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Title :   CRYSTAL STRUCTURE OF HUMAN TRNAHIS GUANYLYLTRANSFERASE (THG1)- NAI DERIVATIVE

Authors :   S. J. Hyde, B. E. Eckenroth, S. Doublie

Date :   11 Sep 10 (Deposition) - 17 Nov 10 (Release) - 09 Apr 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.28

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

Keywords :   Guanylyltransferase, Polymerase-Like Palm Domain, Catalytic Carboxylates, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. J. Hyde, B. E. Eckenroth, B. A. Smith, W. A. Eberley, N. H. Heintz, J. E. Jackman, S. Doublie
Trnahis Guanylyltransferase (Thg1), A Unique 3'-5' Nucleotidyl Transferase, Shares Unexpected Structural Homology With Canonical 5'-3' Dna Polymerases.
Proc. Natl. Acad. Sci. Usa V. 107 20305 2010
PubMed-ID: 21059936 | Reference-DOI: 10.1073/PNAS.1010436107

Molecule 1 - TRNA(HIS) GUANYLYLTRANSFERASE
	Cell Line	:	KATO III
	Chains	:	A, B
	EC Number	:	2.7.7.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PME182-FL
	Expression System Strain	:	ROSETTA (DE3) PLYSS
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 30-298
	Gene	:	ICF45, THG1L
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	TRNA-HISTIDINE GUANYLYLTRANSFERASE, INTERPHASE CYTOPLASMIC FOCI PROTEIN 45

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 10)

No.	Name	Count	Type	Full Name
1	IOD	10	Ligand/Ion	IODIDE ION

Biological Unit 1 (1, 20)

No.	Name	Count	Type	Full Name
1	IOD	20	Ligand/Ion	IODIDE ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	MET A:205	BINDING SITE FOR RESIDUE IOD A 270
02	AC2	SOFTWARE	ARG B:207	BINDING SITE FOR RESIDUE IOD A 271
03	AC3	SOFTWARE	PRO A:204 , MET A:205	BINDING SITE FOR RESIDUE IOD A 272
04	AC4	SOFTWARE	GLN A:166 , GLN A:167	BINDING SITE FOR RESIDUE IOD A 273
05	AC5	SOFTWARE	ARG A:92	BINDING SITE FOR RESIDUE IOD A 274
06	AC6	SOFTWARE	HIS A:152 , ARG A:207	BINDING SITE FOR RESIDUE IOD A 275
07	AC7	SOFTWARE	MET B:205	BINDING SITE FOR RESIDUE IOD B 270
08	AC8	SOFTWARE	PRO B:204 , MET B:205	BINDING SITE FOR RESIDUE IOD B 271
09	AC9	SOFTWARE	ARG B:92	BINDING SITE FOR RESIDUE IOD B 272
10	BC1	SOFTWARE	GLN B:166 , GLN B:167	BINDING SITE FOR RESIDUE IOD B 273

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

Asymmetric Unit

No.	Residues
1	Lys A:44	-	Pro A:45
2	Lys B:44	-	Pro B:45

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_031871	L	232	P	THG1_HUMAN	Polymorphism	2270812	A/B	L	203	P

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_031871	L	232	P	THG1_HUMAN	Polymorphism	2270812	A/B	L	203	P

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

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

(no "Exon" information available for 3OTD)

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:240
 aligned with THG1_HUMAN | Q9NWX6 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:267
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       
           THG1_HUMAN    32 KSKFEYVRDFEADDTCLAHCWVVVRLDGRNFHRFAEKHNFAKPNDSRALQLMTKCAQTVMEELEDIVIAYGQSDEYSFVFKRKTNWFKRRASKFMTHVASQFASSYVFYWRDYFEDQPLLYPPGFDGRVVVYPSNQTLKDYLSWRQADCHINNLYNTVFWALIQQSGLTPVQAQGRLQGTLAADKNEILFSEFNINYNNELPMYRKGTVLIWQKVDEVMTKEIKLPTEMEGKKMAVTRTRTKPVPLHCDIIGDAFWKEHPEILDEDS 298
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh.........eeeeeeee.hhhhhhhhh......hhhhhhhhhhhhhhhhhhh..eeeeeee..eeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhheeeee.---------------------------..eeee.....hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3otd A   3 KSKFEYVRDFEADDTCLAHCWVVVRLDGRNFHRFAEKHNFAKPNDSRALQLMTKCAQTVMEELEDIVIAYGQSDEYSFVFKRKTNWFKRRASKFMTHVASQFASSYVFYWRDYFEDQPLLYPPGFDGRVVVYPSNQTLKDYLSWRQADCHINNLYNTVFWALIQQSGLTPVQAQGRLQGTLAADKNEILFSEFNINYNNELPMYRKGTVLIWQ---------------------------TKPVPLHCDIIGDAFWKEHPEILDEDS 269
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212  |      -         -         -|      252       262       
                                                                                                                                                                                                                                              215                         243

Chain B from PDB  Type:PROTEIN  Length:240
 aligned with THG1_HUMAN | Q9NWX6 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:267
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       
           THG1_HUMAN    32 KSKFEYVRDFEADDTCLAHCWVVVRLDGRNFHRFAEKHNFAKPNDSRALQLMTKCAQTVMEELEDIVIAYGQSDEYSFVFKRKTNWFKRRASKFMTHVASQFASSYVFYWRDYFEDQPLLYPPGFDGRVVVYPSNQTLKDYLSWRQADCHINNLYNTVFWALIQQSGLTPVQAQGRLQGTLAADKNEILFSEFNINYNNELPMYRKGTVLIWQKVDEVMTKEIKLPTEMEGKKMAVTRTRTKPVPLHCDIIGDAFWKEHPEILDEDS 298
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --Thg1-3otdB03 B:5-135                                                                                                               Thg1C-3otdB01 B:136-266                                                                                                            --- Pfam domains (1)
           Pfam domains (2) --Thg1-3otdB04 B:5-135                                                                                                               Thg1C-3otdB02 B:136-266                                                                                                            --- Pfam domains (2)
         Sec.struct. author ...hhhhhhhh.........eeeeeeee.hhhhhhhhh......hhhhhhhhhhhhhhhhhhh..eeeeeee..eeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhheeeee.---------------------------..eeee.....hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3otd B   3 KSKFEYVRDFEADDTCLAHCWVVVRLDGRNFHRFAEKHNFAKPNDSRALQLMTKCAQTVMEELEDIVIAYGQSDEYSFVFKRKTNWFKRRASKFMTHVASQFASSYVFYWRDYFEDQPLLYPPGFDGRVVVYPSNQTLKDYLSWRQADCHINNLYNTVFWALIQQSGLTPVQAQGRLQGTLAADKNEILFSEFNINYNNELPMYRKGTVLIWQ---------------------------TKPVPLHCDIIGDAFWKEHPEILDEDS 269
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212  |      -         -         -|      252       262       
                                                                                                                                                                                                                                              215                         243

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 '\|'

(no "SCOP Domain" information available for 3OTD)

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Thg1C] (4)

Family: Thg1C (4)

Homo sapiens (Human) (4)

1a	Thg1C-3otdB01	B:136-266
1b	Thg1C-3otdB02	B:136-266

Clan: no clan defined [family: Thg1] (4)

Family: Thg1 (4)

Homo sapiens (Human) (4)

2a	Thg1-3otdB03	B:5-135
2b	Thg1-3otdB04	B:5-135

Asymmetric Unit(hide GO term definitions)

Chain A,B (THG1_HUMAN | Q9NWX6)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0000049	tRNA binding	Interacting selectively and non-covalently with transfer RNA.
	GO:0008193	tRNA guanylyltransferase activity	Catalysis of the posttranscriptional addition of a guanyl residue to the 5' end of a tRNA molecule; observed for His tRNAs.
	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:0051289	protein homotetramerization	The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
	GO:0006400	tRNA modification	The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.
	GO:0008033	tRNA processing	The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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