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(-) Description

Title :  THE FIRST STRUCTURE OF UDP-GLUCOSE DEHYDROGENASE (UDPGDH) REVEALS THE CATALYTIC RESIDUES NECESSARY FOR THE TWO-FOLD OXIDATION
 
Authors :  R. E. Campbell, S. C. Mosimann, I. Van De Rijn, M. E. Tanner, N. C. J. Str
Date :  09 Dec 99  (Deposition) - 31 May 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.31
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Rossmann Fold, Ternary Complex, Crystallographic Dimer, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. E. Campbell, S. C. Mosimann, I. Van De Rijn, M. E. Tanner, N. C. Strynadka
The First Structure Of Udp-Glucose Dehydrogenase Reveals Th Catalytic Residues Necessary For The Two-Fold Oxidation.
Biochemistry V. 39 7012 2000
PubMed-ID: 10841783  |  Reference-DOI: 10.1021/BI000181H

(-) Compounds

Molecule 1 - UDP-GLUCOSE DEHYDROGENASE
    Chains: A
    EC Number: 1.1.1.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGAC147
    Expression System Taxid: 562
    Organism Scientific: STREPTOCOCCUS PYOGENES
    Organism Taxid: 1314

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3SO43Ligand/IonSULFATE ION
4UDX1Ligand/IonURIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE
Biological Unit 1 (4, 16)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3SO46Ligand/IonSULFATE ION
4UDX2Ligand/IonURIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:144 , LYS A:147 , GLU A:306 , HOH A:638 , HOH A:655BINDING SITE FOR RESIDUE SO4 A 405
2AC2SOFTWARELYS A:68 , VAL A:364 , ASN A:365 , ASP A:366 , HOH A:581 , HOH A:640BINDING SITE FOR RESIDUE SO4 A 406
3AC3SOFTWAREGLU A:328 , LYS A:332 , GOL A:409 , HOH A:577 , HOH A:599BINDING SITE FOR RESIDUE SO4 A 407
4AC4SOFTWAREGLY A:9 , TYR A:10 , VAL A:11 , ASP A:29 , ILE A:30 , LEU A:31 , LYS A:34 , ALA A:80 , THR A:81 , PRO A:82 , THR A:83 , THR A:99 , SER A:117 , THR A:118 , GLU A:141 , LEU A:143 , GLU A:145 , TYR A:259 , CYS A:260 , LYS A:263 , ARG A:327 , UDX A:404 , GOL A:409 , HOH A:411 , HOH A:415 , HOH A:432 , HOH A:496 , HOH A:582BINDING SITE FOR RESIDUE NAD A 403
5AC5SOFTWAREGLU A:141 , PHE A:142 , LEU A:143 , ARG A:144 , GLU A:145 , LYS A:204 , VAL A:215 , ARG A:244 , TYR A:249 , ASN A:250 , ASN A:251 , SER A:253 , TYR A:256 , GLY A:257 , CYS A:260 , LEU A:261 , MET A:319 , LYS A:320 , ARG A:381 , ASP A:402 , NAD A:403 , HOH A:412 , HOH A:413 , HOH A:414 , HOH A:453 , HOH A:454BINDING SITE FOR RESIDUE UDX A 404
6AC6SOFTWAREPRO A:276 , GLN A:277 , GLU A:281 , HOH A:433 , HOH A:488 , HOH A:560BINDING SITE FOR RESIDUE GOL A 408
7AC7SOFTWAREPRO A:82 , ASN A:84 , TYR A:259 , ARG A:327 , NAD A:403 , SO4 A:407 , HOH A:582 , HOH A:625BINDING SITE FOR RESIDUE GOL A 409
8AC8SOFTWAREPHE A:142 , ARG A:144 , PRO A:155 , SER A:156 , ARG A:244 , HOH A:435 , HOH A:479 , HOH A:627 , HOH A:638BINDING SITE FOR RESIDUE GOL A 410

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1DLI)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1DLI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1DLI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1DLI)

(-) Exons   (0, 0)

(no "Exon" information available for 1DLI)

(-) 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:402
 aligned with UDG_STRPY | P0C0F4 from UniProtKB/Swiss-Prot  Length:402

    Alignment length:402
                                    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       280       290       300       310       320       330       340       350       360       370       380       390       400  
            UDG_STRPY     1 MKIAVAGSGYVGLSLGVLLSLQNEVTIVDILPSKVDKINNGLSPIQDEYIEYYLKSKQLSIKATLDSKAAYKEAELVIIATPTNYNSRINYFDTQHVETVIKEVLSVNSHATLIIKSTIPIGFITEMRQKFQTDRIIFSPEFLRESKALYDNLYPSRIIVSCEENDSPKVKADAEKFALLLKSAAKKNNVPVLIMGASEAEAVKLFANTYLALRVAYFNELDTYAESRKLNSHMIIQGISYDDRIGMHYNNPSFGYGGYCLPKDTKQLLANYNNIPQTLIEAIVSSNNVRKSYIAKQIINVLKEQESPVKVVGVYRLIMKSNSDNFRESAIKDVIDILKSKDIKIIIYEPMLNKLESEDQSVLVNDLENFKKQANIIVTNRYDNELQDVKNKVYSRDIFGRD 402
               SCOP domains d1dlia2 A:1-196 UDP-glucose dehydrogenase (UDPGDH)                                                                                                                                                  d1dlia1 A:197-294 UDP-glucose dehydrogenase (UDPGDH), middle domain                               d1dlia3 A:295-402 UDP-glucose dehydrogenase (UDPGDH), C-terminal (UDP-binding) domain                        SCOP domains
               CATH domains 1dliA01 A:1-204 NAD(P)-binding Rossmann-like Domain                                                                                                                                                         1dliA03 A:205-294 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2               1dliA02 A:295-402  [code=3.40.50.1870, no name defined]                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhh...eeeee..hhhhhhhhhh......hhhhhhhhhhh...eeee.hhhhhhhhh.eeee.....ee....ee.hhhhhhhhhhhhhhh...eeee......hhhhhhhhhhh...eee..........hhhhhh...eeee.....hhhhhhhhhhhhhhhhhhh......eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.................hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee.............hhhhhhhhhhhh...eeeee.............ee..hhhhhhhhh.eee....hhhhhhhhh.ee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1dli A   1 MKIAVAGSGYVGLSLGVLLSLQNEVTIVDILPSKVDKINNGLSPIQDEYIEYYLKSKQLSIKATLDSKAAYKEAELVIIATPTNYNSRINYFDTQHVETVIKEVLSVNSHATLIIKSTIPIGFITEMRQKFQTDRIIFSPEFLRESKALYDNLYPSRIIVSCEENDSPKVKADAEKFALLLKSAAKKNNVPVLIMGASEAEAVKLFANTYLALRVAYFNELDTYAESRKLNSHMIIQGISYDDRIGMHYNNPSFGYGGYCLPKDTKQLLANYNNIPQTLIEAIVSSNNVRKSYIAKQIINVLKEQESPVKVVGVYRLIMKSNSDNFRESAIKDVIDILKSKDIKIIIYEPMLNKLESEDQSVLVNDLENFKKQANIIVTNRYDNELQDVKNKVYSRDIFGRD 402
                                    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       280       290       300       310       320       330       340       350       360       370       380       390       400
   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  (3, 3)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1DLI)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (UDG_STRPY | P0C0F4)
molecular function
    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:0003979    UDP-glucose 6-dehydrogenase activity    Catalysis of the reaction: H(2)O + 2 NAD(+) + UDP-alpha-D-glucose = 3 H(+) + 2 NADH + UDP-alpha-D-glucuronate.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016616    oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
biological process
    GO:0006065    UDP-glucuronate biosynthetic process    The chemical reactions and pathways resulting in the formation of UDP-glucuronate, a substance composed of glucuronic acid in glycosidic linkage with uridine diphosphate.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0000271    polysaccharide biosynthetic process    The chemical reactions and pathways resulting in the formation of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.

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 Related Entries

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

UniProtKB/Swiss-Prot
        UDG_STRPY | P0C0F4: 1dlj 1lty

(-) Related Entries Specified in the PDB File

1dlj CYS260SER UDPGDH FROM S. PYOGENES WITH BOUND UDP-GLUCURONIC ACID AND NAD(H) RESULTING FROM TURNOVER OF THE SLOWLY HYDROLYZING ESTER INTERMEDIATE