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(-) Description

Title :  CRYSTAL STRUCTURE OF UDP-N-ACETYLGLUCOSAMINE 2-EPIMERASE FROM THERMUS THERMOPHILUS HB8
 
Authors :  B. Bagautdinov, T. H. Tahirov, Riken Structural Genomics/Proteomi Initiative (Rsgi)
Date :  19 Nov 03  (Deposition) - 02 Dec 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Udp-Glcnac, Two Domains, Homodimer, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Bagautdinov, T. H. Tahirov
The Structure Of Udp-N-Acetylglucosamine 2-Epimerase From Thermus Thermophilus Hb8
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UDP-N-ACETYLGLUCOSAMINE 2-EPIMERASE
    Chains: A, B
    EC Number: 5.1.3.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CAP5P
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 21)

Asymmetric/Biological Unit (3, 21)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2GOL2Ligand/IonGLYCEROL
3MSE18Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:93 , PRO A:117 , HOH A:1786 , HOH A:1932 , HOH B:1764BINDING SITE FOR RESIDUE ACY A 1400
2AC2SOFTWAREGLN A:176 , GLY A:178 , VAL A:179 , VAL A:182 , GLU A:287 , GLU A:288 , TYR A:348 , HOH A:1557 , HOH A:1572 , HOH A:1699 , HOH A:2058BINDING SITE FOR RESIDUE GOL A 1500
3AC3SOFTWAREPHE A:248 , LEU B:367 , PRO B:369 , HOH B:1507 , HOH B:1632 , HOH B:1812 , HOH B:1853BINDING SITE FOR RESIDUE GOL B 1501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V4V)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Glu A:132 -Pro A:133
2Phe A:134 -Pro A:135
3Gly A:198 -Pro A:199
4Glu B:132 -Pro B:133
5Phe B:134 -Pro B:135
6Gly B:198 -Pro B:199

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V4V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V4V)

(-) Exons   (0, 0)

(no "Exon" information available for 1V4V)

(-) 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:373
 aligned with P83824_THETH | P83824 from UniProtKB/TrEMBL  Length:376

    Alignment length:373
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373   
         P83824_THETH     4 GMKRVVLAFGTRPEATKMAPVYLALRGIPGLKPLVLLTGQHREQLRQALSLFGIQEDRNLDVMQERQALPDLAARILPQAARALKEMGADYVLVHGDTLTTFAVAWAAFLEGIPVGHVEAGLRSGNLKEPFPEEANRRLTDVLTDLDFAPTPLAKANLLKEGKREEGILVTGQTGVDAVLLAAKLGRLPEGLPEGPYVTVTMHRRENWPLLSDLAQALKRVAEAFPHLTFVYPVHLNPVVREAVFPVLKGVRNFVLLDPLEYGSMAALMRASLLLVTDSGGLQEEGAALGVPVVVLRNVTERPEGLKAGILKLAGTDPEGVYRVVKGLLENPEELSRMRKAKNPYGDGKAGLMVARGVAWRLGLGPRPEDWLP 376
               SCOP domains d1v4va_ A: UDP-N-acetylglucosamine 2-epimerase                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1v4vA01 A:4-191,A:349-376 Glycogen Phosphorylase B;                                                                                                                                         1v4vA02 A:192-348 Glycogen Phosphorylase B;                                                                                                                  1v4vA01 A:4-191,A:349-376    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.hhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhh......ee........hhhhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhh.eeee.hhhhhhhhhh...hhh.eee..hhhhhhhhhhhhhh..........eeee...hhhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhh....eeee...hhhhhhhhhhheeeeee.hhhhhhhhhhh...eee......hhhhhhhh.eee...hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v4v A   4 GmKRVVLAFGTRPEATKmAPVYLALRGIPGLKPLVLLTGQHREQLRQALSLFGIQEDRNLDVmQERQALPDLAARILPQAARALKEmGADYVLVHGDTLTTFAVAWAAFLEGIPVGHVEAGLRSGNLKEPFPEEANRRLTDVLTDLDFAPTPLAKANLLKEGKREEGILVTGQTGVDAVLLAAKLGRLPEGLPEGPYVTVTmHRRENWPLLSDLAQALKRVAEAFPHLTFVYPVHLNPVVREAVFPVLKGVRNFVLLDPLEYGSmAALmRASLLLVTDSGGLQEEGAALGVPVVVLRNVTERPEGLKAGILKLAGTDPEGVYRVVKGLLENPEELSRmRKAKNPYGDGKAGLmVARGVAWRLGLGPRPEDWLP 376
                             |      13       |23        33        43        53        63  |     73        83      | 93       103       113       123       133       143       153       163       173       183       193       203 |     213       223       233       243       253       263    |  273       283       293       303       313       323       333       343       353  |    363       373   
                             |              21-MSE                                       66-MSE                  90-MSE                                                                                                            205-MSE                                                        268-MSE                                                                  341-MSE        356-MSE                
                             5-MSE                                                                                                                                                                                                                                                                    272-MSE                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:372
 aligned with P83824_THETH | P83824 from UniProtKB/TrEMBL  Length:376

    Alignment length:372
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374  
         P83824_THETH     5 MKRVVLAFGTRPEATKMAPVYLALRGIPGLKPLVLLTGQHREQLRQALSLFGIQEDRNLDVMQERQALPDLAARILPQAARALKEMGADYVLVHGDTLTTFAVAWAAFLEGIPVGHVEAGLRSGNLKEPFPEEANRRLTDVLTDLDFAPTPLAKANLLKEGKREEGILVTGQTGVDAVLLAAKLGRLPEGLPEGPYVTVTMHRRENWPLLSDLAQALKRVAEAFPHLTFVYPVHLNPVVREAVFPVLKGVRNFVLLDPLEYGSMAALMRASLLLVTDSGGLQEEGAALGVPVVVLRNVTERPEGLKAGILKLAGTDPEGVYRVVKGLLENPEELSRMRKAKNPYGDGKAGLMVARGVAWRLGLGPRPEDWLP 376
               SCOP domains d1v4vb_ B: UDP-N-acetylglucosamine 2-epimerase                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -1v4vB01 B:6-191,B:349-376 Glycogen Phosphorylase B;                                                                                                                                       1v4vB02 B:192-348 Glycogen Phosphorylase B;                                                                                                                  1v4vB01 B:6-191,B:349-376    CATH domains
           Pfam domains (1) ----------------------Epimerase_2-1v4vB01 B:27-361                                                                                                                                                                                                                                                                                                                   --------------- Pfam domains (1)
           Pfam domains (2) ----------------------Epimerase_2-1v4vB02 B:27-361                                                                                                                                                                                                                                                                                                                   --------------- Pfam domains (2)
         Sec.struct. author .eeeeeee.hhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhh......ee........hhhhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhh.eeee.hhhhhhhhhhh..hhh.eee..hhhhhhhhhhhhhh..........eeeee.......hhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhh....eeee...hhhhhhhhhhheeeeee.hhhhhhhhhhhh..eee...............eee...hhhhhhhhhhhhhh...hhhhhhh........hhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1v4v B   5 mKRVVLAFGTRPEATKmAPVYLALRGIPGLKPLVLLTGQHREQLRQALSLFGIQEDRNLDVmQERQALPDLAARILPQAARALKEmGADYVLVHGDTLTTFAVAWAAFLEGIPVGHVEAGLRSGNLKEPFPEEANRRLTDVLTDLDFAPTPLAKANLLKEGKREEGILVTGQTGVDAVLLAAKLGRLPEGLPEGPYVTVTmHRRENWPLLSDLAQALKRVAEAFPHLTFVYPVHLNPVVREAVFPVLKGVRNFVLLDPLEYGSmAALmRASLLLVTDSGGLQEEGAALGVPVVVLRNVTERPEGLKAGILKLAGTDPEGVYRVVKGLLENPEELSRmRKAKNPYGDGKAGLmVARGVAWRLGLGPRPEDWLP 376
                            |       14      | 24        34        44        54        64 |      74        84     |  94       104       114       124       134       144       154       164       174       184       194       204|      214       224       234       244       254       264   |   274       284       294       304       314       324       334      |344       354 |     364       374  
                            5-MSE          21-MSE                                       66-MSE                  90-MSE                                                                                                            205-MSE                                                        268-MSE                                                                  341-MSE        356-MSE                
                                                                                                                                                                                                                                                                                                     272-MSE
   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  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: GT-B (132)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (P83824_THETH | P83824)
molecular function
    GO:0008761    UDP-N-acetylglucosamine 2-epimerase activity    Catalysis of the reaction: UDP-N-acetyl-D-glucosamine = UDP-N-acetyl-D-mannosamine.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.

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