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(-) Description

Title :  TERNARY CRYSTAL STRUCTURE OF PYROCOCCUS FURIOSUS GLYOXYLATE HYDROXYPYRUVATE REDUCTASE IN PRESENCE OF GLYOXALATE
 
Authors :  L. Lassalle, E. Girard
Date :  12 Sep 15  (Deposition) - 02 Mar 16  (Release) - 02 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Oxidoreductase, Glyoxylate Hydroxypyruvate Reductase, Glyoxylate, 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 REDUCTASE
    Chains: A
    EC Number: 1.1.1.26, 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 FURIOSUS
    Organism Taxid: 2261
    Synonym: GLYOXYLATE HYDROXYPYRUVATE REDUCTASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 25)

Asymmetric Unit (5, 25)
No.NameCountTypeFull Name
11PE15Ligand/IonPENTAETHYLENE GLYCOL
2ACY2Ligand/IonACETIC ACID
3EDO5Ligand/Ion1,2-ETHANEDIOL
4GLV2Ligand/IonGLYOXYLIC ACID
5NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 1 (5, 50)
No.NameCountTypeFull Name
11PE30Ligand/IonPENTAETHYLENE GLYCOL
2ACY4Ligand/IonACETIC ACID
3EDO10Ligand/Ion1,2-ETHANEDIOL
4GLV4Ligand/IonGLYOXYLIC ACID
5NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:32 , LYS A:42 , VAL A:76 , THR A:104 , GLY A:157 , PHE A:158 , GLY A:159 , ARG A:160 , ILE A:161 , TYR A:179 , SER A:180 , ARG A:181 , THR A:182 , LYS A:184 , ALA A:211 , VAL A:212 , PRO A:213 , GLU A:217 , THR A:218 , ILE A:239 , ALA A:240 , ARG A:241 , ASP A:265 , HIS A:288 , GLY A:290 , SER A:291 , GLV A:1336 , HOH A:2059 , HOH A:2078 , HOH A:2135 , HOH A:2143 , HOH A:2170 , HOH A:2228 , HOH A:2230 , HOH A:2232 , HOH A:2251 , HOH A:2255 , HOH A:2256 , HOH A:2287 , HOH A:2352 , HOH A:2397BINDING SITE FOR RESIDUE NAP A1335
02AC2SOFTWARELEU A:53 , ALA A:75 , VAL A:76 , GLY A:77 , LEU A:100 , ARG A:241 , HIS A:288 , NAP A:1335 , HOH A:2352 , HOH A:2353BINDING SITE FOR RESIDUE GLV A1336
03AC3SOFTWAREARG A:56 , ASP A:79 , ASN A:80 , ILE A:81 , ASP A:82 , HOH A:2398 , HOH A:2399BINDING SITE FOR RESIDUE 1PE A1337
04AC4SOFTWAREARG A:133BINDING SITE FOR RESIDUE 1PE A1338
05AC5SOFTWAREPHE A:294 , 1PE A:1347 , HOH A:2401 , HOH A:2403BINDING SITE FOR RESIDUE 1PE A1339
06AC6SOFTWARETYR A:220 , ASN A:223 , ARG A:226 , HOH A:2295 , HOH A:2404BINDING SITE FOR RESIDUE 1PE A1340
07AC7SOFTWAREGLU A:13 , TYR A:195BINDING SITE FOR RESIDUE 1PE A1341
08AC8SOFTWAREASN A:173 , MET A:174 , HOH A:2407BINDING SITE FOR RESIDUE 1PE A1342
09AC9SOFTWARETHR A:115 , ALA A:116 , HIS A:118 , LYS A:121 , TYR A:146 , ALA A:260 , ASP A:281 , ASN A:282 , 1PE A:1359 , HOH A:2186 , HOH A:2189 , HOH A:2330BINDING SITE FOR RESIDUE 1PE A1343
10BC1SOFTWAREPHE A:278 , SER A:279 , HOH A:2192 , HOH A:2194 , HOH A:2408BINDING SITE FOR RESIDUE 1PE A1344
11BC2SOFTWARELEU A:214 , THR A:215 , LYS A:216 , HOH A:2046 , HOH A:2290 , HOH A:2409 , HOH A:2410BINDING SITE FOR RESIDUE 1PE A1345
12BC3SOFTWAREASP A:98 , ASN A:102 , TYR A:149 , ARG A:167 , 1PE A:1347 , HOH A:2180 , HOH A:2412 , HOH A:2413BINDING SITE FOR RESIDUE 1PE A1346
13BC4SOFTWARETYR A:146 , TYR A:149 , LYS A:151 , ASP A:206 , THR A:233 , 1PE A:1339 , 1PE A:1346 , HOH A:2220 , HOH A:2221 , HOH A:2223 , HOH A:2285BINDING SITE FOR RESIDUE 1PE A1347
14BC5SOFTWAREGLU A:199 , GLU A:200 , LYS A:203 , LEU A:229BINDING SITE FOR RESIDUE 1PE A1348
15BC6SOFTWAREMET A:219 , TYR A:220 , LYS A:243 , GLU A:268 , GLU A:269 , HOH A:2400 , HOH A:2416BINDING SITE FOR RESIDUE 1PE A1349
16BC7SOFTWAREGLU A:31 , HIS A:139 , TRP A:142 , HOH A:2417BINDING SITE FOR RESIDUE EDO A1350
17BC8SOFTWARETYR A:220 , ASP A:246BINDING SITE FOR RESIDUE EDO A1351
18BC9SOFTWAREGLY A:314BINDING SITE FOR RESIDUE EDO A1352
19CC1SOFTWARELYS A:44 , ASN A:64 , PRO A:66 , HOH A:2117 , HOH A:2419BINDING SITE FOR RESIDUE EDO A1353
20CC2SOFTWARELYS A:330 , PRO A:331 , GLY A:332 , PHE A:333 , ASN A:334 , HOH A:2420BINDING SITE FOR RESIDUE EDO A1354
21CC3SOFTWARETYR A:272 , TYR A:273BINDING SITE FOR RESIDUE 1PE A1355
22CC4SOFTWAREMET A:52 , LEU A:53 , TYR A:74 , ALA A:75 , TRP A:138 , HOH A:2353BINDING SITE FOR RESIDUE GLV A1356
23CC5SOFTWARELYS A:38 , TYR A:78 , ARG A:181 , ACY A:1358 , HOH A:2256 , HOH A:2421BINDING SITE FOR RESIDUE ACY A1357
24CC6SOFTWAREARG A:32 , PRO A:35 , ARG A:181 , GLU A:217 , ACY A:1357 , HOH A:2287 , HOH A:2292BINDING SITE FOR RESIDUE ACY A1358
25CC7SOFTWAREHIS A:118 , TRP A:142 , PHE A:143 , LEU A:144 , TYR A:146 , PHE A:294 , 1PE A:1343 , HOH A:2076 , HOH A:2185 , HOH A:2214 , HOH A:2219 , HOH A:2422BINDING SITE FOR RESIDUE 1PE A1359

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu A:270 -Pro A:271

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5AOV)

(-) 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:334
                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhh..eeee.......hhhhhhhhhhhh.eeee......hhhhhhh.....eeee........hhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................eeeee..hhhhhhhhhhhhh...eeeee....hhhhhhhhh.ee.hhhhhhhhh.eeee............hhhhhhhh....eeee..hhhh.hhhhhhhhhhh....eeee.........hhhhhh...eee.......hhhhhhhhhhhhhhhhhhhhh..........hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5aov A   1 MKPKVFITRAIPENGINMLEEEFEVEVWEEEREIPREKLLEKVKDVDALVTMLSERIDQEVFENAPRLRIVANYAVGYDNIDVEEATRRGIYVTNTPDVLTNATADHAFALLLATARHVVKGDKFVRSGEWKRKGIAWHPKWFLGYELYGKTIGIVGFGRIGQAIARRAKGFNMRILYYSRTRKSQAEKELGAEYRPLEEVLKESDFVILAVPLTKETMYMINEERLKLMKPTAILVNIARGKVVDTKALIKALKEGWIAGAGLDVFEEEPYYNEELFSLDNVVLTPHIGSATFEAREAMAELVARNLIAFKRGEIPPTLVNKEVIKIRKPGFN 334
                                    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
   Legend:   → Mismatch (orange background)
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  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 5AOV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 14)

Asymmetric Unit(hide GO term definitions)

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5aow TERNARY CRYSTAL STRUCTURE OF PYROCOCCUS YAYANOSII GLYOXYLATE HYDROXYPYRUVATE REDUCTASE IN PRESENCE OF D- GLYCERATE