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(-) Description

Title :  CRYSTAL STRUCTURE OF KETOPANTOATE REDUCTASE FROM THERMOCOCCUS KODAKARENSIS COMPLEXED WITH NADP+
 
Authors :  Y. Aikawa, Y. Nishitani, K. Miki
Date :  29 Jan 16  (Deposition) - 18 May 16  (Release) - 18 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Oxidoreductase, Nadp, Rossmann Type Fold (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Aikawa, Y. Nishitani, H. Tomita, H. Atomi, K. Miki
Crystal Structure Of Ketopantoate Reductase From Thermococcus Kodakarensis Complexed With Nadp+
Acta Crystallogr. , Sect. F V. 72 369 2016
PubMed-ID: 27139828  |  Reference-DOI: 10.1107/S2053230X16005033

(-) Compounds

Molecule 1 - 2-DEHYDROPANTOATE 2-REDUCTASE
    Chains: A, B, C, D
    EC Number: 1.1.1.169
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: ROSETTA2(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TK1968
    Mutation: YES
    Organism Scientific: THERMOCOCCUS KODAKARENSIS (STRAIN ATCC BAA-918 / JCM 12380 / KOD1)
    Organism Taxid: 69014
    Strain: ATCC BAA-918 / JCM 12380 / KOD1
    Synonym: KETOPANTOATE REDUCTASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1NAP4Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:7 , GLY A:9 , SER A:10 , ILE A:11 , ILE A:29 , GLY A:30 , ARG A:31 , ALA A:72 , VAL A:73 , LYS A:74 , SER A:77 , ALA A:81 , GLN A:99 , ASN A:100 , THR A:120 , ASN A:122 , GLY A:123 , ALA A:124 , GLU A:262 , HOH A:508 , HOH A:523 , HOH A:525 , HOH A:535 , HOH A:538 , HOH A:553 , HOH A:558 , HOH A:567binding site for residue NAP A 401
2AC2SOFTWAREGLY B:7 , GLY B:9 , SER B:10 , ILE B:11 , GLY B:30 , ARG B:31 , ALA B:72 , VAL B:73 , LYS B:74 , ALA B:81 , ASN B:100 , THR B:120 , ASN B:122 , GLY B:123 , ALA B:124 , GLU B:262 , HOH B:505 , HOH B:549 , HOH B:558 , HOH B:575binding site for residue NAP B 401
3AC3SOFTWAREGLY C:7 , GLY C:9 , SER C:10 , ILE C:11 , ILE C:29 , GLY C:30 , ARG C:31 , ALA C:72 , LYS C:74 , ALA C:81 , GLN C:99 , ASN C:100 , THR C:120 , ASN C:122 , ALA C:124 , GLU C:262 , HOH C:515 , HOH C:534 , HOH C:540 , HOH C:542 , HOH C:551binding site for residue NAP C 401
4AC4SOFTWAREGLY D:7 , GLY D:9 , SER D:10 , ILE D:11 , ILE D:29 , GLY D:30 , ARG D:31 , ALA D:72 , VAL D:73 , LYS D:74 , ALA D:81 , ILE D:98 , GLN D:99 , ASN D:100 , THR D:120 , ASN D:122 , ALA D:124 , GLU D:262 , HOH D:508 , HOH D:512 , HOH D:539 , HOH D:541binding site for residue NAP D 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Tyr A:145 -Pro A:146
2Tyr B:145 -Pro B:146
3Tyr C:145 -Pro C:146
4Tyr D:145 -Pro D:146

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5HWS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5HWS)

(-) Exons   (0, 0)

(no "Exon" information available for 5HWS)

(-) 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:298
                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhheeeee...eee..eee.........eeee..hhhhhhhhhhhhhhhh....eeee.....hhhhhhh.....eeeeee..eeeeee..eeeeee...eeeee.....hhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh....hhhhhhhhhh.......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hws A   1 MRIYVLGAGSIGSLFGALLARAGNDVTLIGRREQVDAINKNGLHVFGAEEFTVKPKATIYAPEEPPDLLILAVKSYSTKTALEAARQCIGRNTWVLSIQNGLGNEELALKYTPNVMGGVTTNGAMLVEWGKVLWAGKGITVIGRYPTGRDDFVDEVASVFNEAGIDTSVTENAIGWKWAKAIVNSVINGLGTVLEVKNGHLKDDPHLEGISVDIAREGCMVAQQLGIEFEIHPLELLWDTIERTRENYNSTLQDIWRGRETEVDYIHGKIVEYARSVGMEAPRNELLWVLVKAKERIN 298
                                    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        


Chain B from PDB  Type:PROTEIN  Length:298
                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhheeeee...eee..eee.........eeee..hhhhhhhhhhhhhhhh....eeee.....hhhhhhh.....eeeeee..eeeeee..eeeeee...eeeee.....hhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh....hhhhhhhhhh.......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hws B   1 MRIYVLGAGSIGSLFGALLARAGNDVTLIGRREQVDAINKNGLHVFGAEEFTVKPKATIYAPEEPPDLLILAVKSYSTKTALEAARQCIGRNTWVLSIQNGLGNEELALKYTPNVMGGVTTNGAMLVEWGKVLWAGKGITVIGRYPTGRDDFVDEVASVFNEAGIDTSVTENAIGWKWAKAIVNSVINGLGTVLEVKNGHLKDDPHLEGISVDIAREGCMVAQQLGIEFEIHPLELLWDTIERTRENYNSTLQDIWRGRETEVDYIHGKIVEYARSVGMEAPRNELLWVLVKAKERIN 298
                                    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        


Chain C from PDB  Type:PROTEIN  Length:303
                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhheeeee...eee..eee.........eeee.....hhhhhhhhhhhhh....eeee.....hhhhhhh.....eeeeee..eeeeee..eeeeee...eeeee.....hhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh....hhhhhhhhh........hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hws C   1 MRIYVLGAGSIGSLFGALLARAGNDVTLIGRREQVDAINKNGLHVFGAEEFTVKPKATIYAPEEPPDLLILAVKSYSTKTALEAARQCIGRNTWVLSIQNGLGNEELALKYTPNVMGGVTTNGAMLVEWGKVLWAGKGITVIGRYPTGRDDFVDEVASVFNEAGIDTSVTENAIGWKWAKAIVNSVINGLGTVLEVKNGHLKDDPHLEGISVDIAREGCMVAQQLGIEFEIHPLELLWDTIERTRENYNSTLQDIWRGRETEVDYIHGKIVEYARSVGMEAPRNELLWVLVKAKERINRGKTR 303
                                    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   


Chain D from PDB  Type:PROTEIN  Length:297
                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhheeeee...eee..eee.........eeee.....hhhhhhhhhhhhh....eeee.....hhhhhhh.....eeeeee..eeeeee..eeeeee...eeeee.....hhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh....hhhhhhhhhh.......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hws D   1 MRIYVLGAGSIGSLFGALLARAGNDVTLIGRREQVDAINKNGLHVFGAEEFTVKPKATIYAPEEPPDLLILAVKSYSTKTALEAARQCIGRNTWVLSIQNGLGNEELALKYTPNVMGGVTTNGAMLVEWGKVLWAGKGITVIGRYPTGRDDFVDEVASVFNEAGIDTSVTENAIGWKWAKAIVNSVINGLGTVLEVKNGHLKDDPHLEGISVDIAREGCMVAQQLGIEFEIHPLELLWDTIERTRENYNSTLQDIWRGRETEVDYIHGKIVEYARSVGMEAPRNELLWVLVKAKERI 297
                                    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
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5HWS)

(-) Gene Ontology  (6, 6)

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        Q5JGC2_THEKO | Q5JGC2: 5ayv

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