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(-) Description

Title :  STRUCTURE OF HYDROXYETHYLPHOSHPHONATE DIOXYGENASE Y98F MUTANT
 
Authors :  H. A. Cooke
Date :  12 May 11  (Deposition) - 20 Jul 11  (Release) - 23 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Non Heme Fe(Ii) Dioxygenase, Cupin, Biosynthetic Protein, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. C. Peck, H. A. Cooke, R. M. Cicchillo, P. Malova, F. Hammerschmidt, S. K. Nair, W. A. Van Der Donk
Mechanism And Substrate Recognition Of 2-Hydroxyethylphosphonate Dioxygenase.
Biochemistry V. 50 6598 2011
PubMed-ID: 21711001  |  Reference-DOI: 10.1021/BI200804R

(-) Compounds

Molecule 1 - HYDROXYETHYLPHOSHPHONATE DIOXYGENASE (PHPD)
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-15B
    Expression System Strain: ROSETTA 2(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PHPD
    Mutation: YES
    Organism Scientific: STREPTOMYCES VIRIDOCHROMOGENES
    Organism Taxid: 1938
    Strain: 1938

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 15)

Asymmetric Unit (1, 15)
No.NameCountTypeFull Name
1CD15Ligand/IonCADMIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:129 , GLU A:176 , HIS A:182 , HOH A:555 , HOH A:563 , HOH A:574BINDING SITE FOR RESIDUE CD A 444
02AC2SOFTWAREHIS A:10 , GLU A:131 , HOH A:579 , HOH A:637 , HOH A:638BINDING SITE FOR RESIDUE CD A 445
03AC3SOFTWAREASP A:142 , HIS A:160 , HIS A:163 , HOH A:517 , HOH A:558 , HOH A:639BINDING SITE FOR RESIDUE CD A 446
04AC4SOFTWAREHIS A:82 , HOH A:470 , HOH A:568 , HOH A:586 , HOH A:617 , HOH A:678BINDING SITE FOR RESIDUE CD A 447
05AC5SOFTWAREGLN A:296 , LYS A:302 , HIS A:330 , HOH A:567 , HOH A:679BINDING SITE FOR RESIDUE CD A 448
06AC6SOFTWARECYS A:180 , ASP A:298 , HOH A:577 , HOH A:580 , HOH A:629BINDING SITE FOR RESIDUE CD A 449
07AC7SOFTWAREARG A:340 , ASP A:342 , HOH A:698BINDING SITE FOR RESIDUE CD A 450
08AC8SOFTWAREGLU A:80 , HOH A:578 , HOH A:644BINDING SITE FOR RESIDUE CD A 451
09AC9SOFTWAREASP A:66 , HOH A:561 , HOH A:640 , HOH A:695BINDING SITE FOR RESIDUE CD A 452
10BC1SOFTWAREHIS A:75 , HOH A:536 , HOH A:687BINDING SITE FOR RESIDUE CD A 453
11BC2SOFTWAREHIS A:94 , ARG A:265 , HOH A:684 , HOH A:688BINDING SITE FOR RESIDUE CD A 454
12BC3SOFTWAREGLU A:209 , HIS A:410 , HOH A:616 , HOH A:669BINDING SITE FOR RESIDUE CD A 455
13BC4SOFTWAREASP A:32 , ASP A:309 , HOH A:565 , HOH A:681BINDING SITE FOR RESIDUE CD A 456
14BC5SOFTWARECYS A:180 , HOH A:593BINDING SITE FOR RESIDUE CD A 457
15BC6SOFTWAREASP A:189 , GLU A:368 , HIS A:397 , HOH A:582 , HOH A:653BINDING SITE FOR RESIDUE CD A 458

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3RZZ)

(-) 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 3RZZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3RZZ)

(-) Exons   (0, 0)

(no "Exon" information available for 3RZZ)

(-) 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:421
 aligned with HEPD_STRVT | Q5IW40 from UniProtKB/Swiss-Prot  Length:443

    Alignment length:434
                                    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       400       410       420       430    
           HEPD_STRVT     1 MRIDPFKLAHWMNARKYTAAQTADLAGLPLDDLRRLLGDEANEPDPAAATALAEALSVEPSQLAADAHRNLTVVHKSAEEMHASRRPIQRDGIHFYNYYTLAAPEGRVAPVVLDILCPSDRLPALNNGHLEPAITVNLGPGDINGRWGEEITPQTWRVLHANHGGDRWITGDSYVEPSYCPHSYSLAGDAPARIVSYTAQSNISPLMTEANNWSTGAFEEALKALSGKVSAGSVLDLFLARRAHTRTSAAEAAGVPPADLEAALRSPASETGLTVLRTLGRALGFDYRVLLPADDQHDGVGKTWTTIEDSRRSRRTFGTYEAASMASAAHLPDLVGSFLRVDADGRGADLIDHAENHYVVTEGRLTLEWDGPDGPASVELEPDGSAWTGPFVRHRWHGTGTVLKFGSGAHLGYQDWLELTNTFEPAATLRRGRR 434
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhh.-------hhhhhhhhhhh..hhhhh.........eeeehhhhhhhh.eeeee..eeeeeeee..........eeeee.................eeeeeeee..eeee.........eeee.............eeee......eeee.....eeeeeee....hhhhhhhhh..hhhhhhhhhhhhh...hhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhh..............hhhhhhhh.eee..eeeee..........eeeeeee.------......eeeeeeee..eeeeeee..eeeeeee....eeee.....eeee..eeeeeeee....hhhhhhhhh...hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rzz A   1 MRIDPFKLAHWMNARKYTAAQTADLAGLPLDDLRRLLG-------PAAATALAEALSVEPSQLAADAHRNLTVVHKSAEEMHASRRPIQRDGIHFYNFYTLAAPEGRVAPVVLDILCPSDRLPALNNGHLEPAITVNLGPGDINGRWGEEITPQTWRVLHANHGGDRWITGDSYVEPSYCPHSYSLAGDAPARIVSYTAQSNISPLMTEANNWSTGAFEEALKALSGKVSAGSVLDLFLARRAHTRTSAAEAAGVPPADLEAALRSPASETGLTVLRTLGRALGFDYRVLLPADDQHDGVGKTWTTIEDSRRSRRTFGTYEAASMASAAHLPDLVGSFLRVD------DLIDHAENHYVVTEGRLTLEWDGPDGPASVELEPDGSAWTGPFVRHRWHGTGTVLKFGSGAHLGYQDWLELTNTFEPAATLRRGRR 434
                                    10        20        30       | -     |  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       400       410       420       430    
                                                                38      46                                                                                                                                                                                                                                                                                                     342    349
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 3RZZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3RZZ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3RZZ)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (HEPD_STRVT | Q5IW40)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0051213    dioxygenase activity    Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
    GO:0008198    ferrous iron binding    Interacting selectively and non-covalently with ferrous iron, Fe(II).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016702    oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from one donor, and two oxygen atoms is incorporated into a donor.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
biological process
    GO:0032923    organic phosphonate biosynthetic process    The chemical reactions and pathways resulting in the formation of phosphonates, any organic compound containing one or more C-PO(OH)2 or C-PO(OR)2 (with R=alkyl, aryl) groups. Synthesis of phosphonic acid itself, an inorganic compound without the biochemically relevant C-P bond, is not included.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:1901766    phosphinothricin biosynthetic process    The chemical reactions and pathways resulting in the formation of phosphinothricin.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HEPD_STRVT | Q5IW40: 3g7d 3gbf 4yar

(-) Related Entries Specified in the PDB File

3g7d NATIVE PHPD WITH CADMIUM ATOMS
3gbf PHPD WITH CADMIUM COMPLEXED WITH HYDROETHYLPHOSPHONATE (HEP)