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(-) Description

Title :  CRYSTAL STRUCTURE OF MICOBACTERIUM TUBERCULOSIS UDP-GALACTOPYRANOSE MUTASE IN COMPLEX WITH SUBSTRATE UDP-GALP
 
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 :  2.40
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
    Fragment: UDP-GALACTOPYRANOSE MUTASE
    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  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1FAD3Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2GDU1Ligand/IonGALACTOSE-URIDINE-5'-DIPHOSPHATE
3UDP2Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2GDU2Ligand/IonGALACTOSE-URIDINE-5'-DIPHOSPHATE
3UDP-1Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2GDU-1Ligand/IonGALACTOSE-URIDINE-5'-DIPHOSPHATE
3UDP2Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL B:13 , GLY 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 , PHE B:226 , THR B:244 , GLY B:245 , LEU B:263 , TYR B:327 , TYR B:328 , GLY B:359 , ARG B:360 , LEU B:367 , ASP B:368 , MET B:369 , GDU B:402 , HOH B:505 , HOH B:507 , HOH B:510 , HOH B:605 , HOH B:619 , HOH B:639 , HOH B:648BINDING SITE FOR RESIDUE FAD B 401
2AC2SOFTWARELEU B:66 , HIS B:89 , VAL B:91 , PHE B:102 , PHE B:157 , VAL B:158 , TYR B:161 , THR B:162 , TRP B:166 , ASN B:177 , ARG B:180 , LEU B:181 , TYR B:191 , PHE B:192 , ASN B:282 , ASN B:284 , ARG B:292 , TYR B:328 , TYR B:366 , FAD B:401 , HOH B:509 , HOH B:513 , HOH B:544 , HOH B:553 , HOH B:591 , HOH B:619BINDING SITE FOR RESIDUE GDU 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 , ASN A:46 , 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 , LEU A:263 , TYR A:327 , TYR A:328 , GLY A:359 , ARG A:360 , LEU A:367 , ASP A:368 , MET A:369 , ALA A:372 , HOH A:501 , HOH A:506 , HOH A:516 , HOH A:630 , HOH A:632BINDING SITE FOR RESIDUE FAD A 401
4AC4SOFTWAREPHE A:102 , LEU A:141 , PHE A:157 , VAL A:158 , TYR A:161 , THR A:162 , TRP A:166 , ASN A:177 , ARG A:180 , LEU A:181 , TYR A:191 , ASN A:282 , ASN A:284 , ARG A:292 , TYR A:328 , TYR A:366 , HOH A:510 , HOH A:521 , HOH A:579 , HOH A:629 , HOH A:633BINDING SITE FOR RESIDUE UDP A 402
5AC5SOFTWAREVAL C:13 , GLY C:14 , GLY C:16 , PHE C:17 , PHE C:18 , LEU C:37 , GLU C:38 , ARG C:39 , ARG C:40 , GLY C:45 , ASN C:46 , TYR C:62 , GLY C:63 , 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 , HOH C:504 , HOH C:505 , HOH C:520 , HOH C:555BINDING SITE FOR RESIDUE FAD C 401
6AC6SOFTWAREPHE 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 , HOH C:507 , HOH C:512 , HOH C:552 , HOH C:571 , HOH C:612 , HOH C:613BINDING SITE FOR RESIDUE UDP C 402

(-) SS Bonds  (0, 0)

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

(-) 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 4RPG)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RPG)

(-) 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:393
                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee..hhhhhhhhhhhhhhhh..eeee......hhhh.eee......eee......eee.hhhhhhhhh...........eeeee..eeee...hhhhhhhhhh...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
                 4rpg A   4 MTARFDLFVVGSGFFGLTIAERVATQLDKRVLVLERRPHIGGNAYSEAEPQTGIEVHKYGAHLFHTSNKRVWDYVRQFTDFTDYRHRVFAMHNGQAYQFPMGLGLVSQFFGKYFTPEQARQLIAEQAAEIDTADAQNLEEKAISLIGRPLYEAFVKGYTAKQWQTDPKELPAANITRLPVRYTFDNRYFSDTYEGLPTDGYTAWLQNMAADHRIEVRLNTDWFDVRGQLRPGSPAAPVVYTGPLDRYFDYAEGRLGWRTLDFEVEVLPIGDFQGTAVMNYNDLDVPYTRIHEFRHFHPERDYRTDKTVIMREYSRFAEDDDEPYYPINTEADRALLATYRARAKSETASSKVLFGGRLGTYQYLDMHMAIASALNMYDNVLAPHLRDGVPLLQ 396
                                    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       383       393   


Chain B 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..eeee...hhhhhhhhh....hhhhhhhhhhhhh.........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
                 4rpg B   4 MTARFDLFVVGSGFFGLTIAERVATQLDKRVLVLERRPHIGGNAYSEAEPQTGIEVHKYGAHLFHTSNKRVWDYVRQFTDFTDYRHRVFAMHNGQAYQFPMGLGLVSQFFGKYFTPEQARQLIAEQAAEIDTADAQNLEEKAISLIGRPLYEAFVKGYTAKQWQTDPKELPAANITRLPVRYTFDNRYFSDTYEGLPTDGYTAWLQNMAADHRIEVRLNTDWFDVRGQLRPGSPAAPVVYTGPLDRYFDYAEGRLGWRTLDFEVEVLPIGDFQGTAVMNYNDLDVPYTRIHEFRHFHPERDYRTDKTVIMREYSRFAEDDDEPYYPINTEADRALLATYRARAKSETASSKVLFGGRLGTYQYLDMHMAIASALNMYDNVLAPHLRDGVPLL 395
                                    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       383       393  


Chain C 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..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
                 4rpg C   4 MTARFDLFVVGSGFFGLTIAERVATQLDKRVLVLERRPHIGGNAYSEAEPQTGIEVHKYGAHLFHTSNKRVWDYVRQFTDFTDYRHRVFAMHNGQAYQFPMGLGLVSQFFGKYFTPEQARQLIAEQAAEIDTADAQNLEEKAISLIGRPLYEAFVKGYTAKQWQTDPKELPAANITRLPVRYTFDNRYFSDTYEGLPTDGYTAWLQNMAADHRIEVRLNTDWFDVRGQLRPGSPAAPVVYTGPLDRYFDYAEGRLGWRTLDFEVEVLPIGDFQGTAVMNYNDLDVPYTRIHEFRHFHPERDYRTDKTVIMREYSRFAEDDDEPYYPINTEADRALLATYRARAKSETASSKVLFGGRLGTYQYLDMHMAIASALNMYDNVLAPHLRDGVPLL 395
                                    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       383       393
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "SCOP Domain" information available for 4RPG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

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 Related Entries

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

(-) Related Entries Specified in the PDB File

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