2ZPA - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF TRNA(MET) CYTIDINE ACETYLTRANSFERASE

Authors :   S. Chimnaronk, T. Manita, M. Yao, I. Tanaka

Date :   08 Jul 08 (Deposition) - 07 Apr 09 (Release) - 02 Jun 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.35

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

Keywords :   Rna Modification Enzyme, Rna Helicase, Acetyltransferase, Gcn5 Acetyltransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Chimnaronk, T. Suzuki, T. Manita, Y. Ikeuchi, M. Yao, T. Suzuki, I. Tanaka
Rna Helicase Module In An Acetyltransferase That Modifies A Specific Trna Anticodon
Embo J. V. 28 1362 2009
PubMed-ID: 19322199 | Reference-DOI: 10.1038/EMBOJ.2009.69
(for further references see the PDB file header)

Molecule 1 - UNCHARACTERIZED PROTEIN YPFI
	Chains	:	A, B
	EC Number	:	2.3.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TMCA
	Organism Scientific	:	ESCHERICHIA COLI K12
	Organism Taxid	:	83333
	Synonym	:	TRNA(MET) CYTIDINE ACETYLTRANSFERASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 25)

No.	Name	Count	Type	Full Name
1	ACO	2	Ligand/Ion	ACETYL COENZYME *A
2	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
3	MSE	21	Mod. Amino Acid	SELENOMETHIONINE
4	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 12)

No.	Name	Count	Type	Full Name
1	ACO	1	Ligand/Ion	ACETYL COENZYME *A
2	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
3	MSE	10	Mod. Amino Acid	SELENOMETHIONINE
4	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 13)

No.	Name	Count	Type	Full Name
1	ACO	1	Ligand/Ion	ACETYL COENZYME *A
2	ADP	-1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
3	MSE	11	Mod. Amino Acid	SELENOMETHIONINE
4	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG B:201 , GLY B:202 , ARG B:203 , GLY B:204 , LYS B:205 , SER B:206 , HOH B:979	BINDING SITE FOR RESIDUE SO4 B 801
2	AC2	SOFTWARE	SER A:459 , ARG A:460 , ILE A:461 , GLN A:468 , ARG A:469 , GLU A:470 , GLY A:471 , THR A:472 , GLY A:473 , ARG A:474 , SER A:493 , GLU A:499 , ARG A:502 , PHE A:503 , ARG A:506 , HOH A:875 , HOH A:887	BINDING SITE FOR RESIDUE ACO A 700
3	AC3	SOFTWARE	LYS B:301 , SER B:459 , ILE B:461 , ARG B:469 , GLU B:470 , GLY B:471 , THR B:472 , GLY B:473 , ARG B:474 , SER B:493 , PHE B:494 , LEU B:500 , PHE B:503 , ARG B:506 , HOH B:906 , HOH B:930	BINDING SITE FOR RESIDUE ACO B 701
4	AC4	SOFTWARE	ALA A:172 , GLY A:174 , ALA A:175 , PRO A:176 , GLN A:180 , ALA A:200 , GLY A:202 , ARG A:203 , GLY A:204 , LYS A:205 , SER A:206 , ALA A:207 , GLN A:211 , PHE A:236 , ILE A:318 , ARG A:319 , HOH A:856 , HOH A:908 , HOH A:968	BINDING SITE FOR RESIDUE ADP A 800

(no "SS Bond" information available for 2ZPA)

(no "Cis Peptide Bond" information available for 2ZPA)

(no "SAP(SNP)/Variant" information available for 2ZPA)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GNAT	PS51186	Gcn5-related N-acetyltransferase (GNAT) domain profile.	TMCA_ECOLI	356-531	2	A:356-531 B:356-531

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GNAT	PS51186	Gcn5-related N-acetyltransferase (GNAT) domain profile.	TMCA_ECOLI	356-531	1	A:356-531 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GNAT	PS51186	Gcn5-related N-acetyltransferase (GNAT) domain profile.	TMCA_ECOLI	356-531	1	- B:356-531

(no "Exon" information available for 2ZPA)

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:658
 aligned with TMCA_ECOLI | P76562 from UniProtKB/Swiss-Prot  Length:671

    Alignment length:669
                                    11        21        31        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       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661         
           TMCA_ECOLI     2 AELTALHTLTAQMKREGIRRLLVLSGEEGWCFEHTLKLRDALPGDWLWISPRPDAENHCSPSALQTLLGREFRHAVFDARHGFDAAAFAALSGTLKAGSWLVLLLPVWEEWENQPDADSLRWSDCPDPIATPHFVQHLKRVLTADNEAILWRQNQPFSLAHFTPRTDWYPATGAPQPEQQQLLKQLMTMPPGVAAVTAARGRGKSALAGQLISRIAGRAIVTAPAKASTDVLAQFAGEKFRFIAPDALLASDEQADWLVVDEAAAIPAPLLHQLVSRFPRTLLTTTVQGYEGTGRGFLLKFCARFPHLHRFELQQPIRWAQGCPLEKMVSEALVFDDENFTHTPQGNIVISAFEQTLWQSDPETPLKVYQLLSGAHYRTSPLDLRRMMDAPGQHFLQAAGENEIAGALWLVDEGGLSQQLSQAVWAGFRRPRGNLVAQSLAAHGNNPLAATLRGRRVSRIAVHPARQREGTGRQLIAGALQYTQDLDYLSVSFGYTGELWRFWQRCGFVLVRMGNHREASSGCYTAMALLPMSDAGKQLAEREHYRLRRDAQALAQWNGETLPVDPLNDAVLSDDDWLELAGFAFAHRPLLTSLGCLLRLLQTSELALPALRGRLQKNASDAQLCTTLKLSGRKMLLVRQREEAAQALFALNDVRTERLRDRITQWQLF 670
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhh....eee....-----------..........eeee.....hhhhhhhhhh......eeeeee.hhhhh....hhhhhhhhh......hhhhhhhhhhhhh.....eeee.......................hhhhhhhhhhhh....eeeeeee....hhhhhhhhhhhhh...eeee......hhhhhhhhhhhh...hhhhhhhh.....eeeee.hhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhh....eeee..........hhhhhhhhhhh...hhhhhh......eeeeee.hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh..eeeeeee....eeeeeeeeeee..hhhhhhhhhh.......hhhhhhhhhhh...hhhh.eeeeeeeeee.......hhhhhhhhhhhhh.....eeeeeee.hhhhhhhhhhh..eeeee...........eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhh......hhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GNAT  PDB: A:356-531 UniProt: 356-531                                                                                                                                           ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zpa A   2 AELTALHTLTAQmKREGIRRLLVLSGEEGWCFEHTLKLRDALPGDWLWISPRP-----------QTLLGREFRHAVFDARHGFDAAAFAALSGTLKAGSWLVLLLPVWEEWENQPDADSLRWSDCPDPIATPHFVQHLKRVLTADNEAILWRQNQPFSLAHFTPRTDWYPATGAPQPEQQQLLKQLmTmPPGVAAVTAARGRGKSALAGQLISRIAGRAIVTAPAKASTDVLAQFAGEKFRFIAPDALLASDEQADWLVVDEAAAIPAPLLHQLVSRFPRTLLTTTVQGYEGTGRGFLLKFCARFPHLHRFELQQPIRWAQGCPLEKmVSEALVFDDENFTHTPQGNIVISAFEQTLWQSDPETPLKVYQLLSGAHYRTSPLDLRRmmDAPGQHFLQAAGENEIAGALWLVDEGGLSQQLSQAVWAGFRRPRGNLVAQSLAAHGNNPLAATLRGRRVSRIAVHPARQREGTGRQLIAGALQYTQDLDYLSVSFGYTGELWRFWQRCGFVLVRmGNHREASSGCYTAmALLPmSDAGKQLAEREHYRLRRDAQALAQWNGETLPVDPLNDAVLSDDDWLELAGFAFAHRPLLTSLGCLLRLLQTSELALPALRGRLQKNASDAQLCTTLKLSGRKmLLVRQREEAAQALFALNDVRTERLRDRITQWQLF 670
                                    11  |     21        31        41        51  |      -    |   71        81        91       101       111       121       131       141       151       161       171       181      |191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381      |391       401       411       421       431       441       451       461       471       481       491       501       511  |    521      |531 |     541       551       561       571       581       591       601       611       621       631    |  641       651       661         
                                       14-MSE                                  54          66                                                                                                                       188-MSE                                                                                                                                      329-MSE                                                    388-MSE                                                                                                                       514-MSE       528-MSE|                                                                                                    636-MSE                              
                                                                                                                                                                                                                      190-MSE                                                                                                                                                                                                389-MSE                                                                                                                                         533-MSE

Chain B from PDB  Type:PROTEIN  Length:662
 aligned with TMCA_ECOLI | P76562 from UniProtKB/Swiss-Prot  Length:671

    Alignment length:670
                                    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       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670
           TMCA_ECOLI     1 MAELTALHTLTAQMKREGIRRLLVLSGEEGWCFEHTLKLRDALPGDWLWISPRPDAENHCSPSALQTLLGREFRHAVFDARHGFDAAAFAALSGTLKAGSWLVLLLPVWEEWENQPDADSLRWSDCPDPIATPHFVQHLKRVLTADNEAILWRQNQPFSLAHFTPRTDWYPATGAPQPEQQQLLKQLMTMPPGVAAVTAARGRGKSALAGQLISRIAGRAIVTAPAKASTDVLAQFAGEKFRFIAPDALLASDEQADWLVVDEAAAIPAPLLHQLVSRFPRTLLTTTVQGYEGTGRGFLLKFCARFPHLHRFELQQPIRWAQGCPLEKMVSEALVFDDENFTHTPQGNIVISAFEQTLWQSDPETPLKVYQLLSGAHYRTSPLDLRRMMDAPGQHFLQAAGENEIAGALWLVDEGGLSQQLSQAVWAGFRRPRGNLVAQSLAAHGNNPLAATLRGRRVSRIAVHPARQREGTGRQLIAGALQYTQDLDYLSVSFGYTGELWRFWQRCGFVLVRMGNHREASSGCYTAMALLPMSDAGKQLAEREHYRLRRDAQALAQWNGETLPVDPLNDAVLSDDDWLELAGFAFAHRPLLTSLGCLLRLLQTSELALPALRGRLQKNASDAQLCTTLKLSGRKMLLVRQREEAAQALFALNDVRTERLRDRITQWQLF 670
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------------------------------------DUF1726-2zpaB05 B:65-153                                                                 ------------------------------------------Helicase_RecD-2zpaB03 B:196-337                                                                                                               ------------------------------GNAT_acetyltr_2-2zpaB01 B:368-534                                                                                                                                      -------------tRNA_bind_2-2zpaB07 B:548-637                                                             --------------------------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------DUF1726-2zpaB06 B:65-153                                                                 ------------------------------------------Helicase_RecD-2zpaB04 B:196-337                                                                                                               ------------------------------GNAT_acetyltr_2-2zpaB02 B:368-534                                                                                                                                      -------------tRNA_bind_2-2zpaB08 B:548-637                                                             --------------------------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh....eee......--------...........eeee.....hhhhhhhhhh......eeeeee.hhhhh....hhhhhhh........hhhhhhhhhhhhhhh...eeee.......................hhhhhhhh.........eeeeee....hhhhhhhhh.................hhhhhhh........hhhhhh........eee.hhhhhhhhhhhhhhhhh..eeeeee.......hhhhhhhhhh....eeeee..........hhhhhhhhhhhh..............eeeee..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh..eeeeeee....eeeeeeeeeee..hhhhhhhhhh.......hhhhhhhhhhh...hhhh.eeeeeeeeee.hhhh..hhhhhhhhhhhhh.....eeeeeee.hhhhhhhhhh...eeeee...........eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...hhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GNAT  PDB: B:356-531 UniProt: 356-531                                                                                                                                           ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zpa B   1 mAELTALHTLTAQmKREGIRRLLVLSGEEGWCFEHTLKLRDALPGDWLWISPRPDA--------LQTLLGREFRHAVFDARHGFDAAAFAALSGTLKAGSWLVLLLPVWEEWENQPDADSLRWSDCPDPIATPHFVQHLKRVLTADNEAILWRQNQPFSLAHFTPRTDWYPATGAPQPEQQQLLKQLmTmPPGVAAVTAARGRGKSALAGQLISRIAGRAIVTAPAKASTDVLAQFAGEKFRFIAPDALLASDEQADWLVVDEAAAIPAPLLHQLVSRFPRTLLTTTVQGYEGTGRGFLLKFCARFPHLHRFELQQPIRWAQGCPLEKmVSEALVFDDENFTHTPQGNIVISAFEQTLWQSDPETPLKVYQLLSGAHYRTSPLDLRRmmDAPGQHFLQAAGENEIAGALWLVDEGGLSQQLSQAVWAGFRRPRGNLVAQSLAAHGNNPLAATLRGRRVSRIAVHPARQREGTGRQLIAGALQYTQDLDYLSVSFGYTGELWRFWQRCGFVLVRmGNHREASSGCYTAmALLPmSDAGKQLAEREHYRLRRDAQALAQWNGETLPVDPLNDAVLSDDDWLELAGFAFAHRPLLTSLGCLLRLLQTSELALPALRGRLQKNASDAQLCTTLKLSGRKmLLVRQREEAAQALFALNDVRTERLRDRITQWQLF 670
                            |       10   |    20        30        40        50     |   -    |   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       440       450       460       470       480       490       500       510   |   520       530  |    540       550       560       570       580       590       600       610       620       630     | 640       650       660       670
                            1-MSE       14-MSE                                    56       65                                                                                                                        188-MSE                                                                                                                                      329-MSE                                                    388-MSE                                                                                                                       514-MSE       528-MSE|                                                                                                    636-MSE                              
                                                                                                                                                                                                                       190-MSE                                                                                                                                                                                                389-MSE                                                                                                                                         533-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 '\|'

(no "SCOP Domain" information available for 2ZPA)

(no "CATH Domain" information available for 2ZPA)

Asymmetric Unit(hide GO term definitions)

Chain A,B (TMCA_ECOLI | P76562)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0008080	N-acetyltransferase activity	Catalysis of the transfer of an acetyl group to a nitrogen atom on the acceptor molecule.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	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:0051392	tRNA N-acetyltransferase activity	Catalysis of the reaction: acetyl-CoA + cytidine = CoA + N4-acetylcytidine. The cytidine is within the polynucleotide chain of a tRNA.
	GO:0000049	tRNA binding	Interacting selectively and non-covalently with transfer RNA.
	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:0016746	transferase activity, transferring acyl groups	Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
biological process
	GO:0051391	tRNA acetylation	The modification of tRNA structure by addition of an acetyl group to tRNA. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid.
	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.
	GO:0002101	tRNA wobble cytosine modification	The process in which a cytosine in position 34 of a tRNA is post-transcriptionally modified.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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Description

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Chains, Units

Ligands, Modified Residues, Ions (4, 25)

Sites (4, 4)

SS Bonds (0, 0)

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