKILDPEAFSGYSIVAFAFDYQRNPSDVIHQNIVRSDLYPARKKHADEHAHMIKEYAKTNDIKGIFDLAQEDTEEYHSILRGVGVNVIRENMQKLISYLKLIRKDYWNAYIVTGGSNVYVAVESENADRLFSIENTFGSKKKMLRIVGGAWHRRPE 318
                                    11        21        31        41        51        61      ||75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315   
                                                                                             68|                                                                                                                                                                                                                                                     
                                                                                              73                                                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:318
                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeee..eeeee................eeeeeee......eeeeeeee.....eee..ee..hhhhhhhhhhhhhhhhhhh....eeeeeeee....hhhhhhhhhhhhhhhhhh...hhhhhhhhhh....hhhhhhhh.eeeeee....eeeeeeehhhhhh.eeeeeee......hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh....eee.....eeeeeee..hhhhhhh.......eeeeeee....ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4rkz B  -1 GSMTYRSIGSTAYPTIGVVLLGGIANPVTRTPLHTSAGIAYSDSCGSIRSETRIYADEATHIYFNGTESDNRSVRRVLDRYSSVFEEAFGTKTVSYSSQNFGILSGSSDAGAASIGAAILGLKPDLDPHDVENDLRAVSESAGRSLFGGLTITWSDGFHAYTEKILDPEAFSGYSIVAFAFDYQRNPSDVIHQNIVRSDLYPARKKHADEHAHMIKEYAKTNDIKGIFDLAQEDTEEYHSILRGVGVNVIRENMQKLISYLKLIRKDYWNAYIVTGGSNVYVAVESENADRLFSIENTFGSKKKMLRIVGGAWHRRPE 318
                                     8        18        28        38        48        58        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310        
                                                                                               67|                                                                                                                                                                                                                                                        
                                                                                                70
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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 4RKZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

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        MV3K_THEAC | Q9HIN1: 4rkp 4rks

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