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(-) Description

Title :  GDP-MANNOSE-3', 5' -EPIMERASE (ARABIDOPSIS THALIANA), K178R, WITH GDP-BETA-L-GULOSE AND GDP-4-KETO-BETA-L-GULOSE BOUND IN ACTIVE SITE.
 
Authors :  L. L. Major, B. A. Wolucka, J. H. Naismith
Date :  25 Oct 05  (Deposition) - 14 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  3' 5'-Epimerase, Short Chain Dehydratase/Reductase, Gdp- Mannose, Gdp-Gulose, Gdp-Galactose, Keto Intermediate, Vitamin C, Sdr, Isomerase, Ascorbate Biosynthesis, 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
    Chains: A, B
    EC Number: 5.1.3.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHISTEV-GME-K178R
    Expression System Strain: ROSETTA (DE3)
    Expression System Taxid: 562
    Mutation: YES
    Organism Common: MOUSE-EAR CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Other Details: GDP-BETA-L-GULOSE WAS REFINED USING GMP (DEFINED AS GDP, MODIFIED IN THE CIF FILE TO REMOVE THE SECOND PHOSPHATE GROUP) AND GULOSE-MONOPHOSPHATE (GUL), LINKING THE GDP O3A TO THE GUL PB. GDP-BETA-L-4-KETO- GULOSE WAS REFINED USING GMP (DEFINED AS GDP, MODIFIED IN THE CIF FILE TO REMOVE THE SECOND PHOSPHATE GROUP) AND 4-KETO-GULOSE- MONOPHOSPHATE (4KG), LINKING THE GDP O3A TO THE 4KG PB NAD WAS REFINED USING ADP AND A NICOTINAMIDE RING (NI3), LINKING THE ADP PB TO THE NI3 O5* NADH WAS REFINED USING ADP AND A SKEWED REDUCED NICOTINAMIDE RING (NDH), LINKING THE ADP PB TO THE NDH O5*
    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, 25)

Asymmetric/Biological Unit (5, 25)
No.NameCountTypeFull Name
1EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
2FMT18Ligand/IonFORMIC ACID
3GKD2Ligand/IonGUANOSINE 5'-DIPHOSPHATE-4-KETO-BETA-L-GULOSE
4GKE2Ligand/IonGUANOSINE 5'-DIPHOSPHATE-BETA-L-GULOSE
5NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY 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 , HOH A:2440 , HOH A:2441 , HOH A:2442BINDING SITE FOR RESIDUE GKE A1372
02AC2SOFTWAREGLY A:103 , GLY A:104 , MET A:105 , SER A:143 , ALA A:144 , 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:1378 , HOH A:2440 , HOH A:2441 , HOH A:2442BINDING SITE FOR RESIDUE GKD A1374
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 , ARG A:178 , PHE A:201 , ASN A:203 , ILE A:204 , LYS A:217 , GKD A:1374 , HOH A:2139 , HOH A:2443 , HOH A:2444 , HOH A:2445 , HOH A:2446 , HOH A:2447 , HOH A:2448 , HOH A:2449 , HOH A:2450BINDING SITE FOR RESIDUE NAD A1378
04AC4SOFTWAREGLU A:162 , SER A:163 , TRP A:166 , GLU A:183 , HOH A:2464 , HOH A:2465 , HOH A:2466 , GLU B:169 , PRO B:170 , ASP B:172BINDING SITE FOR RESIDUE EPE A1390
05AC5SOFTWAREGLY 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 , TRP B:236 , GLN B:241 , ARG B:243 , MET B:277 , PRO B:300 , GLU B:301 , ARG B:306 , SER B:356 , HOH B:2292 , HOH B:2457 , HOH B:2458BINDING SITE FOR RESIDUE GKE B1372
06AC6SOFTWAREGLY B:103 , GLY B:104 , MET B:105 , ILE B:108 , SER B:143 , ALA B:144 , 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 , 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:1375 , HOH B:2292 , HOH B:2457 , HOH B:2458BINDING SITE FOR RESIDUE GKD B1374
07AC7SOFTWAREGLY 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 , 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 , ARG B:178 , PHE B:201 , ASN B:203 , ILE B:204 , LYS B:217 , GKD B:1374 , HOH B:2079 , HOH B:2164 , HOH B:2281 , HOH B:2459 , HOH B:2460 , HOH B:2461 , HOH B:2462 , HOH B:2463 , HOH B:2464BINDING SITE FOR RESIDUE NAD B1375
08AC8SOFTWAREVAL A:77 , ASP A:78 , ASN A:84 , GLY A:368 , SER A:369 , HOH A:2452 , HIS B:295BINDING SITE FOR RESIDUE FMT A1381
09AC9SOFTWAREGLY A:213 , ARG A:224 , LEU A:352 , TYR A:353 , SER A:355 , HOH A:2259BINDING SITE FOR RESIDUE FMT A1382
10BC1SOFTWARETHR A:13 , TYR A:14 , LYS A:15 , GLU A:16 , ARG B:330BINDING SITE FOR RESIDUE FMT A1383
11BC2SOFTWAREGLN A:366 , LEU A:367 , HOH A:2427 , HOH A:2454 , HOH A:2455 , MET B:82 , ILE B:132 , HOH B:2190BINDING SITE FOR RESIDUE FMT A1384
12BC3SOFTWAREARG A:19 , ARG A:46 , ASP A:249 , HOH A:2282BINDING SITE FOR RESIDUE FMT A1385
13BC4SOFTWAREASN A:157 , HOH A:2199 , HOH A:2456 , HOH A:2457BINDING SITE FOR RESIDUE FMT A1386
14BC5SOFTWAREARG A:215 , GLN A:362 , HOH A:2459BINDING SITE FOR RESIDUE FMT A1387
15BC6SOFTWAREPHE A:150 , HOH A:2460 , PRO B:167BINDING SITE FOR RESIDUE FMT A1388
16BC7SOFTWAREGLU A:162 , SER A:163 , HOH A:2462 , HOH A:2463BINDING SITE FOR RESIDUE FMT A1389
17BC8SOFTWARETHR B:210 , TRP B:211 , LYS B:212 , HOH B:2093 , HOH B:2466BINDING SITE FOR RESIDUE FMT B1378
18BC9SOFTWARELYS B:212 , GLY B:213 , LEU B:352 , TYR B:353 , SER B:355 , LYS B:357 , HOH B:2291 , HOH B:2423BINDING SITE FOR RESIDUE FMT B1379
19CC1SOFTWAREGLN B:109 , HIS B:112 , HOH B:2468 , HOH B:2469 , HOH B:2470 , HOH B:2471 , HOH B:2472BINDING SITE FOR RESIDUE FMT B1380
20CC2SOFTWARETYR B:22 , TRP B:23 , PRO B:24 , HOH B:2032 , HOH B:2473BINDING SITE FOR RESIDUE FMT B1381
21CC3SOFTWAREARG B:215 , GLN B:362 , ARG B:371BINDING SITE FOR RESIDUE FMT B1382
22CC4SOFTWAREGLU B:67 , ASP B:68 , HOH B:2108BINDING SITE FOR RESIDUE FMT B1383
23CC5SOFTWAREARG B:19 , ARG B:46 , ASP B:249 , VAL B:252BINDING SITE FOR RESIDUE FMT B1384
24CC6SOFTWAREHOH A:2361 , LYS B:48 , HOH B:2474BINDING SITE FOR RESIDUE FMT B1385
25CC7SOFTWARESER B:229 , THR B:230 , ASP B:231 , ARG B:232 , HOH B:2477 , HOH B:2478BINDING SITE FOR RESIDUE FMT B1386

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2C54)

(-) 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 2C54)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2C54)

(-) Exons   (0, 0)

(no "Exon" information available for 2C54)

(-) 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:362
 aligned with GME_ARATH | Q93VR3 from UniProtKB/Swiss-Prot  Length:377

    Alignment length:362
                                    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 TYKELEREQYWPSENLKISITGAGGFIASHIARRLKHEGHYVIASDWKKNEHMTEDMFCDEFHLVDLRVMENCLKVTEGVDHVFNLAADMGGMGFIQSNHSVIMYNNTMISFNMIEAARINGIKRFFYASSACIYPEFKQLETTNVSLKESDAWPAEPQDAYGLEKLATEELCKHYNKDFGIECRIGRFHNIYGPFGTWKGGREKAPAAFCRKAQTSTDRFEMWGDGLQTRSFTFIDECVEGVLRLTKSDFREPVNIGSDEMVSMNEMAEMVLSFEEKKLPIHHIPGPEGVRGRNSDNNLIKEKLGWAPNMRLKEGLRITYFWIKEQIEKEKAKGSDVSLYGSSKVVGTQAPVQLGSLRAAD 374
               SCOP domains d2c54a1 A:13-374 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.hhh.hhhh......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
                 2c54 A  13 TYKELEREQYWPSENLKISITGAGGFIASHIARRLKHEGHYVIASDWKKNEHMTEDMFCDEFHLVDLRVMENCLKVTEGVDHVFNLAADMGGMGFIQSNHSVIMYNNTMISFNMIEAARINGIKRFFYASSACIYPEFKQLETTNVSLKESDAWPAEPQDAYGLERLATEELCKHYNKDFGIECRIGRFHNIYGPFGTWKGGREKAPAAFCRKAQTSTDRFEMWGDGLQTRSFTFIDECVEGVLRLTKSDFREPVNIGSDEMVSMNEMAEMVLSFEEKKLPIHHIPGPEGVRGRNSDNNLIKEKLGWAPNMRLKEGLRITYFWIKEQIEKEKAKGSDVSLYGSSKVVGTQAPVQLGSLRAAD 374
                                    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:360
 aligned with GME_ARATH | Q93VR3 from UniProtKB/Swiss-Prot  Length:377

    Alignment length:360
                                    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 YTYKELEREQYWPSENLKISITGAGGFIASHIARRLKHEGHYVIASDWKKNEHMTEDMFCDEFHLVDLRVMENCLKVTEGVDHVFNLAADMGGMGFIQSNHSVIMYNNTMISFNMIEAARINGIKRFFYASSACIYPEFKQLETTNVSLKESDAWPAEPQDAYGLEKLATEELCKHYNKDFGIECRIGRFHNIYGPFGTWKGGREKAPAAFCRKAQTSTDRFEMWGDGLQTRSFTFIDECVEGVLRLTKSDFREPVNIGSDEMVSMNEMAEMVLSFEEKKLPIHHIPGPEGVRGRNSDNNLIKEKLGWAPNMRLKEGLRITYFWIKEQIEKEKAKGSDVSLYGSSKVVGTQAPVQLGSLR 371
               SCOP domains d2c54b_ 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...........hhhhhhhhhhhhh...eeee.....ee..eehhhhhhhhhhhhhh.....eee.....eehhhhhhhhhhh......eeee.........ee.hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh......................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2c54 B  12 YTYKELEREQYWPSENLKISITGAGGFIASHIARRLKHEGHYVIASDWKKNEHMTEDMFCDEFHLVDLRVMENCLKVTEGVDHVFNLAADMGGMGFIQSNHSVIMYNNTMISFNMIEAARINGIKRFFYASSACIYPEFKQLETTNVSLKESDAWPAEPQDAYGLERLATEELCKHYNKDFGIECRIGRFHNIYGPFGTWKGGREKAPAAFCRKAQTSTDRFEMWGDGLQTRSFTFIDECVEGVLRLTKSDFREPVNIGSDEMVSMNEMAEMVLSFEEKKLPIHHIPGPEGVRGRNSDNNLIKEKLGWAPNMRLKEGLRITYFWIKEQIEKEKAKGSDVSLYGSSKVVGTQAPVQLGSLR 371
                                    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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2C54)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2C54)

(-) 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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  2c54
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  5.1.3.18
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 Related Entries

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

UniProtKB/Swiss-Prot
        GME_ARATH | Q93VR3: 2c59 2c5a 2c5e

(-) Related Entries Specified in the PDB File

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