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(-) Description

Title :  CRYSTAL STRUCTURE OF MICOBACTERIUM TUBERCULOSIS UDP-GALACTOPYRANOSE MUTASE IN COMPLEX WITH TETRAFLUORINATED SUBSTRATE ANALOG UDP-F4-GALF
 
Authors :  K. E. Van Straaten, D. A. R. Sanders
Date :  30 Oct 14  (Deposition) - 21 Jan 15  (Release) - 11 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  B  (2x)
Biol. Unit 2:  A,C  (1x)
Keywords :  Udp-Galactopyranose Mutase, Mtugm, Flavoenzyme, Fad, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. E. Van Straaten, J. R. Kuttiyatveetil, C. M. Sevrain, S. A. Villaume, J. Jimenez-Barbero, B. Linclau, S. P. Vincent, D. A. Sanders
Structural Basis Of Ligand Binding To Udp-Galactopyranose Mutase From Mycobacterium Tuberculosis Using Substrate And Tetrafluorinated Substrate Analogues.
J. Am. Chem. Soc. V. 137 1230 2015
PubMed-ID: 25562380  |  Reference-DOI: 10.1021/JA511204P

(-) Compounds

Molecule 1 - UDP-GALACTOPYRANOSE MUTASE
    Chains: B, A, C
    EC Number: 5.4.99.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDEST-HIS-MBP
    Expression System Strain: BL21(DE3)CODON+RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: GLF, GLFA, RV3809C
    Mutation: YES
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    Strain: ATCC 25618 / H37RV
    Synonym: UGM, UDP-GALP MUTASE, URIDINE 5-DIPHOSPHATE GALACTOPYRANOSE MUTASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x):  B 
Biological Unit 2 (1x): A C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
13UA3Ligand/Ion(2R,5S)-5-[(1R)-1,2-DIHYDROXYETHYL]-3,3,4,4-TETRAFLUOROTETRAHYDROFURAN-2-YL [(2R,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGENDIPHOSPHATE (NON-PREFERRED NAME)
2FAD3Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
13UA2Ligand/Ion(2R,5S)-5-[(1R)-1,2-DIHYDROXYETHYL]-3,3,4,4-TETRAFLUOROTETRAHYDROFURAN-2-YL [(2R,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGENDIPHOSPHATE (NON-PREFERRED NAME)
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
13UA2Ligand/Ion(2R,5S)-5-[(1R)-1,2-DIHYDROXYETHYL]-3,3,4,4-TETRAFLUOROTETRAHYDROFURAN-2-YL [(2R,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGENDIPHOSPHATE (NON-PREFERRED NAME)
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY B:14 , GLY B:16 , PHE B:17 , PHE B:18 , LEU B:37 , GLU B:38 , ARG B:39 , ARG B:40 , GLY B:45 , ASN B:46 , TYR B:62 , ALA B:64 , HIS B:65 , LEU B:66 , THR B:223 , ASP B:224 , TRP B:225 , GLY B:245 , ARG B:249 , LEU B:263 , TYR B:327 , TYR B:328 , GLY B:359 , ARG B:360 , LEU B:367 , ASP B:368 , MET B:369 , 3UA B:402 , HOH B:505 , HOH B:536 , HOH B:548 , HOH B:570 , HOH B:572 , HOH B:600BINDING SITE FOR RESIDUE FAD B 401
2AC2SOFTWAREALA B:64 , LEU B:66 , HIS B:89 , VAL B:91 , PHE B:102 , PHE B:157 , VAL B:158 , TYR B:161 , THR B:162 , GLN B:165 , TRP B:166 , ASN B:177 , ARG B:180 , LEU B:181 , TYR B:191 , VAL B:280 , ASN B:282 , ASN B:284 , ARG B:292 , TYR B:328 , TYR B:366 , FAD B:401 , HOH B:517 , HOH B:549 , HOH B:551 , HOH B:586 , HOH B:587BINDING SITE FOR RESIDUE 3UA B 402
3AC3SOFTWAREVAL A:13 , GLY A:14 , GLY A:16 , PHE A:17 , PHE A:18 , LEU A:37 , GLU A:38 , ARG A:39 , ARG A:40 , GLY A:45 , TYR A:62 , ALA A:64 , HIS A:65 , LEU A:66 , THR A:223 , ASP A:224 , TRP A:225 , PHE A:226 , GLY A:245 , ARG A:249 , LEU A:263 , TYR A:327 , TYR A:328 , GLY A:359 , ARG A:360 , LEU A:367 , ASP A:368 , MET A:369 , 3UA A:402 , HOH A:505 , HOH A:559 , HOH A:560 , HOH A:563 , HOH A:564 , HOH A:577BINDING SITE FOR RESIDUE FAD A 401
4AC4SOFTWAREALA A:64 , LEU A:66 , HIS A:89 , VAL A:91 , PHE A:102 , PHE A:157 , VAL A:158 , TYR A:161 , THR A:162 , GLN A:165 , TRP A:166 , ASN A:177 , ARG A:180 , LEU A:181 , TYR A:191 , VAL A:280 , ASN A:282 , ASN A:284 , ARG A:292 , TYR A:328 , TYR A:366 , FAD A:401 , HOH A:529 , HOH A:561 , HOH A:578 , HOH A:579 , HOH A:607BINDING SITE FOR RESIDUE 3UA A 402
5AC5SOFTWAREVAL C:13 , GLY C:14 , GLY C:16 , PHE C:17 , LEU C:37 , GLU C:38 , ARG C:39 , ARG C:40 , GLY C:45 , ASN C:46 , TYR C:62 , ALA C:64 , HIS C:65 , LEU C:66 , THR C:223 , ASP C:224 , TRP C:225 , PHE C:226 , GLY C:245 , LEU C:263 , TYR C:327 , TYR C:328 , GLY C:359 , ARG C:360 , LEU C:367 , ASP C:368 , MET C:369 , ALA C:372 , 3UA C:402 , HOH C:502 , HOH C:505 , HOH C:555 , HOH C:556 , HOH C:574BINDING SITE FOR RESIDUE FAD C 401
6AC6SOFTWAREALA C:64 , LEU C:66 , HIS C:89 , VAL C:91 , PHE C:102 , PHE C:157 , VAL C:158 , TYR C:161 , THR C:162 , TRP C:166 , ASN C:177 , ILE C:178 , ARG C:180 , LEU C:181 , TYR C:191 , ASN C:282 , ASN C:284 , ARG C:292 , TYR C:328 , TYR C:366 , FAD C:401 , HOH C:549 , HOH C:584 , HOH C:585 , HOH C:597 , HOH C:598BINDING SITE FOR RESIDUE 3UA C 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Phe B:102 -Pro B:103
2Phe A:102 -Pro A:103
3Phe C:102 -Pro C:103

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RPK)

(-) 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:392
                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..hhhhhhhhhhhhhhhh..eeee......hhhh.eee......eee......eee.hhhhhhhhh...........eeeee..eeeee..hhhhhhhhh....hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh..............eee....hhhhhhhhhh....eeee...hhhhhhhhhhhhh....eee..hhhhhh........eeeeeeeeeee.........eeee........eeee.hhh..........eeeeeeeeee........ee..hhhhhhhhhhhhhhhhhhhhhhheeehhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rpk A   5 TARFDLFVVGSGFFGLTIAERVATQLDKRVLVLERRPHIGGNAYSEAEPQTGIEVHKYGAHLFHTSNKRVWDYVRQFTDFTDYRHRVFAMHNGQAYQFPMGLGLVSQFFGKYFTPEQARQLIAEQAAEIDTADAQNLEEKAISLIGRPLYEAFVKGYTAKQWQTDPKELPAANITRLPVRYTFDNRYFSDTYEGLPTDGYTAWLQNMAADHRIEVRLNTDWFDVRGQLRPGSPAAPVVYTGPLDRYFDYAEGRLGWRTLDFEVEVLPIGDFQGTAVMNYNDLDVPYTRIHEFRHFHPERDYRTDKTVIMREYSRFAEDDDEPYYPINTEADRALLATYRARAKSETASSKVLFGGRLGTYQYLDMHMAIASALNMYDNVLAPHLRDGVPLLQ 396
                                    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       384       394  


Chain B from PDB  Type:PROTEIN  Length:391
                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..hhhhhhhhhhhhhhh...eeee......hhhh.eee......eee......eee.hhhhhhhhh...........eeeee..eeeee..hhhhhhhhh....hhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh..............eee....hhhhhhhhhh....eeee...hhhhhhhhhhhhh....eee..hhhhhh........eeeeeeeeeee.........eeee........eeee.hhhh.........eeeeeeeeee........ee..hhhhhhhhhhhhhhhhhhhhhhheeehhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rpk B   5 TARFDLFVVGSGFFGLTIAERVATQLDKRVLVLERRPHIGGNAYSEAEPQTGIEVHKYGAHLFHTSNKRVWDYVRQFTDFTDYRHRVFAMHNGQAYQFPMGLGLVSQFFGKYFTPEQARQLIAEQAAEIDTADAQNLEEKAISLIGRPLYEAFVKGYTAKQWQTDPKELPAANITRLPVRYTFDNRYFSDTYEGLPTDGYTAWLQNMAADHRIEVRLNTDWFDVRGQLRPGSPAAPVVYTGPLDRYFDYAEGRLGWRTLDFEVEVLPIGDFQGTAVMNYNDLDVPYTRIHEFRHFHPERDYRTDKTVIMREYSRFAEDDDEPYYPINTEADRALLATYRARAKSETASSKVLFGGRLGTYQYLDMHMAIASALNMYDNVLAPHLRDGVPLL 395
                                    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       384       394 


Chain C from PDB  Type:PROTEIN  Length:391
                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..hhhhhhhhhhhhhhh...eeee......hhhh.eee......eee......eee.hhhhhhhhh...........eeeee..eeee...hhhhhhhhh....hhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh..............eee....hhhhhhhhhh....eeee...hhhhhhhhhhhhh....eee..hhhhhh........eeeeeeeeeee.........eeee........eeee.hhhh.........eeeeeeeeee........ee..hhhhhhhhhhhhhhhhhhhhhhheeehhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rpk C   5 TARFDLFVVGSGFFGLTIAERVATQLDKRVLVLERRPHIGGNAYSEAEPQTGIEVHKYGAHLFHTSNKRVWDYVRQFTDFTDYRHRVFAMHNGQAYQFPMGLGLVSQFFGKYFTPEQARQLIAEQAAEIDTADAQNLEEKAISLIGRPLYEAFVKGYTAKQWQTDPKELPAANITRLPVRYTFDNRYFSDTYEGLPTDGYTAWLQNMAADHRIEVRLNTDWFDVRGQLRPGSPAAPVVYTGPLDRYFDYAEGRLGWRTLDFEVEVLPIGDFQGTAVMNYNDLDVPYTRIHEFRHFHPERDYRTDKTVIMREYSRFAEDDDEPYYPINTEADRALLATYRARAKSETASSKVLFGGRLGTYQYLDMHMAIASALNMYDNVLAPHLRDGVPLL 395
                                    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       384       394
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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 4RPK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

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 Related Entries

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

UniProtKB/Swiss-Prot
        GLF_MYCTU | P9WIQ1: 1v0j 4rpg 4rph 4rpj 4rpl

(-) Related Entries Specified in the PDB File

1voj HOLO MTUGM
4rpg MTUGM IN COMPLEX WITH SUBSTRATE UDP-GALP
4rph MTUGM IN COMPLEX WITH SUBSTRATE UDP-GALP (REDUCED)
4rpj MTUGM IN COMPLEX WITH UDP
4rpl MTUGM IN COMPLEX IN COMPLEX WITH TETRAFLUORINATED SUBSTRATE ANALOG UDP-F4-GALP