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(-) Description

Title :  A STRUCTURAL BASIS FOR THE ALLOSTERIC REGULATION OF NON-HYDROLYZING UDP-GLCNAC 2-EPIMERASES
 
Authors :  L. M. Velloso, S. S. Bhaskaran, R. Schuch, V. A. Fischetti, C. E. Stebbins
Date :  19 Nov 07  (Deposition) - 19 Feb 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Epimerase, Udp-Glcnac, Allosteric, Regulation, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. M. Velloso, S. S. Bhaskaran, R. Schuch, V. A. Fischetti, C. E. Stebbins
A Structural Basis For The Allosteric Regulation Of Non-Hydrolysing Udp-Glcnac 2-Epimerases.
Embo Rep. V. 9 199 2008
PubMed-ID: 18188181  |  Reference-DOI: 10.1038/SJ.EMBOR.7401154
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UDP-N-ACETYLGLUCOSAMINE 2-EPIMERASE
    Chains: A, B
    EC Number: 5.1.3.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: BACILLUS ANTHRACIS
    Organism Taxid: 1392

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1UD12Ligand/IonURIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE
2UDP2Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:15 , GLN A:43 , HIS A:44 , ARG A:45 , GLN A:46 , MET A:47 , MET A:66 , LYS A:67 , ASP A:68 , ARG A:69 , GLN A:70 , THR A:101 , THR A:102 , PRO A:135 , GLU A:136 , HIS A:209 , ARG A:210 , ARG A:211 , HIS A:242 , MET A:243 , ASN A:244 , PRO A:245 , UDP A:1081 , HOH A:1092 , HOH A:1101 , HOH A:1181 , HOH A:1322 , HOH A:1325 , HOH A:1341BINDING SITE FOR RESIDUE UD1 A 372
2AC2SOFTWAREARG A:14 , PRO A:15 , ILE A:18 , HIS A:209 , ARG A:210 , PRO A:240 , LEU A:267 , VAL A:269 , PHE A:272 , HIS A:273 , SER A:286 , GLY A:287 , GLY A:288 , GLU A:292 , UD1 A:372 , HOH A:1084 , HOH A:1102 , HOH A:1127 , HOH A:1171 , HOH A:1181BINDING SITE FOR RESIDUE UDP A 1081
3AC3SOFTWAREPRO B:15 , GLN B:43 , HIS B:44 , ARG B:45 , GLN B:46 , MET B:47 , MET B:66 , LYS B:67 , ASP B:68 , ARG B:69 , GLN B:70 , LEU B:72 , ILE B:75 , THR B:101 , THR B:102 , PRO B:135 , GLU B:136 , HIS B:209 , ARG B:210 , ARG B:211 , HIS B:242 , MET B:243 , ASN B:244 , PRO B:245 , UDP B:1081 , HOH B:1198 , HOH B:1209 , HOH B:1228 , HOH B:1292 , HOH B:1295 , HOH B:1300 , HOH B:1391 , HOH B:1413BINDING SITE FOR RESIDUE UD1 B 372
4AC4SOFTWAREARG B:14 , PRO B:15 , ILE B:18 , HIS B:209 , ARG B:210 , PRO B:240 , LEU B:267 , VAL B:269 , PHE B:272 , HIS B:273 , SER B:286 , GLY B:287 , GLY B:288 , GLU B:292 , UD1 B:372 , HOH B:1199 , HOH B:1205 , HOH B:1236 , HOH B:1262 , HOH B:1358BINDING SITE FOR RESIDUE UDP B 1081

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BEO)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ser A:132 -Pro A:133
2Tyr A:134 -Pro A:135
3Ser B:132 -Pro B:133
4Tyr B:134 -Pro B:135

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BEO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3BEO)

(-) Exons   (0, 0)

(no "Exon" information available for 3BEO)

(-) 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:375
 aligned with Q81K32_BACAN | Q81K32 from UniProtKB/TrEMBL  Length:371

    Alignment length:375
                                1                                                                                                                                                                                                                                                                                                                                                                                  
                                |    6        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     
         Q81K32_BACAN     - ----MTERLKVMTIFGTRPEAIKMAPLVLELQKHPEKIESIVTVTAQHRQMLDQVLSIFGITPDFDLNIMKDRQTLIDITTRGLEGLDKVMKEAKPDIVLVHGDTTTTFIASLAAFYNQIPVGHVEAGLRTWDKYSPYPEEMNRQLTGVMADLHFSPTAKSATNLQKENKDESRIFITGNTAIDALKTTVKETYSHPVLEKLGNNRLVLMTAHRRENLGEPMRNMFRAIKRLVDKHEDVQVVYPVHMNPVVRETANDILGDYGRIHLIEPLDVIDFHNVAARSYLMLTDSGGVQEEAPSLGVPVLVLRDTTERPEGIEAGTLKLAGTDEETIFSLADELLSDKEAHDKMSKASNPYGDGRASERIVEAILKHFNK 371
               SCOP domains d3beoa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 3beoA01 A:-3-191,A:353-371 Glycogen Phosphorylase B;                                                                                                                                               3beoA02 A:192-352 Glycogen Phosphorylase B;                                                                                                                      3beoA01             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeee.hhhhhhhhhhhhhhhh.....eeeeeee....hhhhhhhhhhhh....ee........hhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhh.eeee.hhhhhhhhhhh..hhh.eee..hhhhhhhhhhh.....hhhhhh....eeeeee..hhhhhhhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhh....eeee...hhhhhhhhhhh..eeee.hhhhhhhhhhhh..eee......hhhhhhh..eee...hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3beo A  -3 GPVDMTERLKVMTIFGTRPEAIKMAPLVLELQKHPEKIESIVTVTAQHRQMLDQVLSIFGITPDFDLNIMKDRQTLIDITTRGLEGLDKVMKEAKPDIVLVHGDTTTTFIASLAAFYNQIPVGHVEAGLRTWDKYSPYPEEMNRQLTGVMADLHFSPTAKSATNLQKENKDESRIFITGNTAIDALKTTVKETYSHPVLEKLGNNRLVLMTAHRRENLGEPMRNMFRAIKRLVDKHEDVQVVYPVHMNPVVRETANDILGDYGRIHLIEPLDVIDFHNVAARSYLMLTDSGGVQEEAPSLGVPVLVLRDTTERPEGIEAGTLKLAGTDEETIFSLADELLSDKEAHDKMSKASNPYGDGRASERIVEAILKHFNK 371
                                     6        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     


Chain B from PDB  Type:PROTEIN  Length:375
 aligned with Q81K32_BACAN | Q81K32 from UniProtKB/TrEMBL  Length:371

    Alignment length:375
                                1                                                                                                                                                                                                                                                                                                                                                                                  
                                |    6        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     
         Q81K32_BACAN     - ----MTERLKVMTIFGTRPEAIKMAPLVLELQKHPEKIESIVTVTAQHRQMLDQVLSIFGITPDFDLNIMKDRQTLIDITTRGLEGLDKVMKEAKPDIVLVHGDTTTTFIASLAAFYNQIPVGHVEAGLRTWDKYSPYPEEMNRQLTGVMADLHFSPTAKSATNLQKENKDESRIFITGNTAIDALKTTVKETYSHPVLEKLGNNRLVLMTAHRRENLGEPMRNMFRAIKRLVDKHEDVQVVYPVHMNPVVRETANDILGDYGRIHLIEPLDVIDFHNVAARSYLMLTDSGGVQEEAPSLGVPVLVLRDTTERPEGIEAGTLKLAGTDEETIFSLADELLSDKEAHDKMSKASNPYGDGRASERIVEAILKHFNK 371
               SCOP domains d3beob_ B: automated matches                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 3beoB01 B:-3-191,B:353-371 Glycogen Phosphorylase B;                                                                                                                                               3beoB02 B:192-352 Glycogen Phosphorylase B;                                                                                                                      3beoB01             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeee.hhhhhhhhhhhhhhhh.....eeeeeee....hhhhhhhhhhhh....ee........hhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhh....eeee.............hhhhhhhhhhhhh.eeee.hhhhhhhhhhh..hhh.eee..hhhhhhhhhhh.....hhhhhh....eeeeee..hhhhhhhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhh....eeee...hhhhhhhhhhh..eeee.hhhhhhhhhhhh..eee......hhhhhhh..eee...hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3beo B  -3 GPVDMTERLKVMTIFGTRPEAIKMAPLVLELQKHPEKIESIVTVTAQHRQMLDQVLSIFGITPDFDLNIMKDRQTLIDITTRGLEGLDKVMKEAKPDIVLVHGDTTTTFIASLAAFYNQIPVGHVEAGLRTWDKYSPYPEEMNRQLTGVMADLHFSPTAKSATNLQKENKDESRIFITGNTAIDALKTTVKETYSHPVLEKLGNNRLVLMTAHRRENLGEPMRNMFRAIKRLVDKHEDVQVVYPVHMNPVVRETANDILGDYGRIHLIEPLDVIDFHNVAARSYLMLTDSGGVQEEAPSLGVPVLVLRDTTERPEGIEAGTLKLAGTDEETIFSLADELLSDKEAHDKMSKASNPYGDGRASERIVEAILKHFNK 371
                                     6        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
   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  (0, 0)

(no "Pfam Domain" information available for 3BEO)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q81K32_BACAN | Q81K32)
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.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

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