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(-) Description

Title :  CRYSTAL STRUCTURE OF THE WBKC N-FORMYLTRANSFERASE (C47S VARIANT) 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 :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Brucellosis, 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, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
11YJ2Ligand/IonN-[4-({[(6R)-2-AMINO-4-OXO-3,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)BENZOYL]-L-GLUTAMIC ACID
2EDO1Ligand/Ion1,2-ETHANEDIOL
3GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
4GMP1Ligand/IonGUANOSINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:87 , SER A:89 , LEU A:90 , ILE A:91 , ASN A:105 , HIS A:136 , ASP A:139 , ASN A:141 , PHE A:142 , ASP A:143 , HOH A:401 , HOH A:441binding site for residue 1YJ A 301
2AC2SOFTWAREGLU A:128 , GLU A:156 , GLU A:157 , ARG A:220 , ARG A:223binding site for residue EDO A 302
3AC3SOFTWAREARG A:45 , ARG A:88 , THR A:117 , ASN A:118 , VAL A:120 , ALA A:121 , ALA A:161 , ARG A:201 , MET A:225 , PHE A:227 , PHE A:230 , PRO A:231 , HOH A:415 , HOH A:445 , HOH A:472 , HOH A:480binding site for residue GDP A 303
4AC4SOFTWARESER B:89 , ILE B:91 , LEU B:96 , ASN B:105 , HIS B:136 , MET B:138 , ASP B:139 , ASN B:141 , PHE B:142 , ASP B:143 , HOH B:408 , HOH B:417binding site for residue 1YJ B 301
5AC5SOFTWAREARG B:45 , ARG B:88 , ASN B:118 , ALA B:161 , PHE B:165 , LEU B:203 , MET B:225 , PHE B:227 , PHE B:230 , PRO B:231 , HOH B:402 , HOH B:432 , HOH B:443 , HOH B:479binding site for residue GDP B 302
6AC6SOFTWAREARG A:212 , ARG B:88 , SER B:89 , GLY B:116 , THR B:117 , PHE B:142 , ASP B:143 , ARG B:201 , HOH B:406binding site for residue GMP B 303

(-) SS Bonds  (0, 0)

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

(-) 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 5VYS)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5VYS)

(-) 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:248
                                                                                                                                                                                                                                                                                        
               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.....hhhhhhhhhhhhhhhhhhhhhhhhhh............ee...hhhhhh.....hhhhhhhhhhhhh......ee...ee.hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vys A   2 AIAPNTRVLVAGYGLPAEFCVTTLIGMGVEIDKIAVATHREDNRNSGLHSMLRLRNIQFTTAAANSEEFYEFGANFAPDMIISMHYRSLIPGRFLKLAKKGSVNLHPSLLPAYRGTNSVAWVIINGESETGFSYHRMDENFDTGAILLQERISVEETDTAFSLFHRQIARAMLRLEEVILKLDQGDPGFAQLGEASYYARELPFGGVIDPRWSEVQIDRFIRAMFFPPFPPAVLKYYVPSIDIYRSLM 254
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231    || 246        
                                                                                                                                                                                                                                                                    236|            
                                                                                                                                                                                                                                                                     242            


Chain B from PDB  Type:PROTEIN  Length:246
                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeeehhhhhhhhhhhhhhh..hhh.eeee.......hhhhhhhhhhh..eee.....hhhhhhhhhhhh..eeeee......hhhhhh.....eeeee.......ee.hhhhhhhhh...eeeeeee..........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh............ee...hhhhhh.....hhhhhhhhhhhhh.......eee....eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5vys B   1 MAIAPNTRVLVAGYGLPAEFCVTTLIGMGVEIDKIAVATHREDNRNSGLHSMLRLRNIQFTTAAANSEEFYEFGANFAPDMIISMHYRSLIPGRFLKLAKKGSVNLHPSLLPAYRGTNSVAWVIINGESETGFSYHRMDENFDTGAILLQERISVEETDTAFSLFHRQIARAMLRLEEVILKLDQGDPGFAQLGEASYYARELPFGGVIDPRWSEVQIDRFIRAMFFPPFPPAVLKIDGKVYYVPS 246
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
   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 5VYS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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: 5vyr 5vyt 5vyu

(-) Related Entries Specified in the PDB File

5vyr 5vyt 5vyu