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(-) Description

Title :  CRYSTAL STRUCTURE OF UDP-GLCNAC 2-EPIMERASE
 
Authors :  S. C. Chen, C. S. Yang, T. P. Ko, Y. Chen
Date :  27 Apr 15  (Deposition) - 01 Jun 16  (Release) - 09 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.69
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  C,D  (2x)
Keywords :  Inhibitor, Complex, Epimerase, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. C. Chen, C. H. Huang, S. J. Lai, C. S. Yang, T. H. Hsiao, C. H. Lin, P. K. Fu, T. P. Ko, Y. Chen
Mechanism And Inhibition Of Human Udp-Glcnac 2-Epimerase, The Key Enzyme In Sialic Acid Biosynthesis.
Sci Rep V. 6 23274 2016
PubMed-ID: 26980148  |  Reference-DOI: 10.1038/SREP23274

(-) Compounds

Molecule 1 - BIFUNCTIONAL UDP-N-ACETYLGLUCOSAMINE 2-EPIMERASE/N- ACETYLMANNOSAMINE KINASE
    Chains: A, B, C, D
    EC Number: 3.2.1.183
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Fragment: UNP RESIDUES 1-405
    Gene: GNE, GLCNE
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: UDP-GLCNAC-2-EPIMERASE/MANAC KINASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (2x): AB  
Biological Unit 2 (2x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 57)

Asymmetric Unit (4, 57)
No.NameCountTypeFull Name
1BM71Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-BETA-D-MANNOPYRANOSE
2MSE48Mod. Amino AcidSELENOMETHIONINE
3NCC4Ligand/IonCYTIDINE-5'-MONOPHOSPHATE-5-N-ACETYLNEURAMINIC ACID
4UDP4Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 1 (3, 56)
No.NameCountTypeFull Name
1BM7-1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-BETA-D-MANNOPYRANOSE
2MSE48Mod. Amino AcidSELENOMETHIONINE
3NCC4Ligand/IonCYTIDINE-5'-MONOPHOSPHATE-5-N-ACETYLNEURAMINIC ACID
4UDP4Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 2 (4, 58)
No.NameCountTypeFull Name
1BM72Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-BETA-D-MANNOPYRANOSE
2MSE48Mod. Amino AcidSELENOMETHIONINE
3NCC4Ligand/IonCYTIDINE-5'-MONOPHOSPHATE-5-N-ACETYLNEURAMINIC ACID
4UDP4Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:19 , ALA A:20 , SER A:23 , LYS A:24 , ARG A:113 , LEU A:218 , HIS A:220 , LEU A:250 , ASN A:253 , HIS A:281 , VAL A:282 , PHE A:284 , PHE A:287 , SER A:301 , SER A:302 , GLU A:307 , ARG A:321 , HOH A:630binding site for residue UDP A 501
2AC2SOFTWAREASP A:53 , LYS A:259 , ARG A:266 , GLU A:271 , ALA A:278 , VAL A:279 , LYS A:280 , HIS A:281 , HOH A:619 , HOH A:632 , HOH A:640 , ARG B:263 , ARG B:266 , NCC B:502binding site for residue NCC A 502
3AC3SOFTWAREARG B:19 , ALA B:20 , SER B:23 , LYS B:24 , ARG B:113 , LEU B:218 , HIS B:220 , LEU B:250 , ASN B:253 , HIS B:281 , VAL B:282 , PHE B:284 , PHE B:287 , SER B:301 , SER B:302 , GLU B:307 , ARG B:321binding site for residue UDP B 501
4AC4SOFTWAREARG A:263 , ARG A:266 , NCC A:502 , HOH A:606 , ASP B:53 , PHE B:251 , LYS B:259 , ARG B:266 , GLU B:271 , ALA B:278 , VAL B:279 , LYS B:280 , HIS B:281 , HOH B:625 , HOH B:636binding site for residue NCC B 502
5AC5SOFTWAREARG C:19 , SER C:23 , LYS C:24 , ARG C:113 , LEU C:218 , HIS C:220 , LEU C:250 , ASN C:253 , HIS C:281 , VAL C:282 , PHE C:284 , PHE C:287 , SER C:301 , SER C:302 , GLU C:307 , ARG C:321 , BM7 C:503binding site for residue UDP C 501
6AC6SOFTWAREASP C:53 , LYS C:259 , VAL C:262 , ARG C:263 , ARG C:266 , LYS C:267 , GLU C:271 , ALA C:278 , VAL C:279 , LYS C:280 , HIS C:281 , HOH C:637binding site for residue NCC C 502
7AC7SOFTWAREARG C:19 , TYR C:22 , SER C:23 , ALA C:26 , MSE C:60 , ASP C:64 , HIS C:281 , PRO C:283 , PHE C:284 , ASP C:285 , UDP C:501binding site for residue BM7 C 503
8AC8SOFTWAREARG D:19 , SER D:23 , LYS D:24 , ARG D:113 , LEU D:218 , HIS D:220 , LEU D:250 , ASN D:253 , HIS D:281 , VAL D:282 , PHE D:284 , PHE D:287 , SER D:301 , SER D:302 , GLU D:307 , ARG D:321 , HOH D:626binding site for residue UDP D 501
9AC9SOFTWAREASP D:53 , LYS D:259 , VAL D:262 , ARG D:263 , ARG D:266 , GLU D:271 , ALA D:278 , VAL D:279 , LYS D:280 , HIS D:281 , HOH D:611 , HOH D:627 , HOH D:628binding site for residue NCC D 502

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Glu A:381 -Pro A:382
2Glu B:381 -Pro B:382
3Glu C:381 -Pro C:382
4Glu D:381 -Pro D:382

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZHT)

(-) 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:384
                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeee.hhhhhhhhhhhhhhhhh....eeeeeeee.hhhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhh.eeee.hhhhhhhhhhh..hhh.eee...hhhhhhh.....hhhhhhhhhhh........eeee...hhhhhhhhhhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhh..eeee.hhhhhhhhhhhh..eeee............eeee....hhhhhhhhhhhhh.............hhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4zht A   7 NRKLRVCVATCNRADYSKLAPImFGIKTEPEFFELDVVVLGSHLIDDYGNTYRmIEQDDFDINTRLHTIVRGEDEAAmVESVGLALVKLPDVLNRLKPDImIVHGDRFDALALATSAALmNIRILHIEGGEVSGTIDDSIRHAITKLAHYHVCCTRSAEQHLISmCEDHDRILLAGCPSYDKLLSAKNKDYmSIIRmWLGDDVKSKDYIVALQHPVTTDIKHSIKmFELTLDALISFNKRTLVLFPNIDAGSKEmVRVmRKKGIEHHPNFRAVKHVPFDQFIQLVAHAGCmIGNSSCGVREVGAFGTPVINLGTRQIGRETGENVLHVRDADTQDKILQALHLQFGKQYPCSKIYGDGNAVPRILKFLKSIDLQEPLQKKFCFP 390
                                    16        26  |     36        46        56   |    66        76       |86        96       106|      116       126       136       146       156       166    |  176       186       196 |    |206       216       226     | 236       246       256    |  266       276       286       296|      306       316       326       336       346       356       366       376       386    
                                                 29-MSE                         60-MSE                  84-MSE                107-MSE            126-MSE                                      171-MSE                    198-MSE|                          232-MSE                      261-MSE                             297-MSE                                                                                         
                                                                                                                                                                                                                              203-MSE                                                       265-MSE                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:382
                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.hhhhhhhhhhhhhhhhh....eeeeeeee.hhhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhh.eeee.hhhhhhhhhhh..hhh.eee...hhhhhhh.....hhhhhhhhhhh........eeee...hhhhhhhhhhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhh..eeee.hhhhhhhhhhhh..eeee............eeee....hhhhhhhhhhhhh.............hhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zht B   8 RKLRVCVATCNRADYSKLAPImFGIKTEPEFFELDVVVLGSHLIDDYGNTYRmIEQDDFDINTRLHTIVRGEDEAAmVESVGLALVKLPDVLNRLKPDImIVHGDRFDALALATSAALmNIRILHIEGGEVSGTIDDSIRHAITKLAHYHVCCTRSAEQHLISmCEDHDRILLAGCPSYDKLLSAKNKDYmSIIRmWLGDDVKSKDYIVALQHPVTTDIKHSIKmFELTLDALISFNKRTLVLFPNIDAGSKEmVRVmRKKGIEHHPNFRAVKHVPFDQFIQLVAHAGCmIGNSSCGVREVGAFGTPVINLGTRQIGRETGENVLHVRDADTQDKILQALHLQFGKQYPCSKIYGDGNAVPRILKFLKSIDLQEPLQKKFCF 389
                                    17        27 |      37        47        57  |     67        77      | 87        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  
                                                29-MSE                         60-MSE                  84-MSE                107-MSE            126-MSE                                      171-MSE                    198-MSE|                          232-MSE                      261-MSE                             297-MSE                                                                                        
                                                                                                                                                                                                                             203-MSE                                                       265-MSE                                                                                                                        


Chain C from PDB  Type:PROTEIN  Length:383
                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.hhhhhhhhhhhhhhhhh....eeeeeeee.hhhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhh.eeee.hhhhhhhhhhh..hhh.eee...hhhhhhh.....hhhhhhhhhhh........eeee...hhhhhhhhhhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhh..eeee.hhhhhhhhhhhh..eeee............eeee....hhhhhhhhhhhhh.............hhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zht C   6 NNRKLRVCVATCNRADYSKLAPImFGIKTEPEFFELDVVVLGSHLIDDYGNTYRmIEQDDFDINTRLHTIVRGEDEAAmVESVGLALVKLPDVLNRLKPDImIVHGDRFDALALATSAALmNIRILHIEGGEVSGTIDDSIRHAITKLAHYHVCCTRSAEQHLISmCEDHDRILLAGCPSYDKLLSAKNKDYmSIIRmWLGDDVKSKDYIVALQHPVTTDIKHSIKmFELTLDALISFNKRTLVLFPNIDAGSKEmVRVmRKKGIEHHPNFRAVKHVPFDQFIQLVAHAGCmIGNSSCGVREVGAFGTPVINLGTRQIGRETGENVLHVRDADTQDKILQALHLQFGKQYPCSKIYGDGNAVPRILKFLKSIDLQEPLQKKFC 388
                                    15        25   |    35        45        55    |   65        75        85        95       105 |     115       125|      135       145       155       165     | 175       185       195  |    205       215       225      |235       245       255     | 265       275       285       295 |     305       315       325       335       345       355       365       375       385   
                                                  29-MSE                         60-MSE                  84-MSE                107-MSE            126-MSE                                      171-MSE                    198-MSE|                          232-MSE                      261-MSE                             297-MSE                                                                                       
                                                                                                                                                                                                                               203-MSE                                                       265-MSE                                                                                                                       


Chain D from PDB  Type:PROTEIN  Length:383
                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.hhhhhhhhhhhhhhhhh....eeeeeeee.hhhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhh.eeee.hhhhhhhhhhh..hhh.eee...hhhhhhh.....hhhhhhhhhhh........eeee...hhhhhhhhhhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhh..eeee.hhhhhhhhhhhh..eeee............eeee....hhhhhhhhhhhhh.............hhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zht D   8 RKLRVCVATCNRADYSKLAPImFGIKTEPEFFELDVVVLGSHLIDDYGNTYRmIEQDDFDINTRLHTIVRGEDEAAmVESVGLALVKLPDVLNRLKPDImIVHGDRFDALALATSAALmNIRILHIEGGEVSGTIDDSIRHAITKLAHYHVCCTRSAEQHLISmCEDHDRILLAGCPSYDKLLSAKNKDYmSIIRmWLGDDVKSKDYIVALQHPVTTDIKHSIKmFELTLDALISFNKRTLVLFPNIDAGSKEmVRVmRKKGIEHHPNFRAVKHVPFDQFIQLVAHAGCmIGNSSCGVREVGAFGTPVINLGTRQIGRETGENVLHVRDADTQDKILQALHLQFGKQYPCSKIYGDGNAVPRILKFLKSIDLQEPLQKKFCFP 390
                                    17        27 |      37        47        57  |     67        77      | 87        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   
                                                29-MSE                         60-MSE                  84-MSE                107-MSE            126-MSE                                      171-MSE                    198-MSE|                          232-MSE                      261-MSE                             297-MSE                                                                                         
                                                                                                                                                                                                                             203-MSE                                                       265-MSE
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  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 4ZHT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (20, 20)

Asymmetric Unit(hide GO term definitions)

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  4zht
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  GLCNE_HUMAN | Q9Y223
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  3.2.1.183
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        GLCNE_HUMAN | Q9Y223: 2yhw 2yhy 2yi1 3eo3

(-) Related Entries Specified in the PDB File

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