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(-) Description

Title :  2-HYDROXYETHYLPHOSPHONATE DIOXYGENASE (HEPD) E176H
 
Authors :  J. R. Chekan, S. K. Nair
Date :  17 Feb 15  (Deposition) - 04 Mar 15  (Release) - 25 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Dioxygenase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. C. Peck, J. R. Chekan, E. C. Ulrich, S. K. Nair, W. A. Van Der Donk
A Common Late-Stage Intermediate In Catalysis By 2-Hydroxyethyl-Phosphonate Dioxygenase And Methylphosphonat Synthase.
J. Am. Chem. Soc. V. 137 3217 2015
PubMed-ID: 25699631  |  Reference-DOI: 10.1021/JACS.5B00282

(-) Compounds

Molecule 1 - 2-HYDROXYETHYLPHOSPHONATE DIOXYGENASE
    Chains: A
    EC Number: 1.13.11.72
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: HEPD, PHPD, SSQG_01041
    Mutation: YES
    Organism Scientific: STREPTOMYCES VIRIDOCHROMOGENES
    Organism Taxid: 1938
    Synonym: HYDROXYETHYLPHOSPHONATE DIOXYGENASE,PHOSPHINOTHRICIN TRIPEPTIDE BIOSYNTHESIS PROTEIN D

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CD10Ligand/IonCADMIUM ION
3NA1Ligand/IonSODIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CD-1Ligand/IonCADMIUM ION
3NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2CD-1Ligand/IonCADMIUM ION
3NA-1Ligand/IonSODIUM ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:129 , HIS A:176 , HIS A:182 , HOH A:695 , HOH A:696 , HOH A:697 , HOH A:728binding site for residue CD A 501
02AC2SOFTWAREASP A:66 , ARG A:107binding site for residue CD A 502
03AC3SOFTWAREHIS A:75binding site for residue CD A 503
04AC4SOFTWAREHIS A:10 , GLU A:131 , ACT A:512 , HOH A:604 , HOH A:638binding site for residue CD A 504
05AC5SOFTWAREASP A:32 , ASP A:309 , HOH A:601 , HOH A:611 , HOH A:624 , HOH A:641binding site for residue CD A 505
06AC6SOFTWAREHIS A:94 , HOH A:670 , HOH A:705 , HOH A:711binding site for residue CD A 506
07AC7SOFTWAREASP A:142 , HIS A:160 , HIS A:163 , ACT A:513 , HOH A:803binding site for residue CD A 507
08AC8SOFTWAREASP A:189 , CD A:510binding site for residue CD A 508
09AC9SOFTWAREGLU A:80 , HOH A:802binding site for residue CD A 509
10AD1SOFTWAREASP A:189 , GLU A:368 , HIS A:397 , CD A:508binding site for residue CD A 510
11AD2SOFTWAREGLN A:296 , HIS A:330 , HOH A:605 , HOH A:702 , HOH A:783 , HOH A:806binding site for residue NA A 511
12AD3SOFTWAREHIS A:10 , ASN A:13 , LEU A:130 , GLU A:131 , TYR A:179 , CD A:504 , HOH A:604binding site for residue ACT A 512
13AD4SOFTWAREASP A:142 , HIS A:160 , HIS A:163 , ASP A:373 , CD A:507 , HOH A:803binding site for residue ACT A 513

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:139 -Pro A:140
2His A:410 -Leu A:411

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YAR)

(-) 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:429
                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhh..........hhhhhhhhh..hhhhh.........eeeehhhhhhh..eeeee..eeeeeeee..........eeeee.................eeeeeeee..eeee.........eeee.............eeee......eeee.....eeeeeee....hhhhhhhhh..hhhhhhhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhh..............hhhhhhhh.eee..eeeee..........eeeeeeeee...........eeeeeeee..eeeeeee..eeeeeee....eeee.....eeeeeeeeeeeeee....hhhhhhhhhh..hhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yar A   3 IDPFKLAHWMNARKYTAAQTADLAGLPLDDLRRLLGDEANEPDPAAATALAEALSVEPSQLAADAHRNLTVVHKSAEEMHASRRPIQRDGIHFYNYYTLAAPEGRVAPVVLDILCPSDRLPALNNGHLEPAITVNLGPGDINGRWGEEITPQTWRVLHANHGGDRWITGDSYVHPSYCPHSYSLAGDAPARIVSYTAQSNISPLMTEANNWSTGAFEEALKALSGKVSAGSVLDLFLARRAHTRTSAAEAAGVPPADLEAALRSPASETGLTVLRTLGRALGFDYRVLLPADDQHDGVGKTWTTIEDSRRSRRTFGTYEAASMASAAHLPDLVGSFLRVDADGRGADLIDHAENHYVVTEGRLTLEWDGPDGPASVELEPDGSAWTGPFVRHRWHGTGTVLKFGSGAHLGYQDWLELTNTFEPAATLRR 431
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422
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  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 4YAR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly A:139 - Pro A:140   [ RasMol ]  
    His A:410 - Leu A:411   [ RasMol ]  
 
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  4yar
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 Related Entries

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        HEPD_STRVT | Q5IW40: 3g7d 3gbf 3rzz

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