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(-) Description

Title :  STRUCTURAL ANALYSIS OF COFACTOR BINDING OF A PROLYL 4-HYDROXYLASE FROM THE PATHOGENIC BACTERIUM BACILLUS ANTHRACIS
 
Authors :  N. J. Schnicker, M. Dey
Date :  28 Jan 16  (Deposition) - 04 May 16  (Release) - 18 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.63
Chains :  Asym./Biol. Unit :  A,B
Keywords :  P4H, Dioxygenase, Cupin, Fe(Ii)/Alpha-Ketoglutarate, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. J. Schnicker, M. Dey
Structural Analysis Of Cofactor Binding For A Prolyl 4-Hydroxylase From The Pathogenic Bacterium Bacillus Anthracis.
Acta Crystallogr D Struct V. 72 675 2016 Biol
PubMed-ID: 27139630  |  Reference-DOI: 10.1107/S2059798316004198

(-) Compounds

Molecule 1 - PROLYL 4-HYDROXYLASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: BACILLUS ANTHRACIS
    Organism Taxid: 1392
    Synonym: 2OG-FE(II) OXYGENASE SUPERFAMILY PROTEIN,PROLYL 4- HYDROXYLASE,ALPHA SUBUNIT DOMAIN PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 19)

Asymmetric/Biological Unit (4, 19)
No.NameCountTypeFull Name
1AKG2Ligand/Ion2-OXOGLUTARIC ACID
2CD14Ligand/IonCADMIUM ION
3GOL2Ligand/IonGLYCEROL
4K1Ligand/IonPOTASSIUM ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:127 , ASP A:129 , HIS A:193 , AKG A:310binding site for residue CD A 301
02AC2SOFTWAREGLU A:90 , HOH A:532binding site for residue CD A 302
03AC3SOFTWAREGLU A:51 , HOH A:403binding site for residue CD A 303
04AC4SOFTWAREHOH A:432 , HIS B:109 , ARG B:212 , HOH B:415 , HOH B:569binding site for residue CD A 304
05AC5SOFTWAREHIS A:18 , HOH A:414 , HOH A:550 , HOH A:565 , HOH A:586binding site for residue CD A 305
06AC6SOFTWAREGLU A:119 , GLY A:201 , ASP B:50 , ASP B:54binding site for residue CD A 306
07AC7SOFTWAREASP A:121binding site for residue CD A 307
08AC8SOFTWAREGLU A:154 , GLU B:51binding site for residue CD A 308
09AC9SOFTWAREHIS A:134 , HOH A:574 , GLU B:133 , HOH B:427binding site for residue CD A 309
10AD1SOFTWARETYR A:118 , HIS A:127 , ASP A:129 , THR A:159 , HIS A:193 , LYS A:203 , ILE A:205 , THR A:207 , TRP A:209 , CD A:301 , HOH A:437binding site for residue AKG A 310
11AD2SOFTWARETHR A:80 , SER A:82 , HIS A:114 , HOH A:551 , HOH A:576binding site for residue K A 311
12AD3SOFTWARESER A:49 , ASP A:50 , GLU A:51 , ASP A:54 , HOH A:407 , HOH A:419 , HOH A:561binding site for residue GOL A 312
13AD4SOFTWAREHIS B:127 , ASP B:129 , HIS B:193 , AKG B:306binding site for residue CD B 301
14AD5SOFTWAREHIS B:18 , HOH B:417 , HOH B:509 , HOH B:535 , HOH B:572binding site for residue CD B 302
15AD6SOFTWAREGLY B:83 , HIS B:114 , HOH B:566 , HOH B:594 , HOH B:608binding site for residue CD B 303
16AD7SOFTWAREGLU B:119 , GLU B:202 , HOH B:432binding site for residue CD B 304
17AD8SOFTWAREGLU A:133 , HOH A:409 , HIS B:134 , HOH B:574 , HOH B:606binding site for residue CD B 305
18AD9SOFTWARETYR B:118 , HIS B:127 , ASP B:129 , THR B:159 , HIS B:193 , LYS B:203 , ILE B:205 , THR B:207 , TRP B:209 , CD B:301binding site for residue AKG B 306
19AE1SOFTWAREMET A:174 , GLN B:31 , GLY B:45 , ASN B:46 , MET B:174 , HOH B:448 , HOH B:466binding site for residue GOL B 307

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5HV0)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:38 -Pro A:39
2Glu B:38 -Pro B:39

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5HV0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5HV0)

(-) Exons   (0, 0)

(no "Exon" information available for 5HV0)

(-) 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:206
                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eee....eeeeeeee....eeeee...hhhhhhhhhhhhh...................ee...hhhhhhhhhhhhhhhh.hhhhh...eeeee.....eeee.......hhhhhh.eeeeeeee.....ee..ee.....eee......eeeee....hhhhhhh..eee..eee..eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hv0 A   5 NQIKEQTIFDHKGNVIKTEDREIQIISKFEEPLIVVLGNVLSDEECDELIELSKSKLARSKVGSSNDIRTSSGAFLDDNELTAKIEKRISSIMNVPASHGEGLHILNYEVDQQYKAHYDYFAEHSRSAANNRISTLVMYLNDVEEGGETFFPKLNLSVHPRKGMAVYFEYFYQDQSLNELTLHGGAPVTKGEKWIATQWVRRGTYK 216
                              ||    17        27        37        47        57        67    ||  80        90       100       110       120       130       140       150       160       170       180       190       200       210      
                              7|                                                           72|                                                                                                                                            
                              11                                                            76                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:197
                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................eee....eeeeeeee....eeeee...hhhhhhhhhhhhhhhh..ee...hhhhhhhhhhhhhhhh.hhhhh...eeeee.....eeee........hhhhh.eeeeeeee.....ee..ee.....eee......eeeee....hhhhhhh..eee..eee..eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hv0 B   3 NNNQIGENKEQTIFDHKGNVIKTEDREIQIISKFEEPLIVVLGNVLSDEECDELIELSKSKLSGAFLDDNELTAKIEKRISSIMNVPASHGEGLHILNYEVDQQYKAHYDYFAEHSRSAANNRISTLVMYLNDVEEGGETFFPKLNLSVHPRKGMAVYFEYFYQDQSLNELTLHGGAPVTKGEKWIATQWVRRGTYK 216
                                    12        22        32        42        52        62 ||     89        99       109       119       129       139       149       159       169       179       189       199       209       
                                                                                        64|                                                                                                                                      
                                                                                         82
   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 5HV0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5HV0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5HV0)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu A:38 - Pro A:39   [ RasMol ]  
    Glu B:38 - Pro B:39   [ RasMol ]  
 

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        Q81LZ8_BACAN | Q81LZ8: 3itq 5hv4 5iat 5iav 5iax

(-) Related Entries Specified in the PDB File

5hv4