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(-) Description

Title :  CRYSTAL STRUCTURE OF THE K102A MUTANT OF KIJD10, A 3-KETOREDUCTASE FROM ACTINOMADURA KIJANIATA IN COMPLEX WITH TDP-BENZENE AND NADP
 
Authors :  H. M. Holden, R. L. Kubiak
Date :  30 Mar 11  (Deposition) - 08 Jun 11  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.91
Chains :  Asym./Biol. Unit :  A
Keywords :  Sugar Biosynthesis, Ketoreductase, Tdp Binding, Nadp Binding, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. L. Kubiak, H. M. Holden
Combined Structural And Functional Investigation Of A C-3''-Ketoreductase Involved In The Biosynthesis Of Dtdp-L-Digitoxose.
Biochemistry V. 50 5905 2011
PubMed-ID: 21598943  |  Reference-DOI: 10.1021/BI200514B

(-) Compounds

Molecule 1 - SUGAR 3-KETOREDUCTASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: ROSETTA 2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: KIJD10
    Mutation: YES
    Organism Scientific: ACTINOMADURA KIJANIATA
    Organism Taxid: 46161

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 6)

Asymmetric/Biological Unit (5, 6)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2NA1Ligand/IonSODIUM ION
3NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
4PO41Ligand/IonPHOSPHATE ION
5TLO2Ligand/Ion5'-O-[(S)-HYDROXY{[(S)-HYDROXY(PHENOXY)PHOSPHORYL]OXY}PHOSPHORYL]THYMIDINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:16 , CYS A:17 , ALA A:18 , SER A:42 , ARG A:43 , ARG A:47 , TYR A:63 , PRO A:78 , LEU A:79 , PRO A:80 , LEU A:83 , HIS A:84 , ALA A:102 , PRO A:103 , VAL A:175 , ASP A:182 , TLO A:337 , HOH A:462 , HOH A:464BINDING SITE FOR RESIDUE NAP A 333
2AC2SOFTWAREASN A:256 , HIS A:270BINDING SITE FOR RESIDUE CL A 334
3AC3SOFTWAREARG A:323 , THR A:324 , ALA A:326 , ASP A:328BINDING SITE FOR RESIDUE NA A 335
4AC4SOFTWAREHIS A:285 , LYS A:290 , HOH A:423BINDING SITE FOR RESIDUE PO4 A 336
5AC5SOFTWAREILE A:20 , ARG A:23 , ARG A:24 , PHE A:159 , ILE A:161 , PRO A:162 , TYR A:186 , TYR A:240 , THR A:260 , GLN A:274 , NAP A:333 , HOH A:503 , HOH A:519 , HOH A:524 , HOH A:535BINDING SITE FOR RESIDUE TLO A 337
6AC6SOFTWAREMET A:126 , LEU A:132 , HIS A:133 , HIS A:137 , ARG A:138 , ALA A:141 , ARG A:189 , LEU A:193 , GLU A:307 , TRP A:308 , ASP A:311 , HOH A:360 , HOH A:361 , HOH A:370 , HOH A:420 , HOH A:483BINDING SITE FOR RESIDUE TLO A 338

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3RC9)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:102 -Pro A:103
2Phe A:331 -Pro A:332

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3RC9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3RC9)

(-) Exons   (0, 0)

(no "Exon" information available for 3RC9)

(-) Sequences/Alignments

Asymmetric/Biological 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:314
 aligned with B3TMR8_9ACTN | B3TMR8 from UniProtKB/TrEMBL  Length:332

    Alignment length:325
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327     
         B3TMR8_9ACTN     8 NPIRVGVIGCADIAWRRALPALEAEPLTEVTAIASRRWDRAKRFTERFGGEPVEGYPALLERDDVDAVYVPLPAVLHAEWIDRALRAGKHVLAEKPLTTDRPQAERLFAVARERGLLLMENFMFLHHPQHRQVADMLDEGVIGEIRSFAASFTIPPKPQGDIRYQADVGGGALLDIGVYPIRAAGLFLGADLEFVGAVLRHERDRDVVVGGNALLTTRQGVTAQLTFGMEHAYTNNYEFRGSTGRLWMNRVFTPPATYQPVVHIERQDHAEQFVLPAHDQFAKSIRAFAQAVLSGEHPREWSEDSLRQASLVDAVRTGARDIYFP 332
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhh.eeeehhhhhhh.....eeee..hhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhh.....eeeeeeeee...-----------..hhhhhhhhhhhhhhhhhhhh...eeeeeeeeee....eeeeeeeeee.....eeeeeee.....eeeeeeee...eeeee...........eeeeee..eeeeee....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhheeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rc9 A   8 NPIRVGVIGCADIAWRRALPALEAEPLTEVTAIASRRWDRAKRFTERFGGEPVEGYPALLERDDVDAVYVPLPAVLHAEWIDRALRAGKHVLAEAPLTTDRPQAERLFAVARERGLLLMENFMFLHHPQHRQVADMLDEGVIGEIRSFAASFTIPP-----------VGGGALLDIGVYPIRAAGLFLGADLEFVGAVLRHERDRDVVVGGNALLTTRQGVTAQLTFGMEHAYTNNYEFRGSTGRLWMNRVFTPPATYQPVVHIERQDHAEQFVLPAHDQFAKSIRAFAQAVLSGEHPREWSEDSLRQASLVDAVRTGARDIYFP 332
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157     |   -       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327     
                                                                                                                                                                                     163         175
   Legend:   → Mismatch (orange background)
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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 3RC9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3RC9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3RC9)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (B3TMR8_9ACTN | B3TMR8)
molecular function
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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 Related Entries

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

UniProtKB/TrEMBL
        B3TMR8_9ACTN | B3TMR8: 3rbv 3rc1 3rc2 3rc7 3rcb

(-) Related Entries Specified in the PDB File

3rbv SAME PROTEIN, BINARY COMPLEX WITH NADP
3rc1 SAME PROTEIN, TERNARY COMPLEX WITH TDP-BENZENE AND NADP; CLOSED CONFORMATION
3rc2 SAME PROTEIN, TERNARY COMPLEX WITH TDP-BENZENE AND NADP; OPEN CONFORMATION
3rc7 SAME PROTEIN, TERNARY COMPLEX WITH TDP-BENZENE AND NADP; Y186F MUTANT
3rcb