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(-) Description

Title :  CRYSTAL STRUCTURE OF UNLIGANDED, FULL LENGTH HUGDH AT PH 7.0
 
Authors :  A. M. Sidlo, Z. A. Wood
Date :  09 Oct 14  (Deposition) - 31 Dec 14  (Release) - 21 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Oxidoreductase, Rossman Fold, Nucleotide Sugar Dehydrogenase, Nad Binding, Udp-Glucose Binding, Oxidation, Cytosol (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Kadirvelraj, G. S. Custer, N. D. Keul, N. C. Sennett, A. M. Sidlo, R. M. Walsh, Z. A. Wood
Hysteresis In Human Udp-Glucose Dehydrogenase Is Due To A Restrained Hexameric Structure That Favors Feedback Inhibition.
Biochemistry V. 53 8043 2014
PubMed-ID: 25478983  |  Reference-DOI: 10.1021/BI500594X

(-) Compounds

Molecule 1 - UDP-GLUCOSE 6-DEHYDROGENASE
    Chains: A, B, C
    EC Number: 1.1.1.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21-T1R
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: UGDH
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: UDP-GLC DEHYDROGENASE, UDP-GLCDH, UDPGDH

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:75 , ASP A:76 , ARG A:115BINDING SITE FOR RESIDUE CL A 601
2AC2SOFTWAREILE B:75 , ASP B:76 , ARG B:115BINDING SITE FOR RESIDUE CL B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4RJT)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Lys A:434 -Pro A:435
2Lys B:434 -Pro B:435
3Lys C:434 -Pro C:435

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4RJT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4RJT)

(-) Exons   (0, 0)

(no "Exon" information available for 4RJT)

(-) 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:459
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee....hhhhhhhhhhhhh...eeeee..hhhhhhhhh.........hhhhhhhhhh...eeee.hhhhhhhhh.eeee..................hhhhhhhhhhhhhh..eeeeeee......hhhhhhhhhhhhh....eeeeeee........hhhhhhhh...eeeee..hhhhhhhhhhhhhhhh...hhh.eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh..................hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeee.............hhhhhhhhhhhh...eeeee....hhhhhhhhh...hhhhheee..hhhhhh....eeee...hhhhhhhhhhhhhhh.....eeee.......hhhhhhhhh.eeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rjt A   2 FEIKKICCIGAGYVGGPTCSVIAHMCPEIRVTVVDVNESRINAWNSPTLPIYEPGLKEVVESCRGKNLFFSTNIDDAIKEADLVFISVNTPTKTYGMGKGRAADLKYIEACARRIVQNSNGYKIVTEKSTVPVRAAESIRRIFDANTKPNLNLQVLSNPEFLAEGTAIKDLKNPDRVLIGGDETPEGQRAVQALCAVYEHWVPREKILTTNTWSSELSKLAANAFLAQRISSINSISALCEATGADVEEVATAIGMDQRIGNKFLKASVGFGGSCFQKDVLNLVYLCEALNLPEVARYWQQVIDMNDYQRRRFASRIIDSLFNTVTDKKIAILGFAFKKDTGDTRESSSIYISKYLMDEGAHLHIYDPKVPREQIVVDLSHDQVSRLVTISKDPYEACDGAHAVVICTEWDMFKELDYERIHKKMLKPAFIFDGRRVLDGLHNELQTIGFQIETIGKKV 466
                                    11        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       381||     397       407       417       427       437       447       457         
                                                                                                                                                                                                                                                                                                                                                                                                                      382|                                                                             
                                                                                                                                                                                                                                                                                                                                                                                                                       389                                                                             


Chain B from PDB  Type:PROTEIN  Length:460
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee....hhhhhhhhhhhhh...eeeee..hhhhhhhhh.........hhhhhhhhhh...eeee.hhhhhhhhh.eeee..................hhhhhhhhhhhhhh..eeeeeee......hhhhhhhhhhhhh....eeeeeee........hhhhhhhh...eeee...hhhhhhhhhhhhhhhh...hhh.eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh..................hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeee.............hhhhhhhhhhhh...eeeee....hhhhhhhhh...hhhhheee..hhhhhh....eeee...hhhhhhhhhhhhhhh.....eeee.......hhhhhhhhh.eeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rjt B   1 MFEIKKICCIGAGYVGGPTCSVIAHMCPEIRVTVVDVNESRINAWNSPTLPIYEPGLKEVVESCRGKNLFFSTNIDDAIKEADLVFISVNTPTKTYGMGKGRAADLKYIEACARRIVQNSNGYKIVTEKSTVPVRAAESIRRIFDANTKPNLNLQVLSNPEFLAEGTAIKDLKNPDRVLIGGDETPEGQRAVQALCAVYEHWVPREKILTTNTWSSELSKLAANAFLAQRISSINSISALCEATGADVEEVATAIGMDQRIGNKFLKASVGFGGSCFQKDVLNLVYLCEALNLPEVARYWQQVIDMNDYQRRRFASRIIDSLFNTVTDKKIAILGFAFKKDTGDTRESSSIYISKYLMDEGAHLHIYDPKVPREQIVVDLSHDQVSRLVTISKDPYEACDGAHAVVICTEWDMFKELDYERIHKKMLKPAFIFDGRRVLDGLHNELQTIGFQIETIGKKV 466
                                    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 ||    396       406       416       426       436       446       456       466
                                                                                                                                                                                                                                                                                                                                                                                                                       382|                                                                             
                                                                                                                                                                                                                                                                                                                                                                                                                        389                                                                             


Chain C from PDB  Type:PROTEIN  Length:461
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee....hhhhhhhhhhhhh...eeeee..hhhhhhhhh.........hhhhhhhhhh...eeee.hhhhhhhhh.eeee..................hhhhhhhhhhhhhh..eeeeeee......hhhhhhhhhhhhh....eeeeeee........hhhhhhhh...eeee...hhhhhhhhhhhhhhhh...hhh.eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh..................hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeee.............hhhhhhhhhhhh...eeeee....hhhhhhhhh...hhhhhheee..hhhhhh....eeee...hhhhhhhhhhhhhhh.....eeee.......hhhhhhhhh.eeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rjt C   1 MFEIKKICCIGAGYVGGPTCSVIAHMCPEIRVTVVDVNESRINAWNSPTLPIYEPGLKEVVESCRGKNLFFSTNIDDAIKEADLVFISVNTPTKTYGMGKGRAADLKYIEACARRIVQNSNGYKIVTEKSTVPVRAAESIRRIFDANTKPNLNLQVLSNPEFLAEGTAIKDLKNPDRVLIGGDETPEGQRAVQALCAVYEHWVPREKILTTNTWSSELSKLAANAFLAQRISSINSISALCEATGADVEEVATAIGMDQRIGNKFLKASVGFGGSCFQKDVLNLVYLCEALNLPEVARYWQQVIDMNDYQRRRFASRIIDSLFNTVTDKKIAILGFAFKKDTGDTRESSSIYISKYLMDEGAHLHIYDPKVPREQIVVDLSHDDQVSRLVTISKDPYEACDGAHAVVICTEWDMFKELDYERIHKKMLKPAFIFDGRRVLDGLHNELQTIGFQIETIGKKV 466
                                    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 ||    395       405       415       425       435       445       455       465 
                                                                                                                                                                                                                                                                                                                                                                                                                       382|                                                                              
                                                                                                                                                                                                                                                                                                                                                                                                                        388
   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  (0, 0)

(no "SCOP Domain" information available for 4RJT)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4RJT)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4RJT)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)

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    Lys A:434 - Pro A:435   [ RasMol ]  
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  4rjt
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  UGDH_HUMAN | O60701
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  1.1.1.22
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 Related Entries

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

UniProtKB/Swiss-Prot
        UGDH_HUMAN | O60701: 2q3e 2qg4 3itk 3khu 3prj 3ptz 3tdk 3tf5 4edf 4qej 5tjh

(-) Related Entries Specified in the PDB File

2q3e HUGDH:UGA:NAD
2qg4 HUGDH:UGA:NAD
3prj HUGDH:UDX:NAD
3ptz HUGDH:UDX:NAD
3tf5 HUGDH D132 MUTANT
4qej HUDGH APO