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(-) Description

Title :  THE CRYSTAL STRUCTURE OF UDP-GLUCOSE PYROPHOSPHORYLASE COMPLEXED WITH UDP-GLUCOSE
 
Authors :  H. Kim, K. K. Kim
Date :  15 Sep 09  (Deposition) - 31 Mar 10  (Release) - 19 May 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Udp-Glucose Pyrophosphorylase, Helicobacter Pylori, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Kim, J. Choi, T. Kim, N. K. Lokanath, S. C. Ha, S. W. Suh, H. -Y. Hwang, K. K. Kim
Structural Basis For The Reaction Mechanism Of Udp-Glucose Pyrophosphorylase
Mol. Cells V. 29 397 2010
PubMed-ID: 20238176  |  Reference-DOI: 10.1007/S10059-010-0047-6

(-) Compounds

Molecule 1 - UDP-GLUCOSE PYROPHOSPHORYLASE (GALU)
    Chains: A, B, C, D
    EC Number: 2.7.7.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-21A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: HP_0646
    Organism Common: CAMPYLOBACTER PYLORI
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 85962
    Strain: 26695

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 16)

Asymmetric/Biological Unit (2, 16)
No.NameCountTypeFull Name
1MG12Ligand/IonMAGNESIUM ION
2UPG4Ligand/IonURIDINE-5'-DIPHOSPHATE-GLUCOSE

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:8 , ALA A:10 , GLY A:11 , LYS A:25 , GLU A:26 , GLN A:102 , MET A:105 , LYS A:106 , GLY A:107 , LEU A:108 , ALA A:111 , LEU A:128 , ASP A:130 , ASP A:131 , TYR A:170 , GLY A:171 , GLU A:190 , LYS A:191 , VAL A:203 , THR A:231 , ARG A:252 , HOH A:291 , HOH A:292 , MG A:301 , HOH A:326 , HOH A:338 , HOH A:340 , HOH A:348 , HOH A:359 , HOH A:369BINDING SITE FOR RESIDUE UPG A 282
02AC2SOFTWARELYS A:25 , ASP A:130 , UPG A:282 , HOH A:338 , HOH A:346 , HOH A:359BINDING SITE FOR RESIDUE MG A 301
03AC3SOFTWAREVAL A:258BINDING SITE FOR RESIDUE MG A 302
04AC4SOFTWARETHR A:14BINDING SITE FOR RESIDUE MG A 303
05AC5SOFTWAREPRO B:8 , ALA B:9 , ALA B:10 , GLY B:11 , LYS B:25 , GLU B:26 , GLN B:102 , MET B:105 , LYS B:106 , GLY B:107 , LEU B:108 , ALA B:111 , LEU B:128 , ASP B:130 , ASP B:131 , TYR B:170 , GLY B:171 , GLU B:190 , LYS B:191 , VAL B:203 , THR B:231 , MG B:304 , HOH B:311 , HOH B:314 , HOH B:320 , HOH B:333 , HOH B:360 , HOH B:407 , HOH B:531 , HOH B:558BINDING SITE FOR RESIDUE UPG B 282
06AC6SOFTWAREASP B:130 , UPG B:282 , HOH B:354 , HOH B:360 , HOH B:558BINDING SITE FOR RESIDUE MG B 304
07AC7SOFTWAREARG A:272 , HOH A:648 , VAL B:258BINDING SITE FOR RESIDUE MG B 305
08AC8SOFTWARETHR B:14 , ARG B:15BINDING SITE FOR RESIDUE MG B 306
09AC9SOFTWAREPRO C:8 , ALA C:9 , ALA C:10 , GLY C:11 , LYS C:25 , GLU C:26 , GLN C:102 , MET C:105 , LYS C:106 , GLY C:107 , LEU C:108 , ALA C:111 , LEU C:128 , ASP C:130 , ASP C:131 , TYR C:170 , GLY C:171 , GLU C:190 , LYS C:191 , VAL C:203 , THR C:231 , MG C:307 , HOH C:325 , HOH C:331 , HOH C:352 , HOH C:356 , HOH C:385 , HOH C:430 , HOH C:483BINDING SITE FOR RESIDUE UPG C 283
10BC1SOFTWARELYS C:25 , ASP C:130 , UPG C:283 , HOH C:326 , HOH C:356 , HOH C:430BINDING SITE FOR RESIDUE MG C 307
11BC2SOFTWARESER C:257 , VAL C:258BINDING SITE FOR RESIDUE MG C 309
12BC3SOFTWAREPRO D:8 , ALA D:9 , ALA D:10 , GLY D:11 , LYS D:25 , GLU D:26 , GLN D:102 , MET D:105 , LYS D:106 , GLY D:107 , LEU D:108 , ALA D:111 , LEU D:128 , ASP D:130 , ASP D:131 , TYR D:170 , GLY D:171 , GLU D:190 , LYS D:191 , VAL D:203 , THR D:231 , HOH D:300 , MG D:310 , HOH D:316 , HOH D:337 , HOH D:362 , HOH D:367 , HOH D:387 , HOH D:443 , HOH D:559 , HOH D:595BINDING SITE FOR RESIDUE UPG D 284
13BC4SOFTWAREASP D:130 , UPG D:284 , HOH D:367 , HOH D:387 , HOH D:559BINDING SITE FOR RESIDUE MG D 310
14BC5SOFTWARETHR D:14 , ARG D:15BINDING SITE FOR RESIDUE MG D 311
15BC6SOFTWAREVAL D:258BINDING SITE FOR RESIDUE MG D 312

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3JUK)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Leu A:17 -Pro A:18
2Leu B:17 -Pro B:18
3Leu C:17 -Pro C:18
4Leu D:17 -Pro D:18

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3JUK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3JUK)

(-) Exons   (0, 0)

(no "Exon" information available for 3JUK)

(-) 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:265
 aligned with O25363_HELPY | O25363 from UniProtKB/TrEMBL  Length:273

    Alignment length:273
                                    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   
         O25363_HELPY     1 MIKKCLFPAAGYGTRFLPITKTIPKEMLPIVDKPLIQYAVEEAMEAGCEVMAIVTGRNKRSLEDYFDTSYEIEHQIQGTNKENALKSIRNIIEKCCFSYVRQKQMKGLGHAILTGEALIGNEPFAVILADDLCISHDHPSVLKQMTSLYQKYQCSIVAIEEVALEEVSKYGVIRGEWLEEGVYEIKDMVEKPNQEDAPSNLAVIGRYILTPDIFEILSETKPGKNNEIQITDALRTQAKRKRIIAYQFKGKRYDCGSVEGYIEASNAYYKKRL 273
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....hhhhhhhhhh.hhhhh.....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhh....--------.hhhhhhhhhhhhhhhheeeeee.....hhhhhhhhhhhhhh...eeee...eeee.....hhhhhhhhhhhhhh..eeeeee....hhhh.eeeeeeeee..eeeeeeeee..........eeeeeeeee..hhhhhhhh...hhhhh.hhhhhhhhhhhhh..eeee...eeee..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3juk A   1 MIKKCLFPAAGYGTRFLPITKTIPKEMLPIVDKPLIQYAVEEAMEAGCEVMAIVTGRNKRSLEDYFDTSY--------TNKENALKSIRNIIEKCCFSYVRQKQMKGLGHAILTGEALIGNEPFAVILADDLCISHDHPSVLKQMTSLYQKYQCSIVAIEEVALEEVSKYGVIRGEWLEEGVYEIKDMVEKPNQEDAPSNLAVIGRYILTPDIFEILSETKPGKNNEIQITDALRTQAKRKRIIAYQFKGKRYDCGSVEGYIEASNAYYKKRL 273
                                    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   
                                                                                                70       79                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:263
 aligned with O25363_HELPY | O25363 from UniProtKB/TrEMBL  Length:273

    Alignment length:272
                                    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  
         O25363_HELPY     1 MIKKCLFPAAGYGTRFLPITKTIPKEMLPIVDKPLIQYAVEEAMEAGCEVMAIVTGRNKRSLEDYFDTSYEIEHQIQGTNKENALKSIRNIIEKCCFSYVRQKQMKGLGHAILTGEALIGNEPFAVILADDLCISHDHPSVLKQMTSLYQKYQCSIVAIEEVALEEVSKYGVIRGEWLEEGVYEIKDMVEKPNQEDAPSNLAVIGRYILTPDIFEILSETKPGKNNEIQITDALRTQAKRKRIIAYQFKGKRYDCGSVEGYIEASNAYYKKR 272
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee...hhhhhhhhhh.hhhhh.....hhhhhhhhhhhhh...eeeeee...hhhhhhhh....---------hhhhhhhhhhhhhhhheeeeee.....hhhhhhhhhhhhhh...eeee...eeee.....hhhhhhhhhhhhhh..eeeeee....hhhh.eeeeeeeee..eeeeeeeee..hhhhh...eeeeeeeee..hhhhhhhhh..hhhhh.hhhhhhhhhhhhh..eeee...eeee..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3juk B   1 MIKKCLFPAAGYGTRFLPITKTIPKEMLPIVDKPLIQYAVEEAMEAGCEVMAIVTGRNKRSLEDYFDTSY---------NKENALKSIRNIIEKCCFSYVRQKQMKGLGHAILTGEALIGNEPFAVILADDLCISHDHPSVLKQMTSLYQKYQCSIVAIEEVALEEVSKYGVIRGEWLEEGVYEIKDMVEKPNQEDAPSNLAVIGRYILTPDIFEILSETKPGKNNEIQITDALRTQAKRKRIIAYQFKGKRYDCGSVEGYIEASNAYYKKR 272
                                    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  
                                                                                                70        80                                                                                                                                                                                                


Chain C from PDB  Type:PROTEIN  Length:264
 aligned with O25363_HELPY | O25363 from UniProtKB/TrEMBL  Length:273

    Alignment length:273
                                    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   
         O25363_HELPY     1 MIKKCLFPAAGYGTRFLPITKTIPKEMLPIVDKPLIQYAVEEAMEAGCEVMAIVTGRNKRSLEDYFDTSYEIEHQIQGTNKENALKSIRNIIEKCCFSYVRQKQMKGLGHAILTGEALIGNEPFAVILADDLCISHDHPSVLKQMTSLYQKYQCSIVAIEEVALEEVSKYGVIRGEWLEEGVYEIKDMVEKPNQEDAPSNLAVIGRYILTPDIFEILSETKPGKNNEIQITDALRTQAKRKRIIAYQFKGKRYDCGSVEGYIEASNAYYKKRL 273
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee...hhhhhhhhhh.hhhhh.....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhh....---------hhhhhhhhhhhhhhhheeeeee.....hhhhhhhhhhhhhh...eeee...eeee.....hhhhhhhhhhhhhh..eeeeee.hhhhhhh.eeeeeeeee..eeeeeeeee..........eeeeeeeee.hhhhhhhhh...hhhhh.hhhhhhhhhhh....eeee...eeee..hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3juk C   1 MIKKCLFPAAGYGTRFLPITKTIPKEMLPIVDKPLIQYAVEEAMEAGCEVMAIVTGRNKRSLEDYFDTSY---------NKENALKSIRNIIEKCCFSYVRQKQMKGLGHAILTGEALIGNEPFAVILADDLCISHDHPSVLKQMTSLYQKYQCSIVAIEEVALEEVSKYGVIRGEWLEEGVYEIKDMVEKPNQEDAPSNLAVIGRYILTPDIFEILSETKPGKNNEIQITDALRTQAKRKRIIAYQFKGKRYDCGSVEGYIEASNAYYKKRL 273
                                    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   
                                                                                                70        80                                                                                                                                                                                                 


Chain D from PDB  Type:PROTEIN  Length:264
 aligned with O25363_HELPY | O25363 from UniProtKB/TrEMBL  Length:273

    Alignment length:272
                                    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  
         O25363_HELPY     1 MIKKCLFPAAGYGTRFLPITKTIPKEMLPIVDKPLIQYAVEEAMEAGCEVMAIVTGRNKRSLEDYFDTSYEIEHQIQGTNKENALKSIRNIIEKCCFSYVRQKQMKGLGHAILTGEALIGNEPFAVILADDLCISHDHPSVLKQMTSLYQKYQCSIVAIEEVALEEVSKYGVIRGEWLEEGVYEIKDMVEKPNQEDAPSNLAVIGRYILTPDIFEILSETKPGKNNEIQITDALRTQAKRKRIIAYQFKGKRYDCGSVEGYIEASNAYYKKR 272
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----NTP_transferase-3jukD01 D:6-271                                                                                                                                                                                                                                           - Pfam domains (1)
           Pfam domains (2) -----NTP_transferase-3jukD02 D:6-271                                                                                                                                                                                                                                           - Pfam domains (2)
           Pfam domains (3) -----NTP_transferase-3jukD03 D:6-271                                                                                                                                                                                                                                           - Pfam domains (3)
           Pfam domains (4) -----NTP_transferase-3jukD04 D:6-271                                                                                                                                                                                                                                           - Pfam domains (4)
         Sec.struct. author ...eeeeee...hhhhhhhhhh.hhhhh.....hhhhhhhhhhhhh...eeeeee...hhhhhhhh....--------..hhhhhhhhhhhhhhheeeeee.....hhhhhhhhhhhhhh...eeee...eeee.....hhhhhhhhhhhhhh..eeeeee....hhhh.eeeeeeeee..eeeeeeeee..........eeeeeeeee..hhhhhhhhh..hhhhh.hhhhhhhhhhhhh..eeee...eeee..hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3juk D   1 MIKKCLFPAAGYGTRFLPITKTIPKEMLPIVDKPLIQYAVEEAMEAGCEVMAIVTGRNKRSLEDYFDTSY--------TNKENALKSIRNIIEKCCFSYVRQKQMKGLGHAILTGEALIGNEPFAVILADDLCISHDHPSVLKQMTSLYQKYQCSIVAIEEVALEEVSKYGVIRGEWLEEGVYEIKDMVEKPNQEDAPSNLAVIGRYILTPDIFEILSETKPGKNNEIQITDALRTQAKRKRIIAYQFKGKRYDCGSVEGYIEASNAYYKKR 272
                                    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  
                                                                                                70       79
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  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 3JUK)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3JUK)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: GT-A (172)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (O25363_HELPY | O25363)
molecular function
    GO:0003983    UTP:glucose-1-phosphate uridylyltransferase activity    Catalysis of the reaction: alpha-D-glucose 1-phosphate + UTP = diphosphate + UDP-D-glucose.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006011    UDP-glucose metabolic process    The chemical reactions and pathways involving UDP-glucose, uridinediphosphoglucose, a substance composed of glucose in glycosidic linkage with uridine diphosphate.
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.

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  3juk
    Family and Domain Information: ProDom | SYSTERS
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  O25363_HELPY | O25363
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  2.7.7.9
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 Related Entries

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

UniProtKB/TrEMBL
        O25363_HELPY | O25363: 3juj

(-) Related Entries Specified in the PDB File

3juj APO-UGPASE