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(-) Description

Title :  CRYSTAL STRUCTURE OF THE N-FORMYLTRANSFERASE RV3404C FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH YDP-QUI4N AND FOLINIC ACID
 
Authors :  M. M. Dunsirn, J. B. Thoden, H. M. Holden
Date :  26 May 17  (Deposition) - 12 Jul 17  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Formyltransferase, Deoxysugar, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. M. Dunsirn, J. B. Thoden, M. Gilbert, H. M. Holden
Biochemical Investigation Of Rv3404C From Mycobacterium Tuberculosis.
Biochemistry 2017
PubMed-ID: 28665588  |  Reference-DOI: 10.1021/ACS.BIOCHEM.7B00506

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: ROSETTA2(DE3)
    Expression System Taxid: 562
    Gene: J113_23825
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS CAS/NITR204
    Organism Taxid: 1310114

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (9, 18)

Asymmetric/Biological Unit (9, 18)
No.NameCountTypeFull Name
10FX1Ligand/IonDTDP-4-AMINO-4,6-DIDEOXYGLUCOSE
2CL3Ligand/IonCHLORIDE ION
3EDO4Ligand/Ion1,2-ETHANEDIOL
4EP12Ligand/Ion3-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]PROPANE-1-SULFONICACID
5FON1Ligand/IonN-{[4-({[(6R)-2-AMINO-5-FORMYL-4-OXO-1,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)PHENYL]CARBONYL}-L-GLUTAMIC ACID
6K1Ligand/IonPOTASSIUM ION
7LI1Ligand/IonLITHIUM ION
8NA4Ligand/IonSODIUM ION
9TYD1Ligand/IonTHYMIDINE-5'-DIPHOSPHATE

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:64 , GLN A:66 , ARG A:67 , PHE A:68 , ASN A:80 , TRP A:92 , ILE A:112 , ASP A:113 , GLN A:115 , LEU A:116 , ASP A:117 , LEU A:175 , LYS A:176 , 0FX A:302 , LI A:311 , HOH A:414 , HOH A:425 , HOH A:512binding site for residue FON A 301
02AC2SOFTWAREASN A:10 , HIS A:63 , CYS A:64 , LYS A:65 , HIS A:82 , GLY A:91 , PHE A:93 , GLN A:95 , TYR A:139 , HIS A:205 , PHE A:208 , ASN A:210 , FON A:301 , LI A:311 , HOH A:425 , HOH A:433 , HOH A:477 , HOH A:486 , HOH A:489 , HOH A:500binding site for residue 0FX A 302
03AC3SOFTWARESER A:131 , GLY A:194 , ASN A:198 , ARG A:201 , HOH A:430 , HOH A:479 , PHE B:213binding site for residue EDO A 303
04AC4SOFTWAREVAL A:225 , VAL A:226 , LEU A:227 , HOH A:488 , HOH A:514binding site for residue EDO A 304
05AC5SOFTWAREVAL A:53 , TYR A:56 , HOH A:434 , HOH A:480 , HOH A:615binding site for residue NA A 305
06AC6SOFTWAREMET A:1 , THR A:3 , ASP A:57 , HOH A:614 , HOH A:625 , HOH A:630binding site for residue NA A 306
07AC7SOFTWARESER A:134 , GLY A:136 , ASP A:206 , HOH A:567 , HOH A:649binding site for residue CL A 307
08AC8SOFTWAREASP A:206 , ASP A:207 , PHE A:208 , ARG A:209 , HOH A:432 , HOH A:473binding site for residue EP1 A 308
09AC9SOFTWAREARG A:190 , SER A:217 , GLY B:191 , HOH B:622 , HOH B:657binding site for residue CL A 309
10AD1SOFTWARETYR A:30binding site for residue NA A 310
11AD2SOFTWAREASN A:80 , HIS A:82 , ASP A:117 , FON A:301 , 0FX A:302 , HOH A:425binding site for residue LI A 311
12AD3SOFTWAREASN B:10 , HIS B:63 , LYS B:65 , PHE B:93 , GLN B:95 , TYR B:139 , HIS B:205 , PHE B:208 , ASN B:210 , HOH B:414 , HOH B:415 , HOH B:418 , HOH B:424 , HOH B:455 , HOH B:457 , HOH B:558binding site for residue TYD B 301
13AD4SOFTWAREPHE A:213 , SER B:131 , GLY B:194 , ASN B:198 , ARG B:201 , HOH B:412 , HOH B:500binding site for residue EDO B 302
14AD5SOFTWARECYS B:64 , HIS B:110 , GLN B:115 , LEU B:116 , ASP B:117 , HOH B:512 , HOH B:530binding site for residue EDO B 303
15AD6SOFTWARESER B:134 , GLY B:136 , ASP B:206 , HOH B:626 , HOH B:649binding site for residue CL B 304
16AD7SOFTWAREASP B:206 , ASP B:207 , PHE B:208 , ARG B:209 , HOH B:464 , HOH B:565binding site for residue EP1 B 305
17AD8SOFTWAREVAL B:53 , TYR B:56 , HOH B:422 , HOH B:535 , HOH B:586 , HOH B:619binding site for residue NA B 306
18AD9SOFTWAREGLU A:111 , HOH A:648 , HOH A:658 , ASP B:74 , HOH B:470 , HOH B:538 , HOH B:553binding site for residue K B 307

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asn A:86 -Pro A:87
2Asn B:86 -Pro B:87

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5VYQ)

(-) 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:235
                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.eeeee.hhhhhhhhhhhhhhh..eeee.............hhhhhhhhhhhhh.eeeee......hhhhhhhheeeeee.......ee.hhhhhhhhhh..eeeeeee.........eeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhh............eehhhhhhhhhh.....eeehhhhhhhhhhh.......eeee.....eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vyq A  -2 QGHMVTILILTDNVHAHALAVDLQARHGDMDVYQSPIGQLPGVPRCDVAERVAEIVERYDLVLSFHCKQRFPAALIDGVRCVNVHPGFNPYNRGWFPQVFSIIDGQKVGVTIHEIDDQLDHGPIIAQRECAIESWDSSGSVYARLMDIERELVLEHFDAIRDGSYTAKSPATEGNLNLKKDFEQLRRLDLNERGTFGHFLNRLRALTHDDFRNAWFVDASGRKVFVRVVLEPEKP 232
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227     


Chain B from PDB  Type:PROTEIN  Length:234
                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee.hhhhhhhhhhhhhhhh.eeee.............hhhhhhhhhhhhh.eeeee......hhhhhhhheeeeee.......ee.hhhhhhhhhh..eeeeeee.........eeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhh............eehhhhhhhhhh.....eeehhhhhhhhhhh.......eeee.....eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5vyq B  -2 QGHMVTILILTDNVHAHALAVDLQARHGDMDVYQSPIGQLPGVPRCDVAERVAEIVERYDLVLSFHCKQRFPAALIDGVRCVNVHPGFNPYNRGWFPQVFSIIDGQKVGVTIHEIDDQLDHGPIIAQRECAIESWDSSGSVYARLMDIERELVLEHFDAIRDGSYTAKSPATEGNLNLKKDFEQLRRLDLNERGTFGHFLNRLRALTHDDFRNAWFVDASGRKVFVRVVLEPEK 231
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227
   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 5VYQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5VYQ)

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 Related Entries

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(-) Related Entries Specified in the PDB File

5vyr 5vys 5vyt 5vyu