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(-) Description

Title :  X-RAY STRUCTURE OF THE N-FORMYLTRANSFERASE QDTF FROM PROVIDENCIA ALCALIFACIENS, W305A MUTANT, IN THE PRESENCE OF TDP-QUI3N AND N5-THF
 
Authors :  J. B. Thoden, C. R. Woodford, H. M. Holden
Date :  18 Dec 14  (Deposition) - 21 Jan 15  (Release) - 11 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Formyltransferase, Ankyrin Repeat, Lipopolysaccharide, Deoxy Sugar, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. R. Woodford, J. B. Thoden, H. M. Holden
New Role For The Ankyrin Repeat Revealed By A Study Of The N-Formyltransferase From Providencia Alcalifaciens.
Biochemistry V. 54 631 2015
PubMed-ID: 25574689  |  Reference-DOI: 10.1021/BI501539A

(-) Compounds

Molecule 1 - TDP-3-AMINOQUINOVOSE-N-FORMYLTRANSFERASE
    Chains: A
    EC Number: 2.1.2.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PJ411
    Expression System Strain: ROSETTA2(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: QDTF
    Mutation: YES
    Organism Scientific: PROVIDENCIA ALCALIFACIENS
    Organism Taxid: 126385

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 15)

Asymmetric Unit (6, 15)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2EDO5Ligand/Ion1,2-ETHANEDIOL
3FON1Ligand/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
4K1Ligand/IonPOTASSIUM ION
5NA4Ligand/IonSODIUM ION
6T3Q1Ligand/Ion[(3R,4S,5S,6R)-4-AMINO-3,5-DIHYDROXY-6-METHYLOXAN-2-YL][HYDROXY-[[(2R,3S,5R)-3-HYDROXY-5-(5-METHYL-2,4-DIOXOPYRIMIDIN-1-YL)OXOLAN-2-YL]METHOXY]PHOSPHORYL]HYDROGEN PHOSPHATE
Biological Unit 1 (3, 14)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO10Ligand/Ion1,2-ETHANEDIOL
3FON2Ligand/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
4K-1Ligand/IonPOTASSIUM ION
5NA-1Ligand/IonSODIUM ION
6T3Q2Ligand/Ion[(3R,4S,5S,6R)-4-AMINO-3,5-DIHYDROXY-6-METHYLOXAN-2-YL][HYDROXY-[[(2R,3S,5R)-3-HYDROXY-5-(5-METHYL-2,4-DIOXOPYRIMIDIN-1-YL)OXOLAN-2-YL]METHOXY]PHOSPHORYL]HYDROGEN PHOSPHATE

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:76 , ASP A:77 , LYS A:78 , ILE A:79 , ILE A:80 , ASP A:126 , HIS A:127 , GLY A:128 , ILE A:129 , ASP A:130 , TYR A:187 , SER A:189 , LYS A:190 , T3Q A:402 , HOH A:501 , HOH A:721 , HOH A:723 , HOH A:926binding site for residue FON A 401
02AC2SOFTWARELYS A:8 , GLU A:75 , PHE A:76 , GLY A:103 , MET A:104 , TYR A:105 , THR A:106 , SER A:107 , TYR A:152 , TYR A:195 , PHE A:218 , TYR A:221 , GLN A:222 , FON A:401 , HOH A:606 , HOH A:717 , HOH A:718 , HOH A:719 , HOH A:720 , HOH A:721 , HOH A:722 , HOH A:806 , HOH A:809 , HOH A:905 , HOH A:964 , HOH A:965binding site for residue T3Q A 402
03AC3SOFTWAREASN A:39 , SER A:41 , GLN A:43 , HOH A:713 , HOH A:716 , HOH A:971binding site for residue NA A 403
04AC4SOFTWAREILE A:135 , SER A:176 , HOH A:578 , HOH A:630 , HOH A:748binding site for residue NA A 404
05AC5SOFTWARETYR A:105 , LYS A:190 , ILE A:193 , HOH A:644 , HOH A:798 , HOH A:805binding site for residue NA A 405
06AC6SOFTWARESER A:241 , SER A:259 , THR A:260 , HOH A:576 , HOH A:706 , HOH A:1045binding site for residue K A 406
07AC7SOFTWARESER A:288 , LEU A:291 , HOH A:610 , HOH A:643 , HOH A:693binding site for residue NA A 407
08AC8SOFTWARELYS A:149 , PHE A:298 , GLU A:299 , HOH A:732 , HOH A:735 , HOH A:975binding site for residue EDO A 408
09AC9SOFTWAREPRO A:99 , GLU A:179 , SER A:181 , LYS A:289 , HOH A:532 , HOH A:681 , HOH A:794binding site for residue EDO A 409
10AD1SOFTWARETYR A:254 , ASN A:271 , LEU A:290 , LYS A:292 , HOH A:567 , HOH A:705 , HOH A:838 , HOH A:1012binding site for residue EDO A 410
11AD2SOFTWAREILE A:26 , LEU A:28 , PRO A:56binding site for residue EDO A 411
12AD3SOFTWARETRP A:109 , TYR A:188 , SER A:192 , LYS A:204 , HOH A:505 , HOH A:521 , HOH A:558 , HOH A:823binding site for residue EDO A 412
13AD4SOFTWAREILE A:387 , GLU A:388binding site for residue CL A 413
14AD5SOFTWARELYS A:345 , MET A:381 , ASN A:384 , ASN A:386 , HOH A:903binding site for residue CL A 414
15AD6SOFTWARELYS A:8 , ASN A:33 , HOH A:963binding site for residue CL A 415

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4XD1)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu A:98 -Pro A:99

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XD1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XD1)

(-) Exons   (0, 0)

(no "Exon" information available for 4XD1)

(-) 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:397
                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeehhhhhhhhhhhhhhhh...eeeeee............hhhhhhhhh.....hhhhhhhh..eeeeee......hhhhh....eeeee.......ee....hhhhhh...eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.............eehhhhh...........hhhhhhhhhhhh........ee..eeeeeeee...........eeee...eeee......eeeee.hhhhhhhhhh..hhhhhhhhh.hhhhhhh......hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhhhhhhh...hhhhhhhh............hhhhhhhhh.hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xd1 A   1 MKLIIAGKNNIAVDVTKWIIKTISDIELYSVCNENDHGNDSFQLSFKKFCIQFNIPIISLEDAYHLEDAIFLSLEFDKIIHPSKFTHNRIFNIHFSYLPAYKGMYTSAWPILNNEQESGVTLHKIDHGIDTGAIIDQQKFPLDIEETAKTLYLKYIKIGTEIVIKNLPALISGNYSIVEQSAIKSSYYSKKSIDYKNLMIDLNKTAHEILQQIRAFTFRDYQLPRIDDIDIFHGEILSSKSLSKPGTILEKNNYHLILSTIDYDIKLYSDNFDEILTACEDKSPEFISKLLKTENILFEKNHLGASPIIIAAYHGNMDVIEWLVSKGVNINDRNYKGTTVAMYFKDYMLRSGNYTGLENLINLGLDLFLKDNEGLSVFDYMRKNKNIELFNFMSTFN 397
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390
   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 4XD1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XD1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XD1)

(-) Gene Ontology  (3, 3)

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4xcz 4xd0