3P41 - JenaLib

Title :   CRYSTAL STRUCTURE OF POLYPRENYL SYNTHETASE FROM PSEUDOMONAS FLUORESCENS PF-5 COMPLEXED WITH MAGNESIUM AND ISOPRENYL PYROPHOSPHATE

Authors :   Y. Patskovsky, R. Toro, J. M. Sauder, S. K. Burley, C. D. Poulter, J. A. Ge S. C. Almo, New York Sgx Research Center For Structural Genomi (Nysgxrc)

Date :   05 Oct 10 (Deposition) - 20 Oct 10 (Release) - 08 May 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.76

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Structural Genomics, Protein Structure Initiative, New York Structural Genomix Research Consortium, Nysgxrc, Isoprene Biosynthesis, Transferase, Psi-2, New York Sgx Research Center For Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. H. Wallrapp, J. J. Pan, G. Ramamoorthy, D. E. Almonacid, B. S. Hillerich, R. Seidel, Y. Patskovsky, P. C. Babbitt, S. C. Almo, M. P. Jacobson, C. D. Poulter
Prediction Of Function For The Polyprenyl Transferase Subgroup In The Isoprenoid Synthase Superfamily.
Proc. Natl. Acad. Sci. Usa V. 110 E1196 2013
PubMed-ID: 23493556 | Reference-DOI: 10.1073/PNAS.1300632110

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (7, 16)

Sites (8, 8)

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:223 , POP A:301 , HOH A:338 , HOH A:360 , HOH A:375 , HOH A:380	BINDING SITE FOR RESIDUE MG A 296
2	AC2	SOFTWARE	ASP A:83 , ASP A:89 , MG A:298 , DMA A:300 , HOH A:304 , HOH A:383 , HOH A:384	BINDING SITE FOR RESIDUE MG A 297
3	AC3	SOFTWARE	ASP A:83 , ASP A:89 , MG A:297 , DMA A:300 , HOH A:381 , HOH A:382	BINDING SITE FOR RESIDUE MG A 298
4	AC4	SOFTWARE	LYS A:44 , ARG A:45 , VAL A:46 , ARG A:47 , HIS A:76 , ARG A:95 , ILE A:185 , PHE A:218 , ILE A:290 , HOH A:305 , HOH A:306 , HOH A:313 , HOH A:387 , HOH A:389	BINDING SITE FOR RESIDUE DMA A 299
5	AC5	SOFTWARE	SER A:79 , ASP A:83 , ASP A:89 , ARG A:94 , GLN A:157 , LYS A:180 , MG A:297 , MG A:298 , POP A:301 , HOH A:311 , HOH A:381 , HOH A:382 , HOH A:385	BINDING SITE FOR RESIDUE DMA A 300
6	AC6	SOFTWARE	ASP A:160 , MSE A:176 , HIS A:177 , LYS A:180 , MG A:296 , DMA A:300 , HOH A:311 , HOH A:375	BINDING SITE FOR RESIDUE POP A 301
7	AC7	SOFTWARE	ASP A:90 , ASP A:91 , ASP A:92 , LEU A:93 , GLY A:197 , ARG A:198 , HOH A:371	BINDING SITE FOR RESIDUE GOL A 302
8	AC8	SOFTWARE	ALA A:23 , ARG A:36 , LYS A:61 , HOH A:431	BINDING SITE FOR RESIDUE CL A 303

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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:283
 aligned with Q4K5A6_PSEF5 | Q4K5A6 from UniProtKB/TrEMBL  Length:295

    Alignment length:296
                               1                                                                                                                                                                                                                                                                                                    
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287      
         Q4K5A6_PSEF5     - ---MITAYQASSQARVDAAMHTLFTAPSPELARLYEAMRYSVMNGGKRVRPLLAYAACEALGGKPEQANGAACAVELIHAYSLVHDDLPAMDDDDLRRGQPTTHKAFDEACAILAGDGLQSLAFSALLDPALSDASAEIRLRMVTTLAQAAGPAGMVGGQAIDLGSVGLKLDQQALEYMHRHKTGALIEASVILGALASGRAEKGELKALQTYAQAIGLAFQVQDDILDVESDTATLGKRQGADIARDKPTYPALLGLAAAKEYALELRDQALHALRPFDAAAEPLRELARYIVER 293
               SCOP domains d3p41a_ A: automated matches                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------polyprenyl_synt-3p41A01 A:31-285                                                                                                                                                                                                                               -------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.......ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..-------------.hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p41 A  -2 HHHSLTAYQASSQARVDAAmHTLFTAPSPELARLYEAmRYSVmNGGKRVRPLLAYAACEALGGKPEQANGAACAVELIHAYSLVHDDLPAmDDDDLRRGQPTTHKAFDEAcAILAGDGLQSLAFSALLDPALSDASAEIRLRmVTTLAQAAGPAGmVGGQAIDLGSVGLKLDQQALEYmHRHKTGALIEASVILGALASGRAEKGELKALQTYAQAIGLAFQVQDDILDVESDTAT-------------PTYPALLGLAAAKEYALELRDQALHALRPFDAAAEPLRELARYIVER 293
                                     7        17        27       |37  |     47        57        67        77        87|       97       107|      117       127       137  |    147     | 157       167       177       187       197       207       217       227     |   -       247       257       267       277       287      
                                              17-MSE            35-MSE|                                              88-MSE             108-SCY                         140-MSE      153-MSE                176-MSE                                                  233           247                                              
                                                                     40-MSE

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 (1, 1)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (4, 4)

Asymmetric Unit(hide GO term definitions)

Chain A (Q4K5A6_PSEF5 | Q4K5A6)

molecular function
	GO:0004337	geranyltranstransferase activity	Catalysis of the reaction: geranyl diphosphate + isopentenyl diphosphate = 2-trans,6-trans-farnesyl diphosphate + diphosphate.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0045337	farnesyl diphosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of farnesyl diphosphate.
	GO:0008299	isoprenoid biosynthetic process	The chemical reactions and pathways resulting in the formation of any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.

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