3LL9 - JenaLib

Title :   X-RAY STRUCTURES OF ISOPENTENYL PHOSPHATE KINASE

Authors :   C. P. Hill, H. L. Schubert

Date :   28 Jan 10 (Deposition) - 02 Jun 10 (Release) - 02 Jun 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

Chains :   Asym./Biol. Unit : A,B

Keywords :   Mevalonate Biosynthesis Isoprenoid, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. F. Mabanglo, H. L. Schubert, M. Chen, C. P. Hill, C. D. Poulter
X-Ray Structures Of Isopentenyl Phosphate Kinase.
Acs Chem. Biol. V. 5 517 2010
PubMed-ID: 20402538 | Reference-DOI: 10.1021/CB100032G

Compounds

Molecule 1 - ISOPENTENYL PHOSPHATE KINASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28
	Expression System Strain	:	BL21(DE3)CODON PLUS
	Expression System Taxid	:	469008
	Gene	:	MTH47, MTH_47
	Organism Scientific	:	METHANOTHERMOBACTER THERMAUTOTROPHICUS
	Organism Taxid	:	145262

Structural Features

Chains, Units

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (3, 15)

Asymmetric/Biological Unit (3, 15)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	GOL	1	Ligand/Ion	GLYCEROL
3	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

Sites (3, 3)

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA B:47 , GLY B:51 , HIS B:52 , ALA B:55 , GLY B:140	BINDING SITE FOR RESIDUE GOL B 267
2	AC2	SOFTWARE	LYS A:5 , GLY A:7 , GLY A:8 , SER A:9 , THR A:177 , ASP A:178 , VAL A:179 , GLY A:181 , TYR A:183 , ARG A:185 , ASN A:186 , PRO A:187 , LYS A:188 , GLY A:219 , MSE A:220 , HOH A:278 , HOH A:313 , HOH A:317	BINDING SITE FOR RESIDUE ADP A 267
3	AC3	SOFTWARE	GLY B:7 , GLY B:8 , SER B:9 , THR B:177 , ASP B:178 , VAL B:179 , GLY B:181 , TYR B:183 , ARG B:185 , ASN B:186 , PRO B:187 , LYS B:188 , MSE B:220 , LYS B:223 , HOH B:273 , HOH B:289 , HOH B:311 , HOH B:316	BINDING SITE FOR RESIDUE ADP B 268

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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:244
 aligned with IPK_METTH | O26153 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:263
                             1                                                                                                                                                                                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259   
            IPK_METTH     - -MIILKLGGSVITRKDSEEPAIDRDNLERIASEIGNASPSSLMIVHGAGSFGHPFAGEYRIGSEIENEEDLRRRRFGFALTQNWVKKLNSHVCDALLAEGIPAVSMQPSAFIRAHAGRISHADISLIRSYLEEGMVPVVYGDVVLDSDRRLKFSVISGDQLINHFSLRLMPERVILGTDVDGVYTRNPKKHPDARLLDVIGSLDDLESLDGTLNTDVTGGMVGKIRELLLLAEKGVESEIINAAVPGNIERALLGEEVRGTRI 262
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeehhhhhee......eehhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.hhhh.eeee..eeeee.hhhhhhhhhh..eeeee.eeee.......eeeehhhhhhhhhhhhhh..eeeeee......................-------------------..hhhhhhhhhhhhh...eeeee....hhhhhhhhh.....ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ll9 A  -1 HmIILKLGGSVITRKDSEEPAIDRDNLERIASEIGNASPSSLmIVHGAGSFGHPFAGEYRIGSEIENEEDLRRRRFGFALTQNWVKKLNSHVCDALLAEGIPAVSmQPSAFIRAHAGRISHADISLIRSYLEEGmVPVVYGDVVLDSDRRLKFSVISGDQLINHFSLRLmPERVILGTDVDGVYTRNPKKHPDARLLDVI-------------------GmVGKIRELLLLAEKGVESEIINAAVPGNIERALLGEEVRGTRI 262
                            ||       9        19        29        39  |     49        59        69        79        89        99     | 109       119       129    |  139       149       159       169       179       189       199         -       219|      229       239       249       259   
                            ||                                       42-MSE                                                        105-MSE                      134-MSE                            169-MSE                       199                 219|                                          
                           -1|                                                                                                                                                                                                                        220-MSE                                      
                             1-MSE

Chain B from PDB  Type:PROTEIN  Length:249
 aligned with IPK_METTH | O26153 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:264
                             1                                                                                                                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259    
            IPK_METTH     - -MIILKLGGSVITRKDSEEPAIDRDNLERIASEIGNASPSSLMIVHGAGSFGHPFAGEYRIGSEIENEEDLRRRRFGFALTQNWVKKLNSHVCDALLAEGIPAVSMQPSAFIRAHAGRISHADISLIRSYLEEGMVPVVYGDVVLDSDRRLKFSVISGDQLINHFSLRLMPERVILGTDVDGVYTRNPKKHPDARLLDVIGSLDDLESLDGTLNTDVTGGMVGKIRELLLLAEKGVESEIINAAVPGNIERALLGEEVRGTRIT 263
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeehhhhhee......eehhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee.hhhh.eeee..eeeee.hhhhhhhhhh..eeeee.eeee.......eeeehhhhhhhhhhhhhh..eeeeee....................ee....---------------hhhhhhhhhhhhhhh...eeeee....hhhhhhhhh....eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ll9 B  -1 HmIILKLGGSVITRKDSEEPAIDRDNLERIASEIGNASPSSLmIVHGAGSFGHPFAGEYRIGSEIENEEDLRRRRFGFALTQNWVKKLNSHVCDALLAEGIPAVSmQPSAFIRAHAGRISHADISLIRSYLEEGmVPVVYGDVVLDSDRRLKFSVISGDQLINHFSLRLmPERVILGTDVDGVYTRNPKKHPDARLLDVIGSLD---------------GmVGKIRELLLLAEKGVESEIINAAVPGNIERALLGEEVRGTRIT 263
                            ||       9        19        29        39  |     49        59        69        79        89        99     | 109       119       129    |  139       149       159       169       179       189       199   |     -       219|      229       239       249       259    
                           -1|                                       42-MSE                                                        105-MSE                      134-MSE                            169-MSE                           203             219|                                           
                             1-MSE                                                                                                                                                                                                                    220-MSE

Legend:		→ Mismatch	(orange background)
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		→ 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)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (6, 6)

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		Gly A:219 - Mse A:220	[ RasMol ]

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File

3lkk	THERMOPLASMA ACIDOPHILUM ISOPENTENYL PHOSPHATE KINASE SUBSTRATE COMPLEX
3ll5	THERMOPLASMA ACIDOPHILUM ISOPENTENYL PHOSPHATE KINASE PRODUCT COMPLEX

Description