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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN UDP-XYLOSE SYNTHASE R236H SUBSTITUTION
 
Authors :  R. M. Walsh Jr. , S. J. Polizzi, Z. A. Wood
Date :  08 Aug 13  (Deposition) - 28 Aug 13  (Release) - 03 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.86
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Short-Chain Dehydrogenase/Reductase, Decarboxylase, Lyase, Membrane, Rossmann Fold (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. M. Walsh, S. J. Polizzi, R. Kadirvelraj, W. W. Howard, Z. A. Wood
Man O' War Mutation In Udp-Alpha-D-Xylose Synthase Favors The Abortive Catalytic Cycle And Uncovers A Latent Potentia For Hexamer Formation.
Biochemistry V. 54 807 2015
PubMed-ID: 25521717  |  Reference-DOI: 10.1021/BI501357C

(-) Compounds

Molecule 1 - UDP-GLUCURONIC ACID DECARBOXYLASE 1
    Chains: A, B, C, D, E, F
    EC Number: 4.1.1.35
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET 15B
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 85-420
    Gene: UNQ2538/PRO6079, UXS, UXS1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: UDP-GLUCURONATE DECARBOXYLASE 1, UGD, UXS-1

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 13)

Asymmetric/Biological Unit (4, 13)
No.NameCountTypeFull Name
1NAD6Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2POP2Ligand/IonPYROPHOSPHATE 2-
3SO43Ligand/IonSULFATE ION
4UDP2Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY 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 , THR A:178 , ALA A:200 , SER A:201 , THR A:202 , LYS A:235 , ILE A:258 , PHE A:259 , THR A:261 , HIS A:267BINDING SITE FOR RESIDUE NAD A 501
02AC2SOFTWARELYS A:191 , TYR A:245 , LYS B:177BINDING SITE FOR RESIDUE POP A 502
03AC3SOFTWAREHIS A:267 , MET A:268 , ASN A:269BINDING SITE FOR RESIDUE SO4 A 503
04AC4SOFTWAREGLY B:95 , ALA B:97 , 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 , SER B:161 , PRO B:162 , THR B:178 , THR B:202 , LYS B:235 , ILE B:258 , THR B:261 , HIS B:267 , ARG B:272BINDING SITE FOR RESIDUE NAD B 501
05AC5SOFTWARELYS A:177 , PRO B:148 , LEU B:149 , TYR B:150 , LEU B:184 , ASN B:185 , GLY B:188 , LEU B:189 , LYS B:191 , ARG B:192 , TYR B:245BINDING SITE FOR RESIDUE UDP B 502
06AC6SOFTWAREHIS B:267 , MET B:268 , ASN B:269BINDING SITE FOR RESIDUE SO4 B 503
07AC7SOFTWAREGLY C:95 , ALA C:97 , GLY C:98 , PHE C:99 , VAL C:100 , ASP C:119 , ASN C:120 , PHE C:121 , PHE C:122 , THR C:123 , GLY C:124 , HIS C:143 , ASP C:144 , VAL C:145 , LEU C:159 , ALA C:160 , SER C:161 , PRO C:162 , ALA C:163 , THR C:178 , ALA C:200 , THR C:202 , LYS C:235 , ILE C:258 , THR C:261 , HIS C:267 , ARG C:272BINDING SITE FOR RESIDUE NAD C 501
08AC8SOFTWAREGLY C:188 , LYS C:191 , TYR C:245 , LYS D:177BINDING SITE FOR RESIDUE POP C 502
09AC9SOFTWAREHIS C:267 , MET C:268 , ASN C:269BINDING SITE FOR RESIDUE SO4 C 503
10BC1SOFTWAREGLY D:95 , ALA D:97 , GLY D:98 , PHE D:99 , VAL D:100 , GLY D:101 , ASP D:119 , ASN D:120 , PHE D:121 , PHE D:122 , THR D:123 , GLY D:124 , HIS D:143 , ASP D:144 , VAL D:145 , LEU D:159 , ALA D:160 , SER D:161 , THR D:178 , ALA D:200 , THR D:202 , LYS D:235 , ILE D:258 , PHE D:259 , THR D:261 , HIS D:267BINDING SITE FOR RESIDUE NAD D 501
11BC2SOFTWARELYS C:177 , PRO D:148 , LEU D:184 , ASN D:185 , GLY D:188 , LYS D:191 , TYR D:245BINDING SITE FOR RESIDUE UDP D 502
12BC3SOFTWAREGLY E:95 , ALA E:97 , GLY E:98 , PHE E:99 , VAL E:100 , ASP E:119 , ASN E:120 , PHE E:121 , PHE E:122 , THR E:123 , GLY E:124 , HIS E:143 , ASP E:144 , VAL E:145 , LEU E:159 , SER E:161 , PRO E:162 , THR E:178 , THR E:202 , PHE E:259 , THR E:261BINDING SITE FOR RESIDUE NAD E 800
13BC4SOFTWAREALA F:97 , GLY F:98 , PHE F:99 , VAL F:100 , ASP F:119 , ASN F:120 , PHE F:121 , PHE F:122 , THR F:123 , GLY F:124 , HIS F:143 , ASP F:144 , VAL F:145 , LYS F:174 , THR F:178 , THR F:261 , HIS F:267 , ARG F:272BINDING SITE FOR RESIDUE NAD F 800

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4M55)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4M55)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4M55)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4M55)

(-) Exons   (0, 0)

(no "Exon" information available for 4M55)

(-) 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:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains d4m55a_ A: automated matches                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhh..eeeeee.....hhhhhhhhh....eeeee............eeee.....hhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.hhh.hhhhhhhhhhhhhhhh..eeeeee..ee.........hhhhhhhhhhhh...ee..eee.eehhhhhhhhhhhhh......eee....eeehhhhhhhhhhhhh....ee.....hhhhhhhh......hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m55 A  88 RKRILITGGAGFVGSHLTDKLMMDGHEVTVVDNFFTGRKRNVEHWIGHENFELINHDVVEPLYIEVDQIYHLASPYNPIKTLKTNTIGTLNMLGLAKRVGARLLLASTSEVYGKHVAETMCYAYMKQEGVEVRVARIFNTFGPRMHMNDGRVVSNFILQALQGEPLTVQTRAFQYVSDLVNGLVALMNSNVSSPVNLGNPEEHTILEFAQLIKNLVGSGSEIQFRKPDIKKAKLMLGWEPVVPLEEGLNKAIHYFRKELEYQA 399
                                    97       107       117       127       137       147       157    || 174       184       194       204 ||    241       251       261       271       281       296       306       316       326       336       346   ||  366       376       386       396   
                                                                                                    162|                                 206|                                                    289|                                                    350|                                      
                                                                                                     170                                  234                                                     295                                                     361                                      


Chain B from PDB  Type:PROTEIN  Length:272
                                                                                                                                                                                                                                                                                                                
               SCOP domains d4m55b_ B: automated matches                                                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhh..eeeeee.....hhhhhhhhh....eeeee............eeee........hhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.hhh.hhhhhhhhhhhhhhhhh..eeeeee..ee.........hhhhhhhhhhhh...ee.......eee.eehhhhhhhhhhhhhh.....eee....eeehhhhhhhhhhhhh....ee.....hhhhhhhh......hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m55 B  88 RKRILITGGAGFVGSHLTDKLMMDGHEVTVVDNFFTGRKRNVEHWIGHENFELINHDVVEPLYIEVDQIYHLASPASPYNPIKTLKTNTIGTLNMLGLAKRVGARLLLASTSEVYEGKHVAETMCYAYMKQEGVEVRVARIFNTFGPRMHMNDGRVVSNFILQALQGEPLTVYGSGSQTRAFQYVSDLVNGLVALMNSNVSSPVNLGNPEEHTILEFAQLIKNLVGSGSEIQFRKPDIKKAKLMLGWEPVVPLEEGLNKAIHYFRKELEYQA 399
                                    97       107       117       127       137       147       157       171       181       191       201    || 237       247       257       267       277       287       297       307       317       327       337       347  ||   367       377       387       397  
                                                                                                       165|                                 206|                                                                                                                  350|                                      
                                                                                                        170                                  233                                                                                                                   361                                      


Chain C from PDB  Type:PROTEIN  Length:271
                                                                                                                                                                                                                                                                                                               
               SCOP domains d4m55c_ C: automated matches                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhh..eeeeee.....hhhhhhhhh....eeeee............eeee.......hhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.hhh.hhhhhhhhhhhhhhhhh..eeeeee..ee.........hhhhhhhhhhhh...eee......eee.eehhhhhhhhhhhhh......eee....eeehhhhhhhhhhhhh....eee....hhhhhhhh......hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m55 C  88 RKRILITGGAGFVGSHLTDKLMMDGHEVTVVDNFFTGRKRNVEHWIGHENFELINHDVVEPLYIEVDQIYHLASPASYNPIKTLKTNTIGTLNMLGLAKRVGARLLLASTSEVYEGKHVAETMCYAYMKQEGVEVRVARIFNTFGPRMHMNDGRVVSNFILQALQGEPLTVYGSGSQTRAFQYVSDLVNGLVALMNSNVSSPVNLGNPEEHTILEFAQLIKNLVGSGSEIQFLKPDIKKAKLMLGWEPVVPLEEGLNKAIHYFRKELEYQA 399
                                    97       107       117       127       137       147       157      |172       182       192       202   ||  238       248       258       268       278       288       298       308       318       328       338       348  ||   368       378       388       398 
                                                                                                      164|                                 206|                                                                                                                   351|                                     
                                                                                                       170                                  233                                                                                                                    362                                     


Chain D from PDB  Type:PROTEIN  Length:261
                                                                                                                                                                                                                                                                                                     
               SCOP domains d4m55d_ D: automated matches                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhh..eeeee......hhhhh........eeee.............eeee....hhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.hhh.hhhhhhhhhhhhhhhh..eeeeee..ee....hhhhhhhhhhhhhhhhhh..eee...eee.eehhhhhhhhhhhhh......eee....eeehhhhhhhhhhhhh....eee.....hhhhhhhhh.....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m55 D  88 RKRILITGGAGFVGSHLTDKLMMDGHEVTVVDNFFTGRKRNVEHWIGHENFELINHDVVEPLYIEVDQIYHLASYNPIKTLKTNTIGTLNMLGLAKRVGARLLLASTSEVYGKHVAETMCYAYMKQEGVEVRVARIFNTFGPRMHMNDGRVVSNFILQALQGEPLTVYSQTRAFQYVSDLVNGLVALMNSNVSSPVNLGNPEEHTILEFAQLIKNLVGSGSEIQFLRKPDIKKAKLMLGWEPVVPLEEGLNKAIHYFRKEL 395
                                    97       107       117       127       137       147       157   ||  175       185       195       205||     242       252       262       272       282       295       305       315       325       335       345     ||364       374       384       394 
                                                                                                   161|                                 206|                                                     290|                                                      351|                                  
                                                                                                    170                                  234                                                      294                                                       361                                  


Chain E from PDB  Type:PROTEIN  Length:164
                                                                                                                                                                                                    
               SCOP domains d4m55e_ E: automated matches                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...hhhhhhhhhhhhhh...eeeee.....hhhhhhhhh.....eeee............eeee.....hhhhhhhhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhh.....eeee.hhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m55 E  90 RILITGGAGFVGSHLTDKLMMDGHEVTVVDNFFTGRKRNVEHWIGHENFELINHDVVEPLYIEVDQIYHLASPNPIKTLKTNTIGTLNMLGLAKRVGARLLLASTSVAETMCYAYMKQEGVEVRVARIFNTFQYVSDLVNGLVALMNSNVSSPVNLDIKKAKLM 371
                                    99       109       119       129       139       149       159  ||   177       187       197     ||240       250       260 ||    307       317     ||367    
                                                                                                  162|                             203|                      262|                    323|       
                                                                                                   171                              237                       300                     364       


Chain F from PDB  Type:PROTEIN  Length:181
                                                                                                                                                                                                                     
               SCOP domains d4m55f_ F: automated matches                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh........hhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.............hhhhhhhhhhh..hhhhhhhhhhhh.......................................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m55 F  95 GGAGFVGSHLTDKLMVDNFFTGRKRNVEHWIINHDVVEPLYIEVDQYNPIKTLKTNTIGTLNMLGLAKRVGVAETMCYAYMKQEGVETFGPRMHMNDGRVVSNFILQALQVSDLVNGLVALMNSNVSSPVNLTILEFAQLIKNLVDIKKAKLMLGWEPVVPLEEGLNKAIHYFRKELEYQA 399
                                   104    || 122       132||     149     ||173       183       193||     245      |263       273       283|      311       321 ||    337    || 368       378       388       398 
                                        109|            133|           155|                     194|            252|                   283|                  323|         342|                                   
                                         118             141            170                      237             261                    302                   330          364
   Legend:   → Mismatch (orange background)
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    → 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, 6)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4M55)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4M55)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

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  4m55
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

4lk3 CRYSTAL STRUCTURE OF HUMAN UDP-XYLOSE SYNTHASE R236A SUBSTITUTION