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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN UDP-XYLOSE SYNTHASE.
 
Authors :  Z. A. Wood, S. J. Polizzi
Date :  14 Aug 12  (Deposition) - 05 Sep 12  (Release) - 14 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Short-Chain Dehydrogenase/Reductase, Decarboxylase, Lyase, Membrane (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. J. Polizzi, R. M. Walsh, W. B. Peeples, J. M. Lim, L. Wells, Z. A. Wood
Human Udp-Alpha-D-Xylose Synthase And Escherichia Coli Arna Conserve A Conformational Shunt That Controls Whether Xylos Or 4-Keto-Xylose Is Produced.
Biochemistry V. 51 8844 2012
PubMed-ID: 23072385  |  Reference-DOI: 10.1021/BI301135B

(-) Compounds

Molecule 1 - UDP-GLUCURONIC ACID DECARBOXYLASE 1
    Chains: A, B
    EC Number: 4.1.1.35
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: SOLUBLE UXS DOMAIN;
RESIDUES 85-420
    Gene: UNQ2538/PRO6079, UXS, UXS1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: UDP-GLUCURONATE DECARBOXYLASE 1, UGD, UXS-1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1GAI2Ligand/IonGUANIDINE
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3SO42Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:95 , ALA A:97 , GLY A:98 , PHE A:99 , VAL A:100 , ASP A:119 , ASN A:120 , PHE A:121 , PHE A:122 , THR A:123 , GLY A:124 , HIS A:143 , ASP A:144 , VAL A:145 , LEU A:159 , ALA A:160 , SER A:161 , ALA A:163 , THR A:178 , SER A:201 , TYR A:231 , LYS A:235 , ILE A:258 , THR A:261 , HIS A:267 , HOH A:940BINDING SITE FOR RESIDUE NAD A 800
2AC2SOFTWARETHR A:288 , TYR A:290 , ILE A:331 , ASP A:356BINDING SITE FOR RESIDUE GAI A 801
3AC3SOFTWARESER A:203 , PHE A:259 , ASN A:260 , GLN A:359 , ARG A:361BINDING SITE FOR RESIDUE SO4 A 802
4AC4SOFTWAREGLY B:95 , GLY B:98 , PHE B:99 , VAL B:100 , ASP B:119 , ASN B:120 , PHE B:121 , PHE B:122 , THR B:123 , GLY B:124 , HIS B:143 , ASP B:144 , VAL B:145 , LEU B:159 , ALA B:160 , SER B:161 , PRO B:162 , ALA B:163 , LYS B:174 , THR B:178 , ALA B:200 , THR B:202 , TYR B:231 , LYS B:235 , ILE B:258 , PHE B:259 , ASN B:260 , THR B:261 , HIS B:267 , ARG B:272 , HOH B:608BINDING SITE FOR RESIDUE NAD B 501
5AC5SOFTWARETHR B:288 , TYR B:290 , ASP B:356BINDING SITE FOR RESIDUE GAI B 502
6AC6SOFTWARETYR B:150 , ARG B:192 , TYR B:290 , SER B:292 , GLY B:293 , SER B:294 , GLN B:295BINDING SITE FOR RESIDUE SO4 B 503

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1His A:212 -Pro A:213
2Ser B:164 -Pro B:165
3His B:212 -Pro B:213

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GLL)

(-) 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:307
                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains d4glla_ A: automated matches                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhh..eeeeee.....hhhhhhhhh....eeeee............eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.hhhh....................hhhhhhhhhhhhhhhhhhhhhhh.eeeeeee..ee.........hhhhhhhhhhhh...eeee.....ee..eehhhhhhhhhhhhh......eee.....eehhhhhhhhhhhhh....eeee.............hhhhhhhhh.....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gll A  88 RKRILITGGAGFVGSHLTDKLMMDGHEVTVVDNFFTGRKRNVEHWIGHENFELINHDVVEPLYIEVDQIYHLASPASPPNYMYNPIKTLKTNTIGTLNMLGLAKRVGARLLLASTSEVYGDPEVHPQSEDYWGHVNPIGPRACYDEGKRVAETMCYAYMKQEGVEVRVARIFNTFGPRMHMNDGRVVSNFILQALQGEPLTVYGSGSQTRAFQYVSDLVNGLVALMNSNVSSPVNLGNPEEHTILEFAQLIKNLVGSGSEIQFLSEAQDDPQKRKPDIKKAKLMLGWEPVVPLEEGLNKAIHYFRKE 394
                                    97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       


Chain B from PDB  Type:PROTEIN  Length:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4gllb_ B: automated matches                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhh..eeeeee.....hhhhhhhhh....eeeee............eeee........hhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.hhhh....................hhhhhhhhhhhhhhhhhhhhhhh..eeeeee..ee.........hhhhhhhhhhhh...eeee.....ee..eehhhhhhhhhhhhh......eee.....eehhhhhhhhhhhhh....eeee.............hhhhhhhhh.....hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gll B  88 RKRILITGGAGFVGSHLTDKLMMDGHEVTVVDNFFTGRKRNVEHWIGHENFELINHDVVEPLYIEVDQIYHLASPASPNPIKTLKTNTIGTLNMLGLAKRVGARLLLASTSEVYGDPEVHPQSEDYWGHVNPIGPRACYDEGKRVAETMCYAYMKQEGVEVRVARIFNTFGPRMHMNDGRVVSNFILQALQGEPLTVYGSGSQTRAFQYVSDLVNGLVALMNSNVSSPVNLGNPEEHTILEFAQLIKNLVGSGSEIQFLSEAQDDPQKRKPDIKKAKLMLGWEPVVPLEEGLNKAIHYFRKELEYQ 398
                                    97       107       117       127       137       147       157       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392      
                                                                                                       165|                                                                                                                                                                                                                                   
                                                                                                        171
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    His A:212 - Pro A:213   [ RasMol ]  
    His B:212 - Pro B:213   [ RasMol ]  
    Ser B:164 - Pro B:165   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        UXS1_HUMAN | Q8NBZ7: 2b69 4lk3 4m55

(-) Related Entries Specified in the PDB File

2b69 THE SAME PROTEIN COMPLEXED WITH URIDINE DIPHOSPHATE (UDP). THE 2B69 PROTEIN CONSTRUCT HAS A ~20 AMINO ACID TRUNCATION AT THE C-TERMINUS THAT REMOVES A PREDICTED DISORDERED HELIX.