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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   ENGINEERED RABGGTASE IN COMPLEX WITH A PEPTIDOMIMETIC INHIBITOR (COMPOUND 9)

Authors :   Z. Guo, K. Alexandrov, H. Waldmann, R. S. Goody, W. Blankenfeldt

Date :   20 Jun 09 (Deposition) - 08 Sep 09 (Release) - 17 Feb 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

Keywords :   Protein Prenylation Inhibition, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. T. Tan, E. Guiu-Rozas, R. S. Bon, Z. Guo, C. Delon, S. Wetzel, S. Arndt K. Alexandrov, H. Waldmann, R. S. Goody, Y. W. Wu, W. Blankenfeldt
Design, Synthesis, And Characterization Of Peptide-Based Ra Geranylgeranyl Transferase Inhibitors
J. Med. Chem. V. 52 8025 2009
PubMed-ID: 19894725 | Reference-DOI: 10.1021/JM901117D

Molecule 1 - GERANYLGERANYL TRANSFERASE TYPE-2 SUBUNIT ALPHA
	Chains	:	A
	EC Number	:	2.5.1.60
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGATEV
	Expression System Strain	:	BL21 CODON-PLUS RIL (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RABGGTASE ALPHA-SUBUNIT
	Mutation	:	YES
	Organism Common	:	RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	GERANYLGERANYL TRANSFERASE TYPE II SUBUNIT ALPHA, RAB GERANYLGERANYLTRANSFERASE SUBUNIT ALPHA, RAB GERANYL- GERANYLTRANSFERASE SUBUNIT ALPHA, RAB GG TRANSFERASE ALPHA, RAB GGTASE ALPHA

Molecule 2 - GERANYLGERANYL TRANSFERASE TYPE-2 SUBUNIT BETA
	Chains	:	B
	EC Number	:	2.5.1.60
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET30A
	Expression System Strain	:	BL21 CODON-PLUS RIL (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RABGGTASE BETA-SUBUNIT
	Organism Common	:	RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	GERANYLGERANYL TRANSFERASE TYPE II SUBUNIT BETA, GGTASE-II- BETA, TYPE II PROTEIN GERANYL-GERANYLTRANSFERASE SUBUNIT BETA, RAB GERANYLGERANYLTRANSFERASE SUBUNIT BETA, RAB GERANYL- GERANYLTRANSFERASE SUBUNIT BETA, RAB GG TRANSFERASE BETA, RAB GGTASE BETA

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 3)

No.	Name	Count	Type	Full Name
1	BD7	1	Ligand/Ion	N-[(BENZYLOXY)CARBONYL]-L-HISTIDYL-N-METHYL-L-PHENYLALANYL-N-HYDROXY-L-TYROSINAMIDE
2	CA	1	Ligand/Ion	CALCIUM ION
3	ZN	1	Ligand/Ion	ZINC ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP B:238 , CYS B:240 , HIS B:290 , BD7 B:334	BINDING SITE FOR RESIDUE ZN B 332
2	AC2	SOFTWARE	ALA A:138 , HOH A:400 , HIS B:64 , MET B:66 , HOH B:415 , HOH B:509	BINDING SITE FOR RESIDUE CA B 333
3	AC3	SOFTWARE	TRP B:52 , LEU B:96 , ARG B:144 , PHE B:147 , CYS B:148 , GLY B:192 , GLN B:193 , CYS B:196 , ASP B:238 , TYR B:241 , TRP B:244 , PHE B:289 , HIS B:290 , ZN B:332 , HOH B:373 , HOH B:380	BINDING SITE FOR RESIDUE BD7 B 334

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

(no "Cis Peptide Bond" information available for 3HXD)

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

Asymmetric/Biological Unit (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PFTA	PS51147	Protein prenyltransferases alpha subunit repeat profile.	PGTA_RAT	44-78 88-122 124-158 159-193 207-241 363-397	6	A:44-78 A:88-122 A:124-158 A:159-193 A:207-237 A:252-286

Asymmetric/Biological Unit (10, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSRNOT00000048455	1	ENSRNOE00000431461	chr15:33868619-33868585	35	PGTA_RAT	-	0	0	-	-
1.2	ENSRNOT00000048455	2	ENSRNOE00000442687	chr15:33868298-33868241	58	PGTA_RAT	1-1	1	0	-	-
1.3	ENSRNOT00000048455	3	ENSRNOE00000336091	chr15:33868107-33867997	111	PGTA_RAT	2-38	37	1	A:17-38	22
1.4	ENSRNOT00000048455	4	ENSRNOE00000290128	chr15:33867677-33867553	125	PGTA_RAT	39-80	42	1	A:39-80	42
1.5	ENSRNOT00000048455	5	ENSRNOE00000303229	chr15:33867378-33867191	188	PGTA_RAT	80-143	64	1	A:80-143	64
1.6	ENSRNOT00000048455	6	ENSRNOE00000290397	chr15:33866934-33866731	204	PGTA_RAT	143-211	69	1	A:143-211 (gaps)	69
1.7	ENSRNOT00000048455	7	ENSRNOE00000327073	chr15:33866284-33866201	84	PGTA_RAT	211-239	29	1	A:211-237	27
1.8	ENSRNOT00000048455	8	ENSRNOE00000288887	chr15:33866112-33866030	83	PGTA_RAT	239-266	28	0	-	-
1.9	ENSRNOT00000048455	9	ENSRNOE00000339199	chr15:33865939-33865838	102	PGTA_RAT	267-300	34	0	-	-
1.10	ENSRNOT00000048455	10	ENSRNOE00000352360	chr15:33865732-33865627	106	PGTA_RAT	301-336	36	1	A:238-241	4
1.11	ENSRNOT00000048455	11	ENSRNOE00000303916	chr15:33865535-33865484	52	PGTA_RAT	336-353	18	1	A:242-242	1
1.12	ENSRNOT00000048455	12	ENSRNOE00000357522	chr15:33865353-33865265	89	PGTA_RAT	353-383	31	1	A:242-272	31
1.13	ENSRNOT00000048455	13	ENSRNOE00000294255	chr15:33865148-33865060	89	PGTA_RAT	383-412	30	1	A:272-301	30
1.14	ENSRNOT00000048455	14	ENSRNOE00000306932	chr15:33864791-33864675	117	PGTA_RAT	413-451	39	1	A:302-330	29
1.15	ENSRNOT00000048455	15	ENSRNOE00000363642	chr15:33864038-33863925	114	PGTA_RAT	452-489	38	0	-	-
1.16	ENSRNOT00000048455	16	ENSRNOE00000281487	chr15:33863675-33863588	88	PGTA_RAT	490-519	30	0	-	-
1.17	ENSRNOT00000048455	17	ENSRNOE00000307031	chr15:33862501-33862275	227	PGTA_RAT	519-567	49	0	-	-

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:308
 aligned with PGTA_RAT | Q08602 from UniProtKB/Swiss-Prot  Length:567

    Alignment length:425
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436     
             PGTA_RAT    17 KRLEREQKLKLYQSATQAVFQKRQAGELDESVLELTSQILGANPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPKSYGTWHHRCWLLSRLPEPNWARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNYSSWHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTDPNDQSAWFYHRWLLGRAEPHDVLCCVHVSREEACLSVCFSRPLTVGSRMGTLLLMVDEAPLSVEWRTPDGRNRPSHVWLCDLPAASLNDQLPQHTFRVIWTGSDSQKECVLLKDRPECWCRDSATDEQLFRCELSVEKSTVLQSELESCKELQELEPENKWCLLTIILLMRALDPLLYEKETLQYFSTLKAVDPMRAAYLDDLRSKFLLENSVLKMEYA 441
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...------..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh-------------------------------------------------------------------------------------h..h--------------------------hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------PFTA  PDB: A:44-78 UniProt: 44-78  ---------PFTA  PDB: A:88-122 UniProt: 88-122-PFTA  PDB: A:124-158               PFTA  PDB: A:159-193               -------------PFTA  PDB: A:207-237               -------------------------------------------------------------------------------------------------------------------------PFTA  PDB: A:252-286               -------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:17-38Exon 1.4  PDB: A:39-80 UniProt: 39-80     --------------------------------------------------------------Exon 1.6  PDB: A:143-211 (gaps) UniProt: 143-211                     ---------------------------Exon 1.8  PDB: -            Exon 1.9  PDB: - UniProt: 267-300 Exon 1.10  PDB: A:238-241           ----------------Exon 1.12  PDB: A:242-272      -----------------------------Exon 1.14  PDB: A:302-330     Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------Exon 1.5  PDB: A:80-143 UniProt: 80-143                         -------------------------------------------------------------------Exon 1.7  PDB: A:211-237     ------------------------------------------------------------------------------------------------Exon 1.11         -----------------------------Exon 1.13  PDB: A:272-301     ----------------------------- Transcript 1 (2)
                 3hxd A  17 KRLEREQKLKLYQSATQAVFQKRQAGELDESVLELTSQILGANPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPKSYGTWHHRCWLLSRLPEPNWARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNYSSWHYRSCLLPQLHPQP------RLPENVLLKELELVQNAFFTDPNDQSAWFYHRWLLG-------------------------------------------------------------------------------------AGSG--------------------------RCELSVEKSTVLQSELESCKELQELEPENKWCLLTIILLMRALDPLLYEKETLQYFSTLKAVDPMRAAYLDDLRSKFLLENSVLKMEYA 330
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186        |-     | 206       216       226       236|        -         -         -         -         -         -         -         -      |241         -         -      |245       255       265       275       285       295       305       315       325     
                                                                                                                                                                                                            195    202                                237                                                                                   238  |                        242                                                                                        
                                                                                                                                                                                                                                                                                                                                               241

Chain B from PDB  Type:PROTEIN  Length:324
 aligned with PGTB2_RAT | Q08603 from UniProtKB/Swiss-Prot  Length:331

    Alignment length:327
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       
            PGTB2_RAT     5 QKDVTIKSDAPDTLLLEKHADYIASYGSKKDDYEYCMSEYLRMSGVYWGLTVMDLMGQLHRMNKEEILVFIKSCQHECGGVSASIGHDPHLLYTLSAVQILTLYDSIHVINVDKVVAYVQSLQKEDGSFAGDIWGEIDTRFSFCAVATLALLGKLDAINVEKAIEFVLSCMNFDGGFGCRPGSESHAGQIYCCTGFLAITSQLHQVNSDLLGWWLCERQLPSGGLNGRPEKLPDVCYSWWVLASLKIIGRLHWIDREKLRSFILACQDEETGGFADRPGDMVDPFHTLFGIAGLSLLGEEQIKPVSPVFCMPEEVLQRVNVQPELVS 331
               SCOP domains d3hxdb_ B: Rab geranylgerany   ltransferase, beta subunit                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 3hxdB00 B:5-331  [code=1.50.   10.20, no name defined]                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhhhh...---hhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhh..............hhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hxd B   5 QKDVTIKSDAPDTLLLEKHADYIASYGS---DYEYCMSEYLRMSGVYWGLTVMDLMGQLHRMNKEEILVFIKSCQHECGGVSASIGHDPHLLYTLSAVQILTLYDSIHVINVDKVVAYVQSLQKEDGSFAGDIWGEIDTRFSFCAVATLALLGKLDAINVEKAIEFVLSCMNFDGGFGCRPGSESHAGQIYCCTGFLAITSQLHQVNSDLLGWWLCERQLPSGGLNGRPEKLPDVCYSWWVLASLKIIGRLHWIDREKLRSFILACQDEETGGFADRPGDMVDPFHTLFGIAGLSLLGEEQIKPVSPVFCMPEEVLQRVNVQPELVS 331
                                    14        24       | - |      44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       
                                                      32  36

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: alpha/alpha toroid (324)

Superfamily: Terpenoid cyclases/Protein prenyltransferases (151)

Family: Protein prenyltransferases (86)

Protein domain: Rab geranylgeranyltransferase, beta subunit (21)

Norway rat (Rattus norvegicus) [TaxId: 10116] (21)

d3hxdb_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Alpha/alpha barrel (251)

Topology: Glycosyltransferase (233)

Homologous Superfamily: [code=1.50.10.20, no name defined] (105)

Rat (Rattus norvegicus) (21)

3hxdB00

B:5-331

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PGTA_RAT | Q08602)

molecular function
	GO:0017137	Rab GTPase binding	Interacting selectively and non-covalently with Rab protein, any member of the Rab subfamily of the Ras superfamily of monomeric GTPases.
	GO:0004663	Rab geranylgeranyltransferase activity	Catalysis of the reaction: 2 geranylgeranyl diphosphate + protein-cysteine = 2 S-geranylgeranyl-protein + 2 diphosphate. This reaction is the formation of two thioether linkages between the C-1 atom of the geranylgeranyl groups and two cysteine residues within the terminal sequence motifs XXCC, XCXC or CCXX. Known substrates include Ras-related GTPases of a single family and the Rab family.
	GO:0004659	prenyltransferase activity	Catalysis of the transfer of a prenyl group from one compound (donor) to another (acceptor).
	GO:0008318	protein prenyltransferase activity	Catalysis of the covalent addition of an isoprenoid group such as a farnesyl or geranylgeranyl group via thioether linkages to a cysteine residue in a protein.
	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.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0018344	protein geranylgeranylation	The covalent attachment of a geranylgeranyl group to a protein.
	GO:0018342	protein prenylation	The covalent attachment of a prenyl group to a protein; geranyl, farnesyl, or geranylgeranyl groups may be added.
cellular component
	GO:0005968	Rab-protein geranylgeranyltransferase complex	A heterodimeric enzyme complex, which in mammals is composed of an alpha and a beta subunit, and which associates with an accessory protein Rep (Rab escort protein). Catalyzes of the transfer of a geranyl-geranyl group from geranylgeranyl pyrophosphate to a Rab protein.

Chain B (PGTB2_RAT | Q08603)

molecular function
	GO:0017137	Rab GTPase binding	Interacting selectively and non-covalently with Rab protein, any member of the Rab subfamily of the Ras superfamily of monomeric GTPases.
	GO:0004663	Rab geranylgeranyltransferase activity	Catalysis of the reaction: 2 geranylgeranyl diphosphate + protein-cysteine = 2 S-geranylgeranyl-protein + 2 diphosphate. This reaction is the formation of two thioether linkages between the C-1 atom of the geranylgeranyl groups and two cysteine residues within the terminal sequence motifs XXCC, XCXC or CCXX. Known substrates include Ras-related GTPases of a single family and the Rab family.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004659	prenyltransferase activity	Catalysis of the transfer of a prenyl group from one compound (donor) to another (acceptor).
	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.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0018344	protein geranylgeranylation	The covalent attachment of a geranylgeranyl group to a protein.
cellular component
	GO:0005968	Rab-protein geranylgeranyltransferase complex	A heterodimeric enzyme complex, which in mammals is composed of an alpha and a beta subunit, and which associates with an accessory protein Rep (Rab escort protein). Catalyzes of the transfer of a geranyl-geranyl group from geranylgeranyl pyrophosphate to a Rab protein.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3hxd)

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	3hxd
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	PGTA_RAT \| Q08602
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	PGTB2_RAT \| Q08603
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	2.5.1.60
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 6)

Exons (10, 10)

Sequences/Alignments

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SCOP Domains (1, 1)

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Gene Ontology (11, 18)

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