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(-) Description

Title :  PHPD WITH CADMIUM COMPLEXED WITH HYDROETHYLPHOSPHONATE (HEP)
 
Authors :  H. Zhang, S. K. Nair
Date :  19 Feb 09  (Deposition) - 09 Jun 09  (Release) - 09 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.92
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Antibiotic Biosynthesis, Iron Dependent Oxygenase, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. M. Cicchillio, H. Zhang, J. A. V. Blodgett, J. T. Whitteck, G. Li, S. K. Nair, W. A. Van Der Donk, W. W. Metcalf
An Unusual Carbon-Carbon Bond Cleavage Reaction In The Biosynthesis Of The Herbicide Phosphinothricin
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHPD
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-15
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PHPD
    Organism Scientific: STREPTOMYCES VIRIDOCHROMOGENES
    Organism Taxid: 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  (3, 19)

Asymmetric Unit (3, 19)
No.NameCountTypeFull Name
12HE1Ligand/Ion(2-HYDROXYETHYL)PHOSPHONIC ACID
2CD13Ligand/IonCADMIUM ION
3MSE5Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
12HE2Ligand/Ion(2-HYDROXYETHYL)PHOSPHONIC ACID
2CD-1Ligand/IonCADMIUM ION
3MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:16 , ARG A:90 , TYR A:98 , ASN A:126 , HIS A:129 , GLU A:176 , HIS A:182 , SER A:196 , HOH A:500 , CD A:513 , HOH A:720 , HOH A:725BINDING SITE FOR RESIDUE 2HE A 550
02AC2SOFTWARECYS A:180 , CD A:502BINDING SITE FOR RESIDUE CD A 501
03AC3SOFTWARECYS A:180 , CD A:501 , HOH A:672BINDING SITE FOR RESIDUE CD A 502
04AC4SOFTWAREASP A:189 , GLU A:368 , HIS A:397BINDING SITE FOR RESIDUE CD A 503
05AC5SOFTWAREGLU A:80 , HOH A:531 , HOH A:707BINDING SITE FOR RESIDUE CD A 504
06AC6SOFTWAREASP A:32 , ASP A:309 , HOH A:496 , HOH A:528 , HOH A:705BINDING SITE FOR RESIDUE CD A 505
07AC7SOFTWAREHIS A:94BINDING SITE FOR RESIDUE CD A 506
08AC8SOFTWAREHIS A:10 , GLU A:131 , HOH A:481 , HOH A:561 , HOH A:704BINDING SITE FOR RESIDUE CD A 507
09AC9SOFTWAREASP A:142 , HIS A:160 , HIS A:163 , HOH A:451 , HOH A:464BINDING SITE FOR RESIDUE CD A 508
10BC1SOFTWAREASP A:66 , HOH A:519BINDING SITE FOR RESIDUE CD A 509
11BC2SOFTWAREHIS A:75 , HOH A:698BINDING SITE FOR RESIDUE CD A 510
12BC3SOFTWAREHIS A:410 , HOH A:641 , HOH A:717BINDING SITE FOR RESIDUE CD A 511
13BC4SOFTWAREASP A:294 , LYS A:302 , HIS A:330BINDING SITE FOR RESIDUE CD A 512
14BC5SOFTWAREHIS A:129 , GLU A:176 , HIS A:182 , 2HE A:550 , HOH A:725BINDING SITE FOR RESIDUE CD A 513

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:139 -Pro A:140
2Thr A:399 -Gly A:400
3His A:410 -Leu A:411

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GBF)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3GBF)

(-) 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:415
 aligned with HEPD_STRVT | Q5IW40 from UniProtKB/Swiss-Prot  Length:443

    Alignment length:433
                                    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 MRIDPFKLAHWMNARKYTAAQTADLAGLPLDDLRRLLGDEANEPDPAAATALAEALSVEPSQLAADAHRNLTVVHKSAEEMHASRRPIQRDGIHFYNYYTLAAPEGRVAPVVLDILCPSDRLPALNNGHLEPAITVNLGPGDINGRWGEEITPQTWRVLHANHGGDRWITGDSYVEPSYCPHSYSLAGDAPARIVSYTAQSNISPLMTEANNWSTGAFEEALKALSGKVSAGSVLDLFLARRAHTRTSAAEAAGVPPADLEAALRSPASETGLTVLRTLGRALGFDYRVLLPADDQHDGVGKTWTTIEDSRRSRRTFGTYEAASMASAAHLPDLVGSFLRVDADGRGADLIDHAENHYVVTEGRLTLEWDGPDGPASVELEPDGSAWTGPFVRHRWHGTGTVLKFGSGAHLGYQDWLELTNTFEPAATLRRGR 433
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh.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....hhhhhhhhhh..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gbf A   1 mRIDPFKLAHWmNARKYTAAQTADLAGLPLDDLRRLL--------PAAATALAEALSVEPSQLAADAHRNLTVVHKSAEEmHASRRPIQRDGIHFYNYYTLAAPEGRVAPVVLDILCPSDRLPALNNGHLEPAITVNLGPGDINGRWGEEITPQTWRVLHANHGGDRWITGDSYVEPSYCPHSYSLAGDAPARIVSYTAQSNISPLmTEANNWSTGAFEEALKALSGKVSAGSVLDLFLARRAHTRTSAAEAAGVPPADLEAALRSPASETGLTVLRTLGRALGFDYRVLLPADDQ---VGKTWTTIEDSRRSRRTFGTYEAASmASAAHLPDLVGSFLRV-------DLIDHAENHYVVTEGRLTLEWDGPDGPASVELEPDGSAWTGPFVRHRWHGTGTVLKFGSGAHLGYQDWLELTNTFEPAATLRRGR 433
                            |       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   
                            |         12-MSE                   37       46                                 81-MSE                                                                                                                       207-MSE                                                                                  296 300                      325-MSE         341     349                                                                                    
                            1-MSE
   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 3GBF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 3rzz 4yar

(-) Related Entries Specified in the PDB File

3g7d NATIVE PHPD WITH CADMIUM ATOMS