1LI7 - JenaLib

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Title :   CRYSTAL STRUCTURE OF CYSTEINYL-TRNA SYNTHETASE WITH CYSTEINE SUBSTRATE BOUND

Authors :   K. J. Newberry, Y. -M. Hou, J. J. Perona

Date :   17 Apr 02 (Deposition) - 26 Apr 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Trna Synthetase, Cysteine, E. Coli, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. J. Newberry, Y. -M. Hou, J. J. Perona
Structural Origins Of Amino Acid Selection Without Editing By Cysteinyl-Trna Synthetase
Embo J. V. 21 2778 2002
PubMed-ID: 12032090 | Reference-DOI: 10.1093/EMBOJ/21.11.2778
(for further references see the PDB file header)

Molecule 1 - CYSTEINYL-TRNA SYNTHETASE
	Chains	:	A, B
	EC Number	:	6.1.1.16
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	CYSTEINE--TRNA LIGASE

		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 (2, 4)

No.	Name	Count	Type	Full Name
1	CYS	2	Mod. Amino Acid	CYSTEINE
2	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CYS	1	Mod. Amino Acid	CYSTEINE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CYS	1	Mod. Amino Acid	CYSTEINE
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:28 , CYS A:209 , HIS A:234 , GLU A:238 , CYS A:1000	BINDING SITE FOR RESIDUE ZN A 963
2	AC2	SOFTWARE	CYS B:28 , CYS B:209 , HIS B:234 , GLU B:238 , CYS B:1001	BINDING SITE FOR RESIDUE ZN B 964
3	AC3	SOFTWARE	CYS A:28 , GLY A:29 , ILE A:30 , THR A:31 , THR A:68 , TRP A:205 , CYS A:209 , LEU A:230 , HIS A:234 , ZN A:963	BINDING SITE FOR RESIDUE CYS A 1000
4	AC4	SOFTWARE	CYS B:28 , GLY B:29 , ILE B:30 , THR B:31 , THR B:68 , TRP B:205 , CYS B:209 , HIS B:234 , ZN B:964	BINDING SITE FOR RESIDUE CYS B 1001

(no "SS Bond" information available for 1LI7)

(no "Cis Peptide Bond" information available for 1LI7)

(no "SAP(SNP)/Variant" information available for 1LI7)

(no "PROSITE Motif" information available for 1LI7)

(no "Exon" information available for 1LI7)

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:386
 aligned with SYC_ECOLI | P21888 from UniProtKB/Swiss-Prot  Length:461

    Alignment length:402
                                    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  
            SYC_ECOLI     1 MLKIFNTLTRQKEEFKPIHAGEVGMYVCGITVYDLCHIGHGRTFVAFDVVARYLRFLGYKLKYVRNITDIDDKIIKRANENGESFVAMVDRMIAEMHKDFDALNILRPDMEPRATHHIAEIIELTEQLIAKGHAYVADNGDVMFDVPTDPTYGVLSRQDLDQLQAGARVDVVDDKRNPMDFVLWKMSKEGEPSWPSPWGAGRPGWHIECSAMNCKQLGNHFDIHGGGSDLMFPHHENEIAQSTCAHDGQYVNYWMHSGMVMVDREKMSKSLGNFFTVRDVLKYYDAETVRYFLMSGHYRSQLNYSEENLKQARAALERLYTALRGTDKTVAPAGGEAFEARFIEAMDDDFNTPEAYSVLFDMAREVNRLKAEDMAAANAMASHLRKLSAVLGLLEQEPEAFL 402
               SCOP domains d1li7a2 A:1-315 Cysteinyl-tRNA synthetase (CysRS)                                                                                                                                                                                                                                                                          d1li7a1 A:316-402 Cysteinyl-tRNA synthetase (CysRS)                                     SCOP domains
               CATH domains ----------------1li7A01 A:17-305 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                                                                           ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee......eee.......eeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeee..hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh..eee.....eee.hhhh.........----------------......eeeeee..............ee..hhhhhhhhhhhhhh..eeeeeee.hhh.hhhhhhhhhhhh......eeeeeee..ee..............hhhhhhh..hhhhhhhhhhh......ee.hhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1li7 A   1 MLKIFNTLTRQKEEFKPIHAGEVGMYVCGITVYDLCHIGHGRTFVAFDVVARYLRFLGYKLKYVRNITDIDDKIIKRANENGESFVAMVDRMIAEMHKDFDALNILRPDMEPRATHHIAEIIELTEQLIAKGHAYVADNGDVMFDVPTDPTYGVLSRQ----------------KRNPMDFVLWKMSKEGEPSWPSPWGAGRPGWHIECSAMNCKQLGNHFDIHGGGSDLMFPHHENEIAQSTCAHDGQYVNYWMHSGMVMVDREKMSKSLGNFFTVRDVLKYYDAETVRYFLMSGHYRSQLNYSEENLKQARAALERLYTALRGTDKTVAPAGGEAFEARFIEAMDDDFNTPEAYSVLFDMAREVNRLKAEDMAAANAMASHLRKLSAVLGLLEQEPEAFL 402
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       | -         -    |  180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400  
                                                                                                                                                                                       158              175

Chain B from PDB  Type:PROTEIN  Length:375
 aligned with SYC_ECOLI | P21888 from UniProtKB/Swiss-Prot  Length:461

    Alignment length:402
                                    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  
            SYC_ECOLI     1 MLKIFNTLTRQKEEFKPIHAGEVGMYVCGITVYDLCHIGHGRTFVAFDVVARYLRFLGYKLKYVRNITDIDDKIIKRANENGESFVAMVDRMIAEMHKDFDALNILRPDMEPRATHHIAEIIELTEQLIAKGHAYVADNGDVMFDVPTDPTYGVLSRQDLDQLQAGARVDVVDDKRNPMDFVLWKMSKEGEPSWPSPWGAGRPGWHIECSAMNCKQLGNHFDIHGGGSDLMFPHHENEIAQSTCAHDGQYVNYWMHSGMVMVDREKMSKSLGNFFTVRDVLKYYDAETVRYFLMSGHYRSQLNYSEENLKQARAALERLYTALRGTDKTVAPAGGEAFEARFIEAMDDDFNTPEAYSVLFDMAREVNRLKAEDMAAANAMASHLRKLSAVLGLLEQEPEAFL 402
               SCOP domains d1li7b2 B:1-315 Cysteinyl-tRNA synthetase (CysRS)                                                                                                                                                                                                                                                                          d1li7b1 B:316-402 Cysteinyl-tRNA synthetase (CysRS)                                     SCOP domains
               CATH domains ----------------1li7B01 B:17-305 Tyrosyl-Transfer RNA Synthetase , subunit E,      domain 1                                                                                                                                                                                                                      ------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------tRNA-synt_1e-1li7B03 B:14-314                                                                                                                                                                                                                                                                                --------------------------DALR_2-1li7B01 B:341-402                                       Pfam domains (1)
           Pfam domains (2) -------------tRNA-synt_1e-1li7B04 B:14-314                                                                                                                                                                                                                                                                                --------------------------DALR_2-1li7B02 B:341-402                                       Pfam domains (2)
         Sec.struct. author ..eee......eee.......eeeeee.........hhhhhhhhhhhhhhhhhhhhh..eeeeee.....hhhhhh.-----..hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh..eee.....eee.hhhh.........-----------------.....eeeeee..............eeehhhhhhhhhhhhhhh..eeeeeee.hhh.hhhhhhhhhhhhhh....eeeeeee..eee.....-----...hhhhhhhhhhhhhhhhhhhh......eeehhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1li7 B   1 MLKIFNTLTRQKEEFKPIHAGEVGMYVCGITVYDLCHIGHGRTFVAFDVVARYLRFLGYKLKYVRNITDIDDKIIKR-----ESFVAMVDRMIAEMHKDFDALNILRPDMEPRATHHIAEIIELTEQLIAKGHAYVADNGDVMFDVPTDPTYGVLSRQ-----------------RNPMDFVLWKMSKEGEPSWPSPWGAGRPGWHIECSAMNCKQLGNHFDIHGGGSDLMFPHHENEIAQSTCAHDGQYVNYWMHSGMVMVDREKM-----NFFTVRDVLKYYDAETVRYFLMSGHYRSQLNYSEENLKQARAALERLYTALRGTDKTVAPAGGEAFEARFIEAMDDDFNTPEAYSVLFDMAREVNRLKAEDMAAANAMASHLRKLSAVLGLLEQEPEAFL 402
                                    10        20        30        40        50        60        70      |  -  |     90       100       110       120       130       140       150       | -         -     | 180       190       200       210       220       230       240       250       260      |  -  |    280       290       300       310       320       330       340       350       360       370       380       390       400  
                                                                                                       77    83                                                                        158               176                                                                                        267   273

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 '\|'

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1 (328)

Escherichia coli. Organism_taxid: 562. (13)

1a	1li7B01	B:17-305
1b	1li7A01	A:17-305

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: DALR (5)

Family: DALR_2 (3)

Escherichia coli (strain K12) (3)

1a	DALR_2-1li7B01	B:341-402
1b	DALR_2-1li7B02	B:341-402

Clan: HUP (230)

Family: tRNA-synt_1e (3)

Escherichia coli (strain K12) (3)

2a	tRNA-synt_1e-1li7B03	B:14-314
2b	tRNA-synt_1e-1li7B04	B:14-314

Asymmetric Unit(hide GO term definitions)

Chain A,B (SYC_ECOLI | P21888)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004812	aminoacyl-tRNA ligase activity	Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP.
	GO:0004817	cysteine-tRNA ligase activity	Catalysis of the reaction: ATP + L-cysteine + tRNA(Cys) = AMP + diphosphate + L-cysteinyl-tRNA(Cys).
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	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:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0006423	cysteinyl-tRNA aminoacylation	The process of coupling cysteine to cysteinyl-tRNA, catalyzed by cysteinyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA.
	GO:0006418	tRNA aminoacylation for protein translation	The synthesis of aminoacyl tRNA by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA, to be used in ribosome-mediated polypeptide synthesis.
	GO:0006412	translation	The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
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.

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1li5	UNLIGANDED STRUCTURE OF CYSRS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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