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(-) Description

Title :  CRYSTAL STRUCTURE OF N-TERMINALLY TAGGED APO-UBID FROM E. COLI
 
Authors :  S. A. Marshall, D. Leys
Date :  07 Oct 16  (Deposition) - 11 Jan 17  (Release) - 29 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Ubid, Decarboxylase, Ubiquinone Biosynthesis, Prfmn Binding, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. A. Marshall, K. Fisher, A. Ni Cheallaigh, M. D. White, K. A. Payne, D. A. Parker, S. E. Rigby, D. Leys
Oxidative Maturation And Structural Characterization Of Prenylated Fmn Binding By Ubid, A Decarboxylase Involved In Bacterial Ubiquinone Biosynthesis.
J. Biol. Chem. V. 292 4623 2017
PubMed-ID: 28057757  |  Reference-DOI: 10.1074/JBC.M116.762732

(-) Compounds

Molecule 1 - 3-OCTAPRENYL-4-HYDROXYBENZOATE CARBOXY-LYASE
    Chains: A, B, C
    EC Number: 4.1.1.98
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: UBID, C4790
    Organism Taxid: 199310
    Strain: CFT073 / ATCC 700928 / UPEC
    Synonym: POLYPRENYL P-HYDROXYBENZOATE DECARBOXYLASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1PG41Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1PG42Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR B:160 , ILE B:178 , HIS B:291 , PRO B:329binding site for residue PG4 B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5M1C)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Gly A:286 -Pro A:287
2Pro A:325 -Pro A:326
3Gly B:286 -Pro B:287
4Pro B:325 -Pro B:326
5Pro C:325 -Pro C:326

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5M1C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5M1C)

(-) Exons   (0, 0)

(no "Exon" information available for 5M1C)

(-) 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:437
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh..eeee.......hhhhhhhhhhhhh...eeee.........eee....hhhhhhhhh......hhhhhhh..eee..hhhhheeee.hhhhhhhh............ee...eeee..eee...eeeee..eee......hhhhhhhhhhhhhh....eeeeeee..hhhhhhh............eeee......eee....eeeeeeeeeeeeeee..ee.....ee..eeeeeeeeeeeee.....ee........hhhhhhhhhhhh.hhhhhhhhh..eeeee.hhhhh...eeeeee.....hhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhhheeeeeeee............eeeeeeee...................hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5m1c A   8 DLRDFLTLLEQQGELKRITLPVDPHLEITEIADRTLRAGGPALLFENPKGYSMPVLCNLFGTPKRVAMGMGQEDVSALREVGKPTKRLRGAPCQQKIVSGDDVDLNRIPIMTCWPEDAAPLITWGLTVTRQNLGIYRQQLIGKNKLIMRWLSHRGGALDYQEWCAAHPGERFPVSVALGADPATILGAVTAGLLRGTKTEVVKCISNDLEVPASAEIVLEGYIEQGETAPEGPYGDHTGYYNEVDSFPVFTVTHITQREDAIYHSTYTGRPPDEPAVLGVALNEVFVPILQKQFPEIVDFYLPPEGCSYRLAVVTIKKQYAGHAKRVMMGVWSFLRQFMYTKFVIVCDDDVNARDWNDVIWAITTRMDPARDTVLVENTPIDYLDFASPVSGLGSKMGLDATNKWPGETQREWGRPIKKDPDVVAHIDAIWDELAIF 491
                                    17        27        37        47        57        67        77        87  ||   127       137       147       157       173       183       193       203       213       223       233|      254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       
                                                                                                             90|                                          166|                                                         233|                                                                                                                                                                                                                                                      
                                                                                                             121                                           173                                                          245                                                                                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:460
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..eeee.......hhhhhhhhhhhhh...eeee.........eee....hhhhhhhhh...hhhhhhhhhhhhhhh...ee...hhhhheeee.hhhhhhhh............ee...eeeee......eeee...eeeee..eee......hhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhh......hhhhhhhhhh....eeee......eee....eeeeeeeeeeeeeee..ee.....ee..eeeeeeeeeeeee.....ee........hhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh...eeeeee.....hhhhhhhhhhh..hhhhh...eeeeee......hhhhhhhhhhhhhhhhhheeeeeeee............eeeeeeee...................hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5m1c B   7 NDLRDFLTLLEQQGELKRITLPVDPHLEITEIADRTLRAGGPALLFENPKGYSMPVLCNLFGTPKRVAMGMGQEDVSALREVGKLLAFLKPTKRLRGAPCQQKIVSGDDVDLNRIPIMTCWPEDAAPLITWGLTVTRGPHKERQNLGIYRQQLIGKNKLIMRWLSHRGGALDYQEWCAAHPGERFPVSVALGADPATILGAVTPVPDTLSEYAFAGLLRGTKTEVVKCISNDLEVPASAEIVLEGYIEQGETAPEGPYGDHTGYYNEVDSFPVFTVTHITQREDAIYHSTYTGRPPDEPAVLGVALNEVFVPILQKQFPEIVDFYLPPEGCSYRLAVVTIKKQYAGHAKRVMMGVWSFLRQFMYTKFVIVCDDDVNARDWNDVIWAITTRMDPARDTVLVENTPIDYLDFASPVSGLGSKMGLDATNKWPGETQREWGRPIKKDPDVVAHIDAIWDELAI 490
                                    16        26        36        46        56        66        76        86        96|      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       400       410       420       430       440       450       460       470       480       490
                                                                                                                    96|                                                                                                                                                                                                                                                                                                                                                                                 
                                                                                                                    121                                                                                                                                                                                                                                                                                                                                                                                 


Chain C from PDB  Type:PROTEIN  Length:448
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..eeee.......hhhhhhhhhhhhh...eeee.........eee....hhhhhhhhh...hhhhhhhhhhhhhhh.hhhhheeee.hhhhhhhh............ee...eeeee......eeee...eeeee..eee......hhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhh...hhhhhhh.....eee......eee....eeeeeeeeeeeeeee..ee.....ee..eeeeeeeeeeeee.....ee........hhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh...eeeeee.....hhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhhheeeeeeee............eeeeeeee...................hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5m1c C   7 NDLRDFLTLLEQQGELKRITLPVDPHLEITEIADRTLRAGGPALLFENPKGYSMPVLCNLFGTPKRVAMGMGQEDVSALREVGKLLAFLGAPCQQKIVSGDDVDLNRIPIMTCWPEDAAPLITWGLTVTRGPHKERQNLGIYRQQLIGKNKLIMRWLSHRGGALDYQEWCAAHPGERFPVSVALGADPATILGAVTPVYAFAGLLRGTKTEVVKCISNDLEVPASAEIVLEGYIEQGETAPEGPYGDHTGYYNEVDSFPVFTVTHITQREDAIYHSTYTGRPPDEPAVLGVALNEVFVPILQKQFPEIVDFYLPPEGCSYRLAVVTIKKQYAGHAKRVMMGVWSFLRQFMYTKFVIVCDDDVNARDWNDVIWAITTRMDPARDTVLVENTPIDYLDFASPVSGLGSKMGLDATNKWPGETQREWGRPIKKDPDVVAHIDAIWDELAIF 491
                                    16        26        36        46        56        66        76        86       127       137       147       157       167       177       187       197       207       217       227       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483        
                                                                                                                   95|                                                                                                         235|                                                                                                                                                                                                                                                         
                                                                                                                   127                                                                                                          242
   Legend:   → Mismatch (orange background)
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    → 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 5M1C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5M1C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5M1C)

(-) Gene Ontology  (12, 22)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
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    Pro A:325 - Pro A:326   [ RasMol ]  
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  5m1c
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  UBID_ECOL6 | P0AAB5
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  UBID_ECOLI | P0AAB4
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 Related Entries

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

UniProtKB/Swiss-Prot
        UBID_ECOL6 | P0AAB5: 5m1b 5m1d 5m1e
        UBID_ECOLI | P0AAB4: 2idb 5m1b 5m1d 5m1e

(-) Related Entries Specified in the PDB File

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