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(-) Description

Title :  CRYSTAL STRUCTURE OF BETA-DECARBOXYLATING DEHYDROGENASE (TK0280) FROM THERMOCOCCUS KODAKARENSIS COMPLEXED WITH MN AND ISOCITRATE
 
Authors :  T. Shimizu, T. Tomita, M. Nishiyama
Date :  18 Jan 16  (Deposition) - 07 Dec 16  (Release) - 04 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Homoisocitrate Dehydrogenase, Beta-Decarboxylating Dehydrogenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Shimizu, L. Yin, A. Yoshida, Y. Yokooji, S. I. Hachisuka, T. Sato, T. Tomita, H. Nishida, H. Atomi, T. Kuzuyama, M. Nishiyama
Structure And Function Of An Ancestral-Type Beta-Decarboxylating Dehydrogenase From Thermococcus Kodakarensis
Biochem. J. V. 474 105 2017
PubMed-ID: 27831491  |  Reference-DOI: 10.1042/BCJ20160699

(-) Compounds

Molecule 1 - HOMOISOCITRATE DEHYDROGENASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 CODONPLUS (RIL)
    Expression System Taxid: 562
    Gene: TK0280
    Organism Scientific: THERMOCOCCUS KODAKARENSIS (STRAIN ATCC BAA-918 / JCM 12380 / KOD1)
    Organism Taxid: 69014
    Strain: ATCC BAA-918 / JCM 12380 / KOD1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1ICT1Ligand/IonISOCITRIC ACID
2MN1Ligand/IonMANGANESE (II) ION
3MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1ICT2Ligand/IonISOCITRIC ACID
2MN-1Ligand/IonMANGANESE (II) ION
3MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:80 , ARG A:86 , ARG A:96 , ARG A:111 , TYR A:118 , LYS A:163 , ASP A:194 , ASP A:218 , MN A:402 , HOH A:502 , HOH A:504binding site for residue ICT A 401
2AC2SOFTWAREASP A:194 , ASP A:218 , ICT A:401 , HOH A:504 , HOH A:510binding site for residue MN A 402
3AC3SOFTWAREILE A:12 , SER A:230 , HIS A:250 , ALA A:262 , ASN A:263 , ASP A:301binding site for residue MPD A 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5HN5)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

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(-) Sequences/Alignments

Asymmetric Unit
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Chain A from PDB  Type:PROTEIN  Length:327
                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..hhhhhhhhhhhhhhh....eeeee...hhhhhhhhh...hhhhhhhhh...eeeeee...........hhhhhhhhhh...eeeeeee......eeeeeee..hhhhh..eee....eee....hhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhh.eeeee....eeeee....hhhhh......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh....hhhhh...hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hn5 A   1 MYRVAVIPGDGIGPEVIDGAVRVLKAVTGRVRFEYYEGGVDVFQECGSPIREEDLEEIRRSDAVLFGATTTPFDLPGYRSLILTLRKELGLYANLRIIPDLRTGREIVIVRENSEGLYFGIGAVVNGRAVDVRLITREGAERIARFAVEQAKARGSFITFVHKANVLTGDKFFRRIVREVAGEEGVEVRDAIIDSFTIKLVRNPWEHGVILSENLFGDILSDLATVHAGSIGIVPSGNYGDGIALFEPVHGSAPDIAGKGIANPIGAILSGAMLLDYLGLDGSLIRAAVRGYVVNGELTPDMGGRARTEDVVRGIIGEIEDLLSMDE 327
                                    10        20        30        40        50        60        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       320
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5HN5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5HN5)

(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (7, 7)

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  Q5JFV8_THEKO | Q5JFV8
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 Related Entries

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UniProtKB/TrEMBL
        Q5JFV8_THEKO | Q5JFV8: 5hn3 5hn4 5hn6

(-) Related Entries Specified in the PDB File

5hn3 5hn4 5hn6