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(-) Description

Title :  CRYSTAL STRUCUTRE OF OXIDIZED UDP-GALACTOPYRANOSE MUTASE FROM CORYNEBACTERIUM DIPHTHERIAE WITH UDP BOUND IN CLOSED FORM
 
Authors :  K. Wangkanont, L. L. Kiessling, K. T. Forest
Date :  12 Nov 15  (Deposition) - 23 Nov 16  (Release) - 23 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Keywords :  Galactofuranose, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Wangkanont, L. L. Kiessling, K. T. Forest
Structures Of Udp-Galactopyranose Mutase From Corynebacterium Diphtheriae
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UDP-GALACTOPYRANOSE MUTASE
    Chains: A, B
    EC Number: 5.4.99.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMAL C5X
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 18-404
    Gene: GLF, DIP2203
    Organism Scientific: CORYNEBACTERIUM DIPHTHERIAE
    Organism Taxid: 257309
    Strain: ATCC 700971 / NCTC 13129 / BIOTYPE GRAVIS

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x): A 
Biological Unit 3 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2SO46Ligand/IonSULFATE ION
3UDP2Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2SO46Ligand/IonSULFATE ION
3UDP2Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2SO44Ligand/IonSULFATE ION
3UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 3 (3, 4)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2SO42Ligand/IonSULFATE ION
3UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:98 , LEU A:137 , PHE A:153 , ILE A:154 , TYR A:157 , THR A:158 , TRP A:162 , ASN A:173 , ARG A:176 , LEU A:177 , TYR A:187 , ASN A:278 , ASN A:280 , ARG A:288 , TYR A:326 , TYR A:364 , HOH A:529 , HOH A:548 , HOH A:559 , HOH A:564 , HOH A:614 , HOH A:623binding site for residue UDP A 401
02AC2SOFTWAREVAL A:9 , GLY A:10 , GLY A:12 , LEU A:13 , PHE A:14 , VAL A:33 , GLU A:34 , LYS A:35 , ARG A:36 , GLY A:41 , ASN A:42 , TYR A:58 , GLY A:59 , ALA A:60 , HIS A:61 , LEU A:62 , THR A:219 , ASP A:220 , TRP A:221 , PHE A:222 , LEU A:259 , TYR A:325 , TYR A:326 , GLY A:357 , ARG A:358 , LEU A:359 , LEU A:365 , ASP A:366 , MET A:367 , HOH A:502 , HOH A:525 , HOH A:560 , HOH A:583 , HOH A:590 , HOH A:623binding site for residue FAD A 402
03AC3SOFTWAREARG A:293 , HIS A:294 , PRO A:297 , GLU A:300 , HIS A:303binding site for residue SO4 A 403
04AC4SOFTWAREARG A:36 , SER A:37 , HIS A:38 , TYR A:58 , ARG B:69binding site for residue SO4 A 404
05AC5SOFTWAREARG A:180 , ASN A:189 , HOH A:503binding site for residue SO4 A 405
06AC6SOFTWAREGLN A:76 , PHE A:77 , THR A:78binding site for residue SO4 A 406
07AC7SOFTWAREPHE B:98 , LEU B:137 , PHE B:153 , ILE B:154 , TYR B:157 , THR B:158 , TRP B:162 , ASN B:173 , ILE B:174 , ARG B:176 , LEU B:177 , TYR B:187 , ASN B:278 , ASN B:280 , ARG B:288 , TYR B:326 , TYR B:364 , HOH B:535 , HOH B:540 , HOH B:542binding site for residue UDP B 401
08AC8SOFTWAREGLY B:10 , GLY B:12 , LEU B:13 , PHE B:14 , VAL B:33 , GLU B:34 , LYS B:35 , ARG B:36 , GLY B:41 , ASN B:42 , ALA B:60 , HIS B:61 , LEU B:62 , HIS B:64 , THR B:219 , ASP B:220 , TRP B:221 , LEU B:259 , TYR B:325 , TYR B:326 , GLY B:357 , ARG B:358 , LEU B:365 , ASP B:366 , MET B:367 , ALA B:370binding site for residue FAD B 402
09AC9SOFTWARETYR B:286 , LYS B:312binding site for residue SO4 B 403
10AD1SOFTWAREARG B:293 , GLU B:300binding site for residue SO4 B 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5EQF)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:98 -Pro A:99
2Phe B:98 -Pro B:99

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5EQF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5EQF)

(-) Exons   (0, 0)

(no "Exon" information available for 5EQF)

(-) 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:386
                                                                                                                                                                                                                                                                                                                                                                                                                                  
               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...hhhhhhhhhh...hhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh...............eee...hhhhhhhhhhhh...eeee...hhhhhhhhhhhhh....eee..hhhhhh........eeeeeeeeeee.........eeee........eeee.hhhhhhhhhhh....eeeeeeeeee........ee..hhhhhhhhhhhhhhhhhhhhhhheeehhhhhh....hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5eqf A   2 SDFDLIVVGSGLFGLTVAERAASQLGKKVLIVEKRSHLGGNAYSEAEPETGIEIHKYGAHLFHTSNKRVWDYVNQFTAFTGYQHRVFAMHNGTAYQFPMGLGLINQFFGRYYTPDEARELIKEQSAEIDSKDATNLEEKAISLIGRPLYEAFIRDYTAKQWQTDPKELPAGNITRLPVRYNFDNRYFNDTYEGLPVDGYAQWLSNMADHENIEVRLDTDWFEVREDLRAQNPEAPVVYTGPLDRYFDYSEGHLGWRTLDFETEVLNTGDFQGTPVMNYNDAEFPYTRIHEFRHFHPEREDRHPKDKTVIMKEYSRFAEEGDEPYYPINTPSDREMLFKYRELADAETESGKVYFGGRLGTYQYLDMHMAIASALSMFDNKLVDALK 387
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381      


Chain B from PDB  Type:PROTEIN  Length:385
                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..hhhhhhhhhhhhhhh...eeee......hhhhh.ee......ee.......eee.hhhhhhhhh...........eeeee..eeeee..hhhhhhhhhh...hhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhh.................eee...hhhhhhhhhhhh...eeee...hhhhhhhhhh.......eee..hhhhhh........eeeeeeeeeee.........eeee........eeee.hhhhhhhhhhh....eeeeeeeeee........ee..hhhhhhhhhhhhhhhhhhhhhhheeehhhhhhh...hhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5eqf B   2 SDFDLIVVGSGLFGLTVAERAASQLGKKVLIVEKRSHLGGNAYSEAEPETGIEIHKYGAHLFHTSNKRVWDYVNQFTAFTGYQHRVFAMHNGTAYQFPMGLGLINQFFGRYYTPDEARELIKEQSAEIDSKDATNLEEKAISLIGRPLYEAFIRDYTAKQWQTDPKELPAGNITRLPVRYNFDNRYFNDTYEGLPVDGYAQWLSNMADHENIEVRLDTDWFEVREDLRAQNPEAPVVYTGPLDRYFDYSEGHLGWRTLDFETEVLNTGDFQGTPVMNYNDAEFPYTRIHEFRHFHPEREDRHPKDKTVIMKEYSRFAEEGDEPYYPINTPSDREMLFKYRELADAETESGKVYFGGRLGTYQYLDMHMAIASALSMFDNKLVDAL 386
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381
   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  (0, 0)

(no "SCOP Domain" information available for 5EQF)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5EQF)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5EQF)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)

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5eqd 5er9