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(-) Description

Title :  GDP-MANNOSE-3', 5' -EPIMERASE (ARABIDOPSIS THALIANA), WITH GDP-ALPHA-D-MANNOSE AND GDP-BETA-L-GALACTOSE BOUND IN THE ACTIVE SITE.
 
Authors :  L. L. Major, B. A. Wolucka, J. H. Naismith
Date :  26 Oct 05  (Deposition) - 14 Nov 05  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
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 (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
    Chains: A, B
    EC Number: 5.1.3.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHISTEV-GME-WT
    Expression System Strain: ROSETTA (DE3)
    Expression System Taxid: 562
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: GDP-MAN 3,5-EPIMERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 15)

Asymmetric/Biological Unit (5, 15)
No.NameCountTypeFull Name
1BTB1Ligand/Ion2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2FMT8Ligand/IonFORMIC ACID
3GDC2Ligand/IonGUANOSINE-5'-DIPHOSPHATE-BETA-L-GALACTOSE
4GDD2Ligand/IonGUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE
5NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
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 , ASN A:203 , GLU A:216 , LYS 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 , ARG A:306 , SER A:356 , HOH A:2217 , HOH A:2295 , HOH A:2380BINDING SITE FOR RESIDUE GDD A1377
02AC2SOFTWAREMET A:102 , GLY A:103 , GLY A:104 , MET A:105 , ILE A:108 , SER A:143 , CYS A:145 , TYR A:174 , PHE A:201 , HIS A:202 , ASN A:203 , GLU A:216 , LYS 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 , ARG A:306 , SER A:356 , NAD A:1379 , HOH A:2217 , HOH A:2295 , HOH A:2380BINDING SITE FOR RESIDUE GDC A1378
03AC3SOFTWAREGLY 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 , LYS A:217 , GDC A:1378 , HOH A:2097 , HOH A:2381 , HOH A:2382 , HOH A:2383 , HOH A:2384 , HOH A:2385 , HOH A:2386 , HOH A:2387 , HOH A:2388BINDING SITE FOR RESIDUE NAD A1379
04AC4SOFTWAREFMT A:1382 , HOH A:2319 , LYS B:29 , TYR B:53 , ILE B:55 , GLU B:73 , LYS B:87 , GLU B:90 , GLY B:91 , HOH B:2141 , HOH B:2448BINDING SITE FOR RESIDUE BTB B1376
05AC5SOFTWAREMET B:102 , GLY B:103 , GLY B:104 , MET B:105 , ILE B:108 , SER B:143 , CYS B:145 , TYR B:174 , PHE B:201 , HIS B:202 , ASN B:203 , GLU B:216 , LYS 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 , HOH B:2449 , HOH B:2450 , HOH B:2451BINDING SITE FOR RESIDUE GDD B1377
06AC6SOFTWAREMET B:102 , GLY B:103 , GLY B:104 , MET B:105 , ILE B:108 , SER B:143 , CYS B:145 , TYR B:174 , PHE B:201 , ASN B:203 , GLU B:216 , LYS 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 , ARG B:306 , SER B:356 , NAD B:1380 , HOH B:2449 , HOH B:2450 , HOH B:2451BINDING SITE FOR RESIDUE GDC B1378
07AC7SOFTWAREGLY 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 , LYS B:217 , ARG B:371 , GDC B:1378 , HOH B:2152 , HOH B:2156 , HOH B:2282 , HOH B:2452 , HOH B:2453 , HOH B:2454 , HOH B:2455 , HOH B:2456BINDING SITE FOR RESIDUE NAD B1380
08AC8SOFTWARELYS A:212 , GLY A:213 , ARG A:224 , LEU A:352 , TYR A:353 , SER A:355 , LYS A:357 , HOH A:2218BINDING SITE FOR RESIDUE FMT A1380
09AC9SOFTWAREPHE A:150 , PRO B:167BINDING SITE FOR RESIDUE FMT A1381
10BC1SOFTWAREGLU A:18 , ARG A:257 , GLY A:318 , TRP A:319 , LYS B:29 , BTB B:1376 , HOH B:2147BINDING SITE FOR RESIDUE FMT A1382
11BC2SOFTWAREHOH B:2440BINDING SITE FOR RESIDUE FMT B1371
12BC3SOFTWAREARG B:215 , GLN B:362BINDING SITE FOR RESIDUE FMT B1372
13BC4SOFTWARESER B:229 , THR B:230 , ASP B:231 , ARG B:232BINDING SITE FOR RESIDUE FMT B1373
14BC5SOFTWAREVAL A:77 , ASP A:78 , ASN A:84 , GLY A:368 , SER A:369 , HIS B:295 , HOH B:2444BINDING SITE FOR RESIDUE FMT B1374
15BC6SOFTWAREPRO A:167 , PHE B:150 , HOH B:2445 , HOH B:2446BINDING SITE FOR RESIDUE FMT B1375

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2C59)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Trp A:166 -Pro A:167
2Asp A:374 -Gly A:375
3Trp B:166 -Pro B:167

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2C59)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2C59)

(-) Exons   (0, 0)

(no "Exon" information available for 2C59)

(-) 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:364
 aligned with GME_ARATH | Q93VR3 from UniProtKB/Swiss-Prot  Length:377

    Alignment length:364
                                    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 YTYKELEREQYWPSENLKISITGAGGFIASHIARRLKHEGHYVIASDWKKNEHMTEDMFCDEFHLVDLRVMENCLKVTEGVDHVFNLAADMGGMGFIQSNHSVIMYNNTMISFNMIEAARINGIKRFFYASSACIYPEFKQLETTNVSLKESDAWPAEPQDAYGLEKLATEELCKHYNKDFGIECRIGRFHNIYGPFGTWKGGREKAPAAFCRKAQTSTDRFEMWGDGLQTRSFTFIDECVEGVLRLTKSDFREPVNIGSDEMVSMNEMAEMVLSFEEKKLPIHHIPGPEGVRGRNSDNNLIKEKLGWAPNMRLKEGLRITYFWIKEQIEKEKAKGSDVSLYGSSKVVGTQAPVQLGSLRAADG 375
               SCOP domains -d2c59a1 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.....eee.eehhhhhhhhhhhhhh.....eee....eeehhhhhhhhhhh......eeee.........ee.hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh.................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c59 A  12 YTYKELEREQYWPSENLKISITGAGGFIASHIARRLKHEGHYVIASDWKKNEHMTEDMFCDEFHLVDLRVMENCLKVTEGVDHVFNLAADMGGMGFIQSNHSVIMYNNTMISFNMIEAARINGIKRFFYASSACIYPEFKQLETTNVSLKESDAWPAEPQDAYGLEKLATEELCKHYNKDFGIECRIGRFHNIYGPFGTWKGGREKAPAAFCRKAQTSTDRFEMWGDGLQTRSFTFIDECVEGVLRLTKSDFREPVNIGSDEMVSMNEMAEMVLSFEEKKLPIHHIPGPEGVRGRNSDNNLIKEKLGWAPNMRLKEGLRITYFWIKEQIEKEKAKGSDVSLYGSSKVVGTQAPVQLGSLRAADG 375
                                    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    


Chain B from PDB  Type:PROTEIN  Length:362
 aligned with GME_ARATH | Q93VR3 from UniProtKB/Swiss-Prot  Length:377

    Alignment length:362
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369  
            GME_ARATH    10 GAYTYKELEREQYWPSENLKISITGAGGFIASHIARRLKHEGHYVIASDWKKNEHMTEDMFCDEFHLVDLRVMENCLKVTEGVDHVFNLAADMGGMGFIQSNHSVIMYNNTMISFNMIEAARINGIKRFFYASSACIYPEFKQLETTNVSLKESDAWPAEPQDAYGLEKLATEELCKHYNKDFGIECRIGRFHNIYGPFGTWKGGREKAPAAFCRKAQTSTDRFEMWGDGLQTRSFTFIDECVEGVLRLTKSDFREPVNIGSDEMVSMNEMAEMVLSFEEKKLPIHHIPGPEGVRGRNSDNNLIKEKLGWAPNMRLKEGLRITYFWIKEQIEKEKAKGSDVSLYGSSKVVGTQAPVQLGSLR 371
               SCOP domains d2c59b_ B: automated matches                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................eeeee...hhhhhhhhhhhhhh..eeeeee.......hhhhh..eeee....hhhhhhhh.....eeee......hhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhhhhhh......eehhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.eeeeeee..ee...........hhhhhhhhhhhhh...eeee.....ee..eehhhhhhhhhhhhhh.....eee.....eehhhhhhhhhhh......eeee.........ee.hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c59 B  10 GAYTYKELEREQYWPSENLKISITGAGGFIASHIARRLKHEGHYVIASDWKKNEHMTEDMFCDEFHLVDLRVMENCLKVTEGVDHVFNLAADMGGMGFIQSNHSVIMYNNTMISFNMIEAARINGIKRFFYASSACIYPEFKQLETTNVSLKESDAWPAEPQDAYGLEKLATEELCKHYNKDFGIECRIGRFHNIYGPFGTWKGGREKAPAAFCRKAQTSTDRFEMWGDGLQTRSFTFIDECVEGVLRLTKSDFREPVNIGSDEMVSMNEMAEMVLSFEEKKLPIHHIPGPEGVRGRNSDNNLIKEKLGWAPNMRLKEGLRITYFWIKEQIEKEKAKGSDVSLYGSSKVVGTQAPVQLGSLR 371
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369
   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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2C59)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2C59)

(-) 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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  Cis Peptide Bonds
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  2c59
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 Related Entries

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

UniProtKB/Swiss-Prot
        GME_ARATH | Q93VR3: 2c54 2c5a 2c5e

(-) 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
2c5a GDP-MANNOSE-3,5-EPIMERASE (ARABIDOPSIS THALIANA), Y174F, WITH GDP- BETA-L-GALACTOSE BOUND IN THE ACTIVE SITE
2c5e GDP-MANNOSE-3, 5-EPIMERASE (ARABIDOPSIS THALIANA), K217A, WITH GDP- ALPHA-D-MANNOSE BOUND IN THE ACTIVE SITE