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(-) Description

Title :  CRYSTAL STRUCTURE OF THE WBKC FORMYL TRANSFERASE FROM BRUCELLA MELITENSIS
 
Authors :  A. S. Riegert, D. P. Chantigian, J. B. Thoden, H. M. Holden
Date :  26 May 17  (Deposition) - 05 Jul 17  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  N-Formyltransferase, Deoxysugar, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. S. Riegert, D. P. Chantigian, J. B. Thoden, P. A. Tipton, H. M. Holden
Biochemical Characterization Of Wbkc, An N-Formyltransferas From Brucella Melitensis.
Biochemistry 2017
PubMed-ID: 28636341  |  Reference-DOI: 10.1021/ACS.BIOCHEM.7B00494

(-) Compounds

Molecule 1 - GDP-MANNOSE 4,6-DEHYDRATASE / GDP-4-AMINO-4,6-DIDEOXY-D- MANNOSE FORMYLTRANSFERASE
    Chains: A, B
    EC Number: 2.1.2.-, 4.2.1.47
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: ROSETTA2(DE3)
    Expression System Taxid: 562
    Gene: BMEI1418
    Mutation: YES
    Organism Scientific: BRUCELLA MELITENSIS BIOTYPE 1 (STRAIN 16M / ATCC 23456 / NCTC 10094)
    Organism Taxid: 224914
    Strain: 16M / ATCC 23456 / NCTC 10094

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1B622Ligand/Ion(6R)-2-AMINO-6-METHYL-5,6,7,8-TETRAHYDROPTERIDIN-4(3H)-ONE
2CL1Ligand/IonCHLORIDE ION
3EDO1Ligand/Ion1,2-ETHANEDIOL
4GMP3Ligand/IonGUANOSINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:87 , SER A:89 , LEU A:90 , ILE A:91 , LEU A:96 , ASN A:105 , HIS A:136 , MET A:138 , ASP A:139 , ASN A:141 , PHE A:142 , ASP A:143 , HOH A:409 , HOH A:457 , HOH A:463 , HOH A:482binding site for residue B62 A 301
2AC2SOFTWAREGLU A:128 , VAL A:155 , GLU A:156 , GLU A:157 , ARG A:220 , ARG A:223 , HOH A:415binding site for residue EDO A 302
3AC3SOFTWARELEU A:110 , THR A:131binding site for residue CL A 303
4AC4SOFTWAREMET A:225 , PHE A:227 , PHE A:230 , PRO A:231 , HOH A:407 , HOH A:439binding site for residue GMP A 304
5AC5SOFTWARESER B:89 , LEU B:90 , ILE B:91 , ASN B:105 , HIS B:136 , MET B:138 , ASP B:139 , ASN B:141 , PHE B:142 , ASP B:143 , HOH B:415 , HOH B:433 , HOH B:457 , HOH B:476binding site for residue B62 B 301
6AC6SOFTWAREARG A:212 , ARG B:88 , GLY B:116 , THR B:117 , PHE B:142 , ASP B:143 , ARG B:201 , HOH B:471 , HOH B:511binding site for residue GMP B 302
7AC7SOFTWARELEU B:203 , MET B:225 , PHE B:230 , PRO B:231 , HOH B:477binding site for residue GMP B 303

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:47 -B:47

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Leu A:111 -Pro A:112
2Pro A:228 -Pro A:229
3Leu B:111 -Pro B:112
4Pro B:228 -Pro B:229

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5VYR)

(-) 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:244
                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeehhhhhhhhhhhhhhh..hhh.eeee.......hhhhhhhhhhhh.eee.....hhhhhhhhhhhh..eeeee......hhhhhh.....eeeee.......ee.hhhhhhhhh...eeeeeee..........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh...........ee...hhhhhh.....hhhhhhhhhhhhh.............hhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vyr A   2 AIAPNTRVLVAGYGLPAEFCVTTLIGMGVEIDKIAVATHREDNRNCGLHSMLRLRNIQFTTAAANSEEFYEFGANFAPDMIISMHYRSLIPGRFLKLAKKGSVNLHPSLLPAYRGTNSVAWVIINGESETGFSYHRMDENFDTGAILLQERISVEETDTAFSLFHRQIARAMLRLEEVILKLDQGDPGFAQLGEASYYARELPFGGVIDPRWSEVQIDRFIRAMFFPPFPPAVLYYVPSIDIYR 251
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231   ||  247    
                                                                                                                                                                                                                                                                   235|         
                                                                                                                                                                                                                                                                    242         


Chain B from PDB  Type:PROTEIN  Length:245
                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeehhhhhhhhhhhhhhh..hhh.eeee.......hhhhhhhhhhhh.eee.....hhhhhhhhhhhh..eeeee......hhhhhhh....eeeee.......ee.hhhhhhhhh...eeeeeee..........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh............ee...hhhhhh.....hhhhhhhhhhhhh.......eeee..eeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vyr B   2 AIAPNTRVLVAGYGLPAEFCVTTLIGMGVEIDKIAVATHREDNRNCGLHSMLRLRNIQFTTAAANSEEFYEFGANFAPDMIISMHYRSLIPGRFLKLAKKGSVNLHPSLLPAYRGTNSVAWVIINGESETGFSYHRMDENFDTGAILLQERISVEETDTAFSLFHRQIARAMLRLEEVILKLDQGDPGFAQLGEASYYARELPFGGVIDPRWSEVQIDRFIRAMFFPPFPPAVLKIDGKVYYVPS 246
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 5VYR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        F8WJP6_BRUME | F8WJP6: 5vys 5vyt 5vyu

(-) Related Entries Specified in the PDB File

5vyq 5vys 5vyt 5vyu