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(-) Description

Title :  CRYSTAL STRUCTURE OF UDP-GLUCOSE PYROPHOSPHORYLASE FROM CORYNEBACTERIA GLUTAMICUM IN COMPLEX WITH MAGNESIUM AND UDP-GLUCOSE
 
Authors :  H. M. Holden, J. B. Thoden
Date :  27 Mar 07  (Deposition) - 10 Apr 07  (Release) - 08 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  B,C  (1x)
Biol. Unit 3:  A,D  (1x)
Keywords :  Phosphorylase, Nucleotidyltransferase, Metabolism, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. B. Thoden, H. M. Holden
Active Site Geometry Of Glucose-1-Phosphate Uridylyltransferase.
Protein Sci. V. 16 1379 2007
PubMed-ID: 17567737  |  Reference-DOI: 10.1110/PS.072864707

(-) Compounds

Molecule 1 - UTP-GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
    ChainsA, B, C, D
    EC Number2.7.7.9
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET31
    Expression System StrainROSETTA(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneGALU1
    Organism ScientificCORYNEBACTERIUM GLUTAMICUM ATCC 13032
    Organism Taxid196627
    StrainATCC-13032

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)ABCD
Biological Unit 2 (1x) BC 
Biological Unit 3 (1x)A  D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1MG8Ligand/IonMAGNESIUM ION
2UPG4Ligand/IonURIDINE-5'-DIPHOSPHATE-GLUCOSE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2UPG4Ligand/IonURIDINE-5'-DIPHOSPHATE-GLUCOSE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2UPG2Ligand/IonURIDINE-5'-DIPHOSPHATE-GLUCOSE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2UPG2Ligand/IonURIDINE-5'-DIPHOSPHATE-GLUCOSE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREUPG A:326 , HOH A:332 , HOH A:333 , HOH A:334 , HOH A:335 , HOH A:405BINDING SITE FOR RESIDUE MG A 324
02AC2SOFTWAREASP A:142 , UPG A:326 , HOH A:336 , HOH A:337 , HOH A:363BINDING SITE FOR RESIDUE MG A 325
03AC3SOFTWAREUPG B:326 , HOH B:331 , HOH B:332 , HOH B:333 , HOH B:379 , HOH B:380BINDING SITE FOR RESIDUE MG B 324
04AC4SOFTWAREASP B:142 , UPG B:326 , HOH B:335 , HOH B:336 , HOH B:382BINDING SITE FOR RESIDUE MG B 325
05AC5SOFTWAREUPG C:326 , HOH C:332 , HOH C:333 , HOH C:404 , HOH C:405 , HOH C:407BINDING SITE FOR RESIDUE MG C 324
06AC6SOFTWAREASP C:142 , UPG C:326 , HOH C:336 , HOH C:408 , HOH C:409BINDING SITE FOR RESIDUE MG C 325
07AC7SOFTWAREUPG D:326 , HOH D:332 , HOH D:333 , HOH D:339 , HOH D:350 , HOH D:351BINDING SITE FOR RESIDUE MG D 324
08AC8SOFTWARELYS D:35 , ASP D:142 , UPG D:326 , HOH D:335 , HOH D:336 , HOH D:349BINDING SITE FOR RESIDUE MG D 325
09AC9SOFTWAREPRO A:18 , ALA A:19 , ALA A:20 , GLY A:21 , LYS A:35 , GLU A:36 , GLN A:112 , PRO A:115 , LEU A:116 , GLY A:117 , LEU A:118 , ALA A:121 , LEU A:140 , PRO A:141 , ASP A:142 , ASP A:143 , TYR A:179 , GLY A:180 , GLU A:201 , LYS A:202 , ALA A:214 , THR A:242 , ARG A:264 , MG A:324 , MG A:325 , HOH A:330 , HOH A:332 , HOH A:334 , HOH A:335 , HOH A:336 , HOH A:337 , HOH A:363 , HOH A:366 , HOH A:475BINDING SITE FOR RESIDUE UPG A 326
10BC1SOFTWAREPRO B:18 , ALA B:19 , ALA B:20 , GLY B:21 , LYS B:35 , GLU B:36 , GLN B:112 , PRO B:115 , LEU B:116 , GLY B:117 , LEU B:118 , ALA B:121 , LEU B:140 , PRO B:141 , ASP B:142 , ASP B:143 , TYR B:179 , GLY B:180 , GLU B:201 , LYS B:202 , ALA B:214 , GLY B:216 , THR B:242 , MG B:324 , MG B:325 , HOH B:329 , HOH B:331 , HOH B:335 , HOH B:336 , HOH B:352 , HOH B:379 , HOH B:380 , HOH B:382 , HOH B:399 , HOH B:402BINDING SITE FOR RESIDUE UPG B 326
11BC2SOFTWAREPRO C:18 , ALA C:19 , ALA C:20 , GLY C:21 , LYS C:35 , GLU C:36 , GLN C:112 , PRO C:115 , LEU C:116 , GLY C:117 , LEU C:118 , ALA C:121 , LEU C:140 , PRO C:141 , ASP C:142 , ASP C:143 , TYR C:179 , GLY C:180 , GLU C:201 , LYS C:202 , ALA C:214 , THR C:242 , MG C:324 , MG C:325 , HOH C:332 , HOH C:333 , HOH C:336 , HOH C:402 , HOH C:404 , HOH C:406 , HOH C:407 , HOH C:408 , HOH C:409 , HOH C:412BINDING SITE FOR RESIDUE UPG C 326
12BC3SOFTWAREPRO D:18 , ALA D:19 , ALA D:20 , GLY D:21 , LYS D:35 , GLU D:36 , GLN D:112 , PRO D:115 , LEU D:116 , GLY D:117 , LEU D:118 , ALA D:121 , LEU D:140 , PRO D:141 , ASP D:142 , ASP D:143 , TYR D:179 , GLY D:180 , GLU D:201 , LYS D:202 , ALA D:214 , THR D:215 , GLY D:216 , THR D:242 , MG D:324 , MG D:325 , HOH D:330 , HOH D:333 , HOH D:335 , HOH D:336 , HOH D:339 , HOH D:349 , HOH D:350 , HOH D:351 , HOH D:392 , HOH D:412BINDING SITE FOR RESIDUE UPG D 326

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PA4)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Leu A:27 -Pro A:28
2Leu A:146 -Pro A:147
3Leu B:27 -Pro B:28
4Leu B:146 -Pro B:147
5Leu C:27 -Pro C:28
6Leu C:146 -Pro C:147
7Leu D:27 -Pro D:28
8Leu D:146 -Pro D:147

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PA4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PA4)

(-) Exons   (0, 0)

(no "Exon" information available for 2PA4)

(-) 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:294
                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee....hhhhhhhhhh.hhhh.ee..eehhhhhhhhhhhh...eeeeee....hhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhhhheeeeee.....hhhhhhhhhhhhh.....eeeee...eeee..hhhhhhhhhhhh...eeeeeee.hhhhhhh.eeeeeee......eeeeeeeee..........eeeeeeeeeehhhhhhhhhh..hhhhh.hhhhhhhhhhhh...eeeee...eeee..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2pa4 A  12 VKTVVVPAAGLGTRFLPATKTVPKELLPVVDTPGIELIAAEAAELGATRLAIITAPNKAGVLAHFERSSELEETLMERGKTDQVEIIRRAADLIKAVPVTQDKPLGLGHAVGLAESVLDDDEDVVAVMLPDDLVLPTGVMERMAQVRAEFGGSVLCAVEVSEADVSKYGIFEIEADTKDSDVKKVKGMVEKPAIEDAPSRLAATGRYLLDRKIFDALRRITPGAGGELQLTDAIDLLIDEGHPVHIVIHQGKRHDLGNPGGYIPACVDFGLSHPVYGAQLKDAIKQILAEHEAA 305
                                    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    

Chain B from PDB  Type:PROTEIN  Length:299
                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee....hhhhhhhhhh.hhhh.ee..eehhhhhhhhhhhh...eeeeee....hhhhhh...hhhhhhhhhh..hhhhhhhhhhhhhhheeeeee.....hhhhhhhhhhhhh.....eeeee...eee...hhhhhhhhhhhhhh.eeeeeee....hhhh.eeeeeee......eeeeeeeee..hhhhh...eeeeeeeeee.hhhhhhhhh..hhhhh.hhhhhhhhhhhh...eeeee....eee..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pa4 B  10 NAVKTVVVPAAGLGTRFLPATKTVPKELLPVVDTPGIELIAAEAAELGATRLAIITAPNKAGVLAHFERSSELEETLMERGKTDQVEIIRRAADLIKAVPVTQDKPLGLGHAVGLAESVLDDDEDVVAVMLPDDLVLPTGVMERMAQVRAEFGGSVLCAVEVSEADVSKYGIFEIEADTKDSDVKKVKGMVEKPAIEDAPSRLAATGRYLLDRKIFDALRRITPGAGGELQLTDAIDLLIDEGHPVHIVIHQGKRHDLGNPGGYIPACVDFGLSHPVYGAQLKDAIKQILAEHEAAERI 308
                                    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         

Chain C from PDB  Type:PROTEIN  Length:299
                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee....hhhhhhhhhh.hhhh.ee..eehhhhhhhhhhhh...eeeeee....hhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhhhheeeeee.....hhhhhhhhhhhhh.....eeeee...eee...hhhhhhhhhhhhhh.eeeeeee.hhhhhh..eeeeeeee.....eeeeeeeee..hhhhh...eeeeeeeeeehhhhhhhh....hhhhh.hhhhhhhhhhhh...eeeee....eee..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pa4 C  10 NAVKTVVVPAAGLGTRFLPATKTVPKELLPVVDTPGIELIAAEAAELGATRLAIITAPNKAGVLAHFERSSELEETLMERGKTDQVEIIRRAADLIKAVPVTQDKPLGLGHAVGLAESVLDDDEDVVAVMLPDDLVLPTGVMERMAQVRAEFGGSVLCAVEVSEADVSKYGIFEIEADTKDSDVKKVKGMVEKPAIEDAPSRLAATGRYLLDRKIFDALRRITPGAGGELQLTDAIDLLIDEGHPVHIVIHQGKRHDLGNPGGYIPACVDFGLSHPVYGAQLKDAIKQILAEHEAAERI 308
                                    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         

Chain D from PDB  Type:PROTEIN  Length:295
                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....hhhhhhhhhh.hhhh.ee..eehhhhhhhhhhhh...eeeeee...hhhhhhh...hhhhhhhhh...hhhhhhhhhhhheeeeee.....hhhhhhhhhhhhh.....eeeee...eeee..hhhhhhhhhhhhhh.eeeeeee.hhhhh...eeeeeee......eeeeeeeee..........eeeeeeeeee.hhhhhhhhh........hhhhhhhhhhhh...eeeee...eeee..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pa4 D  11 AVKTVVVPAAGLGTRFLPATKTVPKELLPVVDTPGIELIAAEAAELGATRLAIITAPNKAGVLAHFERSSELEETLMERDQVEIIRRAADLIKAVPVTQDKPLGLGHAVGLAESVLDDDEDVVAVMLPDDLVLPTGVMERMAQVRAEFGGSVLCAVEVSEADVSKYGIFEIEADTKDSDVKKVKGMVEKPAIEDAPSRLAATGRYLLDRKIFDALRRITPGAGGELQLTDAIDLLIDEGHPVHIVIHQGKRHDLGNPGGYIPACVDFGLSHPVYGAQLKDAIKQILAEHEAAERI 308
                                    20        30        40        50        60        70        80        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303     
                                                                                                         89|                                                                                                                                                                                                                       
                                                                                                          93                                                                                                                                                                                                                       

   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 2PA4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2PA4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2PA4)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2PA4)

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