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(-) Description

Title :  TERNARY CRYSTAL STRUCTURE OF PYROCOCCUS YAYANOSII GLYOXYLATE HYDROXYPYRUVATE REDUCTASE IN PRESENCE OF D-GLYCERATE
 
Authors :  L. Lassalle, E. Girard
Date :  12 Sep 15  (Deposition) - 02 Mar 16  (Release) - 02 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase, Glyoxylate Hydroxypyruvate Reductase, D-Glycerate, Archaea (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Lassalle, S. Engilberge, D. Madern, P. Vauclare, B. Franzetti, E. Girard
New Insights Into The Mechanism Of Substrates Trafficking In Glyoxylate/Hydroxypyruvate Reductases.
Sci. Rep. V. 6 20629 2016
PubMed-ID: 26865263  |  Reference-DOI: 10.1038/SREP20629

(-) Compounds

Molecule 1 - GLYOXYLATE HYDROXYPYRUVATE REDUCTASE
    Chains: A, B
    EC Number: 1.1.1.81, 1.1.1.79
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: RIL
    Expression System Vector: PET41
    Expression System Vector Type: PLASMID
    Organism Scientific: PYROCOCCUS YAYANOSII
    Organism Taxid: 529709
    Strain: CH1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 13)

Asymmetric/Biological Unit (4, 13)
No.NameCountTypeFull Name
1DGY2Ligand/Ion(2R)-2,3-DIHYDROXYPROPANOIC ACID
2GOL7Ligand/IonGLYCEROL
3MLI2Ligand/IonMALONATE ION
4NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:76 , GLY A:77 , THR A:104 , GLY A:157 , PHE A:158 , GLY A:159 , ARG A:160 , ILE A:161 , ALA A:180 , ARG A:181 , SER A:182 , LYS A:184 , ALA A:211 , VAL A:212 , PRO A:213 , GLU A:217 , THR A:218 , VAL A:239 , ALA A:240 , ARG A:241 , ASP A:265 , VAL A:266 , HIS A:288 , GLY A:290 , DGY A:1335 , MLI A:1338 , HOH A:2122 , HOH A:2162 , HOH A:2240 , HOH A:2243 , HOH A:2264 , HOH A:2269 , HOH A:2293 , HOH A:2372 , HOH A:2416 , HOH A:2417 , HOH A:2418 , HOH A:2419 , HOH A:2420 , HOH A:2421BINDING SITE FOR RESIDUE NAP A1334
02AC2SOFTWAREHOH A:2217 , VAL B:76 , GLY B:77 , THR B:104 , GLY B:157 , PHE B:158 , GLY B:159 , ARG B:160 , ILE B:161 , ALA B:180 , ARG B:181 , SER B:182 , LYS B:184 , VAL B:212 , PRO B:213 , THR B:218 , VAL B:239 , ALA B:240 , ARG B:241 , ASP B:265 , HIS B:288 , GLY B:290 , SER B:291 , DGY B:1335 , HOH B:2063 , HOH B:2089 , HOH B:2134 , HOH B:2137 , HOH B:2154 , HOH B:2157 , HOH B:2160 , HOH B:2268 , HOH B:2269 , HOH B:2270 , HOH B:2271 , HOH B:2272BINDING SITE FOR RESIDUE NAP B1334
03AC3SOFTWARETRP A:138 , HOH A:2217 , LEU B:53 , ALA B:75 , VAL B:76 , GLY B:77 , LEU B:100 , ARG B:241 , HIS B:288 , NAP B:1334 , HOH B:2262BINDING SITE FOR RESIDUE DGY B1335
04AC4SOFTWARELEU A:53 , ALA A:75 , VAL A:76 , GLY A:77 , LEU A:100 , ARG A:241 , HIS A:288 , NAP A:1334 , HOH A:2372 , HOH A:2374 , TRP B:138BINDING SITE FOR RESIDUE DGY A1335
05AC5SOFTWAREVAL A:99 , LEU A:100 , ASP A:102 , ALA A:103 , GLY A:295 , ALA A:296 , HOH A:2174 , HOH A:2422 , ASP B:147BINDING SITE FOR RESIDUE GOL A1336
06AC6SOFTWAREASN A:14 , GLU A:298 , HOH A:2423 , HOH A:2424 , HOH A:2425 , HOH A:2426 , ARG B:183 , GLU B:188 , GLU B:194 , PHE B:195BINDING SITE FOR RESIDUE GOL A1337
07AC7SOFTWAREGLU A:217 , MET A:221 , ARG A:226 , ARG A:330 , NAP A:1334 , HOH A:2419 , HOH A:2427BINDING SITE FOR RESIDUE MLI A1338
08AC8SOFTWARELYS B:184 , PRO B:185 , GLU B:186 , ALA B:187 , HOH B:2139 , HOH B:2158BINDING SITE FOR RESIDUE GOL B1336
09AC9SOFTWAREHIS A:30 , GLU A:31 , HIS A:32 , HOH A:2428BINDING SITE FOR RESIDUE GOL A1339
10BC1SOFTWARETYR A:78 , ASN A:95 , ARG A:160 , HOH A:2243 , HOH A:2417BINDING SITE FOR RESIDUE GOL A1340
11BC2SOFTWARETYR B:78 , ASN B:95 , ARG B:160 , HOH B:2087 , HOH B:2137 , HOH B:2269 , HOH B:2274BINDING SITE FOR RESIDUE GOL B1337
12BC3SOFTWARELYS A:151 , ASP A:206 , THR A:233 , HOH A:2227 , HOH A:2228BINDING SITE FOR RESIDUE GOL A1341
13BC4SOFTWAREGLU A:31 , LYS B:141 , MET B:142BINDING SITE FOR RESIDUE MLI B1338

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:270 -Pro A:271
2Glu B:270 -Pro B:271

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5AOW)

(-) 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:333
                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhh..eeee.......hhhhhhhhhhhh.eeee......hhhhhhhh....eeee........hhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................eeeee..hhhhhhhhhhhhhh..eeeee....hhhhhhhhheee.hhhhhhhhh.eeee............hhhhhhhh....eeee..hhhh.hhhhhhhhhhh....eeee.........hhhhhh...eee.......hhhhhhhhhhhhhhhhhhhhh........hhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5aow A   1 MKPKVLITRAIPENGIELLREHFEVEVWEHEHEIPREVLLEKVKDVDALVTMLSEKIDREVFDAAPRLRIVANYAVGYDNIDIEEATKRGIYVTNTPDVLTDATADLAWALLLAAARHVVKGDKFVRSGEWKRRGIAWHPKMFLGYDVYGKTIGIVGFGRIGQAIAKRAKGFGMRILYTARSRKPEAEKELGAEFKPLEELLRESDFVVLAVPLTKETYHMINEERLRLMKPTAVLVNVARGKVVDTKALIRALKEGWIAAAGLDVFEEEPYYDEELFALDNVVLTPHIGSATFGAREGMAELVAKNLIAFKNGEVPPTLVNREVLKVRRPGF 333
                                    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       330   


Chain B from PDB  Type:PROTEIN  Length:332
                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhh..eeee.......hhhhhhhhhhhh.eeee......hhhhhhhh....eeee........hhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................eeeee..hhhhhhhhhhhhhh..eeeee....hhhhhhhhheee.hhhhhhhhh.eeee............hhhhhhhh....eeee..hhhh.hhhhhhhhhhhh...eeee.........hhhhhh...eee.......hhhhhhhhhhhhhhhhhhhhh........hhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5aow B   2 KPKVLITRAIPENGIELLREHFEVEVWEHEHEIPREVLLEKVKDVDALVTMLSEKIDREVFDAAPRLRIVANYAVGYDNIDIEEATKRGIYVTNTPDVLTDATADLAWALLLAAARHVVKGDKFVRSGEWKRRGIAWHPKMFLGYDVYGKTIGIVGFGRIGQAIAKRAKGFGMRILYTARSRKPEAEKELGAEFKPLEELLRESDFVVLAVPLTKETYHMINEERLRLMKPTAVLVNVARGKVVDTKALIRALKEGWIAAAGLDVFEEEPYYDEELFALDNVVLTPHIGSATFGAREGMAELVAKNLIAFKNGEVPPTLVNREVLKVRRPGF 333
                                    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       321       331
   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 5AOW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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5aov TERNARY CRYSTAL STRUCTURE OF PYROCOCCUS FURIOSUS GLYOXYLATE HYDROXYPYRUVATE REDUCTASE IN PRESENCE OF GLYCOLATE