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(-) Description

Title :  GDP-MANNOSE-3', 5' -EPIMERASE (ARABIDOPSIS THALIANA), K217A, WITH GDP-ALPHA-D-MANNOSE BOUND IN THE ACTIVE SITE.
 
Authors :  L. L. Major, B. A. Wolucka, J. H. Naismith
Date :  26 Oct 05  (Deposition) - 14 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  3' 5'-Epimerase, Short Chain Dehydratase/Reductase, Gdp- Mannose, Gdp-Gulose, Gdp-Galactose, Keto Intermediate, Vitamin C, Ascorbate Biosynthesis, Isomerase, Nad (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. L. Major, B. A. Wolucka, J. H. Naismith
Structure And Function Of Gdp-Mannose-3', 5'- Epimerase: An Enzyme Which Performs Three Chemical Reactions At The Same Active Site.
J. Am. Chem. Soc. V. 127 18309 2005
PubMed-ID: 16366586  |  Reference-DOI: 10.1021/JA056490I

(-) Compounds

Molecule 1 - GDP-MANNOSE-3', 5'-EPIMERASE
    ChainsA, B
    EC Number5.1.3.18
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPHISTEV-GME-K217A
    Expression System StrainROSETTA (DE3)
    Expression System Taxid562
    MutationYES
    Organism CommonMOUSE-EAR CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702
    Other DetailsGDP-ALPHA-D-MANNOSE WAS REFINED USING GMP (DEFINED AS GDP, MODIFIED IN THE CIF FILE TO REMOVE THE SECOND PHOSPHATE GROUP) AND MANNOSE-MONOPHOSPHATE (MA7), LINKING THE GDP O3A TO THE MA7 PB
    SynonymGDP-MAN 3,5-EPIMERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric/Biological Unit (3, 14)
No.NameCountTypeFull Name
1FMT10Ligand/IonFORMIC ACID
2GDD2Ligand/IonGUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE
3NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREMET A:102 , GLY A:103 , GLY A:104 , MET A:105 , ILE A:108 , SER A:143 , ALA A:144 , CYS A:145 , TYR A:174 , PHE A:201 , HIS A:202 , ASN A:203 , GLU A:216 , ALA A:217 , ALA A:218 , ALA A:221 , PHE A:222 , LYS A:225 , TRP A:236 , GLN A:241 , ARG A:243 , MET A:277 , PRO A:300 , GLU A:301 , SER A:356 , NAD A:1381 , HOH A:2381 , HOH A:2382 , HOH A:2383BINDING SITE FOR RESIDUE GDD A1375
02AC2SOFTWAREGLY A:34 , GLY A:36 , GLY A:37 , PHE A:38 , ILE A:39 , ASP A:58 , TRP A:59 , LYS A:60 , VAL A:77 , ASP A:78 , LEU A:79 , ARG A:80 , LEU A:98 , ALA A:99 , ALA A:100 , MET A:102 , ILE A:122 , ALA A:141 , SER A:142 , SER A:143 , TYR A:174 , LYS A:178 , PHE A:201 , ASN A:203 , ILE A:204 , GDD A:1375 , HOH A:2210 , HOH A:2388 , HOH A:2389 , HOH A:2390 , HOH A:2391 , HOH A:2392 , HOH A:2393 , HOH A:2394 , HOH A:2395 , HOH A:2396BINDING SITE FOR RESIDUE NAD A1381
03AC3SOFTWAREMET B:102 , GLY B:103 , GLY B:104 , MET B:105 , ILE B:108 , SER B:143 , ALA B:144 , CYS B:145 , TYR B:174 , PHE B:201 , HIS B:202 , ASN B:203 , GLU B:216 , ALA B:217 , ALA B:218 , ALA B:221 , PHE B:222 , LYS B:225 , MET B:235 , TRP B:236 , GLN B:241 , ARG B:243 , MET B:277 , PRO B:300 , GLU B:301 , SER B:356 , NAD B:1373 , HOH B:2270 , HOH B:2452 , HOH B:2453 , HOH B:2461BINDING SITE FOR RESIDUE GDD B1372
04AC4SOFTWAREGLY B:34 , GLY B:36 , GLY B:37 , PHE B:38 , ILE B:39 , ASP B:58 , TRP B:59 , LYS B:60 , VAL B:77 , ASP B:78 , LEU B:79 , ARG B:80 , LEU B:98 , ALA B:99 , ALA B:100 , MET B:102 , ILE B:122 , ALA B:141 , SER B:142 , SER B:143 , TYR B:174 , LYS B:178 , PHE B:201 , ASN B:203 , ILE B:204 , ARG B:371 , GDD B:1372 , HOH B:2139 , HOH B:2263 , HOH B:2454 , HOH B:2455 , HOH B:2456 , HOH B:2457 , HOH B:2458 , HOH B:2459 , HOH B:2460 , HOH B:2461BINDING SITE FOR RESIDUE NAD B1373
05AC5SOFTWAREASN A:157 , VAL A:158 , SER A:159 , MET A:274 , ASN A:307 , HOH A:2384 , HOH A:2385BINDING SITE FOR RESIDUE FMT A1376
06AC6SOFTWARETRP A:335 , GLU A:338BINDING SITE FOR RESIDUE FMT A1377
07AC7SOFTWAREVAL A:77 , ASP A:78 , ASN A:84 , GLY A:368 , SER A:369 , HOH A:2386 , HOH A:2387 , HIS B:295BINDING SITE FOR RESIDUE FMT A1378
08AC8SOFTWARETYR A:14 , LYS A:15 , GLU A:16 , ARG B:330BINDING SITE FOR RESIDUE FMT A1379
09AC9SOFTWAREARG A:19 , ARG A:46 , ASP A:249 , VAL A:252 , HOH A:2036BINDING SITE FOR RESIDUE FMT A1380
10BC1SOFTWAREGLN B:109 , SER B:110 , HOH B:2462 , HOH B:2463 , HOH B:2464 , HOH B:2465 , HOH B:2466 , HOH B:2467BINDING SITE FOR RESIDUE FMT B1374
11BC2SOFTWARELYS B:212 , GLY B:213 , LEU B:352 , TYR B:353 , SER B:355 , LYS B:357 , HOH B:2271 , HOH B:2415BINDING SITE FOR RESIDUE FMT B1375
12BC3SOFTWAREGLU B:183 , LYS B:186 , HIS B:187 , LYS B:190BINDING SITE FOR RESIDUE FMT B1376
13BC4SOFTWAREGLU B:162 , SER B:163 , HOH B:2469 , HOH B:2470 , HOH B:2471BINDING SITE FOR RESIDUE FMT B1377
14BC5SOFTWARETHR B:210 , TRP B:211 , LYS B:212 , HOH B:2076 , HOH B:2472 , HOH B:2474BINDING SITE FOR RESIDUE FMT B1378

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2C5E)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Trp A:166 -Pro A:167
2Trp B:166 -Pro B:167

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2C5E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2C5E)

(-) Exons   (0, 0)

(no "Exon" information available for 2C5E)

(-) 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:363
 aligned with GME_ARATH | Q93VR3 from UniProtKB/Swiss-Prot  Length:377

    Alignment length:363
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372   
            GME_ARATH    13 TYKELEREQYWPSENLKISITGAGGFIASHIARRLKHEGHYVIASDWKKNEHMTEDMFCDEFHLVDLRVMENCLKVTEGVDHVFNLAADMGGMGFIQSNHSVIMYNNTMISFNMIEAARINGIKRFFYASSACIYPEFKQLETTNVSLKESDAWPAEPQDAYGLEKLATEELCKHYNKDFGIECRIGRFHNIYGPFGTWKGGREKAPAAFCRKAQTSTDRFEMWGDGLQTRSFTFIDECVEGVLRLTKSDFREPVNIGSDEMVSMNEMAEMVLSFEEKKLPIHHIPGPEGVRGRNSDNNLIKEKLGWAPNMRLKEGLRITYFWIKEQIEKEKAKGSDVSLYGSSKVVGTQAPVQLGSLRAADG 375
               SCOP domains d2c5ea1 A:13-375 GDP-mannose-3', 5'-epimerase                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeeee...hhhhhhhhhhhhhh..eeeeee.......hhhhhh.eeee....hhhhhhhhhh...eeee......hhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhhhhhh......eehhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.eeeeeee..ee...........hhhhhhhhhhhhh...eeee.....ee..eehhhhhhhhhhhhhh.....eee.....eehhhhhhhhhhh......eeee.........ee.hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh.................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c5e A  13 TYKELEREQYWPSENLKISITGAGGFIASHIARRLKHEGHYVIASDWKKNEHMTEDMFCDEFHLVDLRVMENCLKVTEGVDHVFNLAADMGGMGFIQSNHSVIMYNNTMISFNMIEAARINGIKRFFYASSACIYPEFKQLETTNVSLKESDAWPAEPQDAYGLEKLATEELCKHYNKDFGIECRIGRFHNIYGPFGTWKGGREAAPAAFCRKAQTSTDRFEMWGDGLQTRSFTFIDECVEGVLRLTKSDFREPVNIGSDEMVSMNEMAEMVLSFEEKKLPIHHIPGPEGVRGRNSDNNLIKEKLGWAPNMRLKEGLRITYFWIKEQIEKEKAKGSDVSLYGSSKVVGTQAPVQLGSLRAADG 375
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372   

Chain B from PDB  Type:PROTEIN  Length:361
 aligned with GME_ARATH | Q93VR3 from UniProtKB/Swiss-Prot  Length:377

    Alignment length:361
                                    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       341       351       361       371 
            GME_ARATH    12 YTYKELEREQYWPSENLKISITGAGGFIASHIARRLKHEGHYVIASDWKKNEHMTEDMFCDEFHLVDLRVMENCLKVTEGVDHVFNLAADMGGMGFIQSNHSVIMYNNTMISFNMIEAARINGIKRFFYASSACIYPEFKQLETTNVSLKESDAWPAEPQDAYGLEKLATEELCKHYNKDFGIECRIGRFHNIYGPFGTWKGGREKAPAAFCRKAQTSTDRFEMWGDGLQTRSFTFIDECVEGVLRLTKSDFREPVNIGSDEMVSMNEMAEMVLSFEEKKLPIHHIPGPEGVRGRNSDNNLIKEKLGWAPNMRLKEGLRITYFWIKEQIEKEKAKGSDVSLYGSSKVVGTQAPVQLGSLRA 372
               SCOP domains d2c5eb_ B: automated matches                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeee...hhhhhhhhhhhhhh..eeeeee.......hhhhh..eeee....hhhhhhhhhh...eeee......hhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhhhhhh......eehhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.eeeeeee..ee...........hhhhhhhhhhhh....eeee.....ee..eehhhhhhhhhhhhhh.....eee.....eehhhhhhhhhhh......eeee.........ee.hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.......................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c5e B  12 YTYKELEREQYWPSENLKISITGAGGFIASHIARRLKHEGHYVIASDWKKNEHMTEDMFCDEFHLVDLRVMENCLKVTEGVDHVFNLAADMGGMGFIQSNHSVIMYNNTMISFNMIEAARINGIKRFFYASSACIYPEFKQLETTNVSLKESDAWPAEPQDAYGLEKLATEELCKHYNKDFGIECRIGRFHNIYGPFGTWKGGREAAPAAFCRKAQTSTDRFEMWGDGLQTRSFTFIDECVEGVLRLTKSDFREPVNIGSDEMVSMNEMAEMVLSFEEKKLPIHHIPGPEGVRGRNSDNNLIKEKLGWAPNMRLKEGLRITYFWIKEQIEKEKAKGSDVSLYGSSKVVGTQAPVQLGSLRA 372
                                    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       341       351       361       371 

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2C5E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2C5E)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (GME_ARATH | Q93VR3)
molecular function
    GO:0047918    GDP-mannose 3,5-epimerase activity    Catalysis of the reaction: GDP-mannose = GDP-L-galactose.
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0050662    coenzyme binding    Interacting selectively and non-covalently with a coenzyme, any of various nonprotein organic cofactors that are required, in addition to an enzyme and a substrate, for an enzymatic reaction to proceed.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    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.
biological process
    GO:0019853    L-ascorbic acid biosynthetic process    The chemical reactions and pathways resulting in the formation of L-ascorbic acid; L-ascorbic acid ionizes to give L-ascorbate, (2R)-2-[(1S)-1,2-dihydroxyethyl]-4-hydroxy-5-oxo-2,5-dihydrofuran-3-olate, which is required as a cofactor in the oxidation of prolyl residues to hydroxyprolyl, and other reactions.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GME_ARATH | Q93VR32c54 2c59 2c5a

(-) Related Entries Specified in the PDB File

2c54 GDP-MANNOSE-3,5-EPIMERASE (ARABIDOPSIS THALIANA),K178R, WITH GDP-BETA-L-GULOSE AND GDP-4-KETO-BETA-L-GULOSE BOUND IN ACTIVE SITE
2c59 GDP-MANNOSE-3,5-EPIMERASE (ARABIDOPSIS THALIANA), WITH GDP-ALPHA-D-MANNOSE AND GDP-BETA-L-GALACTOSE BOUND IN THE ACTIVE SITE
2c5a GDP-MANNOSE-3,5-EPIMERASE (ARABIDOPSIS THALIANA), Y174F, WITH GDP-BETA-L-GALACTOSE BOUND IN THE ACTIVE SITE