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Title :   CRYSTAL STRUCTURE OF HTE CRYPTOSPORIDIUM MURIS CYTOSOLIC LEUCYL-TRNA SYNTHETASE EDITING DOMAIN COMPLEX WITH A POST-TRANSFER EDITING ANALOGUE OF NORVALINE (NV2AA)

Authors :   A. Palencia, R. J. Liu, M. Lukarska, J. Gut, A. Bougdour, B. Touquet, E. D M. R. K. Alley, P. J. Rosenthal, M. A. Hakimi, S. Cusack

Date :   20 Nov 15 (Deposition) - 03 Aug 16 (Release) - 05 Oct 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x),D (1x)
Biol. Unit 2: B (1x),C (1x)
Biol. Unit 3: A (1x),D (1x)
Biol. Unit 4: B (1x),C (1x)

Keywords :   Lyase, Cryptosporidium, Leucine-Trna Ligase (Leurs) Activity, Atp + L-Leucine + Trna(Leucine) Give Amp + Diphosphate + L-Leucyl-Trna(Leucine), Post-Transfer Editing Activity Of Leurs, Aminoacyl-Trna Synthetase, Protein Biosynthesis, Novel Boron Inhibitors Of The Editing Site Of Leurs (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Palencia, R. Liu, M. Lukarska, J. Gut, A. Bougdour, B. Touquet, E. Wang, X. Li, M. R. K. Alley, Y. R. Freund, P. J. Rosenthal, M. Hakimi, S. Cusack
Cryptosporidium And Toxoplasma Parasites Are Inhibited By A Benzoxaborole Targeting Leucyl-Trna Synthetase.
Antimicrob. Agents Chemother. V. 60 5817 2016
PubMed-ID: 27431220 | Reference-DOI: 10.1128/AAC.00873-16

Molecule 1 - LEUCYL-TRNA SYNTHETASE
	Chains	:	A, B, C, D
	EC Number	:	6.1.1.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	K-12
	Expression System Taxid	:	83333
	Expression System Variant	:	DE3 BL21 RIL
	Expression System Vector	:	PETM-11
	Expression System Vector Type	:	PLASMID
	Fragment	:	EDITING DOMAIN, UNP RESIDUES 254-541
	Organism Scientific	:	CRYPTOSPORIDIUM MURIS
	Organism Taxid	:	441375
	Strain	:	RN66

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A (1x)			D (1x)
Biological Unit 2 (1x)	:		B (1x)	C (1x)
Biological Unit 3 (1x)	:	A (1x)			D (1x)
Biological Unit 4 (1x)	:		B (1x)	C (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 10)

No.	Name	Count	Type	Full Name
1	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
2	K	2	Ligand/Ion	POTASSIUM ION
3	VRT	4	Ligand/Ion	2'-(L-NORVALYL)AMINO-2'-DEOXYADENOSINE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	K	-1	Ligand/Ion	POTASSIUM ION
3	VRT	1	Ligand/Ion	2'-(L-NORVALYL)AMINO-2'-DEOXYADENOSINE

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	K	-1	Ligand/Ion	POTASSIUM ION
3	VRT	1	Ligand/Ion	2'-(L-NORVALYL)AMINO-2'-DEOXYADENOSINE

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
2	K	-1	Ligand/Ion	POTASSIUM ION
3	VRT	1	Ligand/Ion	2'-(L-NORVALYL)AMINO-2'-DEOXYADENOSINE

Biological Unit 4 (2, 2)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	K	-1	Ligand/Ion	POTASSIUM ION
3	VRT	1	Ligand/Ion	2'-(L-NORVALYL)AMINO-2'-DEOXYADENOSINE

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ALA A:286 , THR A:287 , LEU A:288 , THR A:292 , SER A:415 , LYS A:418 , GLY A:421 , VAL A:423 , THR A:424 , ASP A:433 , LYS A:496 , HOH A:2006 , HOH A:2007 , HOH A:2049	BINDING SITE FOR RESIDUE VRT A1542
02	AC2	SOFTWARE	TYR A:434 , ARG A:438 , LYS A:441 , PRO A:460	BINDING SITE FOR RESIDUE EDO A1543
03	AC3	SOFTWARE	TYR B:258 , ALA B:286 , THR B:287 , LEU B:288 , ARG B:289 , THR B:292 , SER B:415 , LYS B:418 , GLY B:421 , VAL B:423 , THR B:424 , SER B:430 , ASP B:433 , LYS B:496 , HOH B:2009 , HOH B:2010 , HOH B:2052	BINDING SITE FOR RESIDUE VRT B1542
04	AC4	SOFTWARE	PHE A:412 , LYS A:449 , TYR B:505 , LYS B:518 , CYS B:520	BINDING SITE FOR RESIDUE EDO B1543
05	AC5	SOFTWARE	ALA C:286 , THR C:287 , LEU C:288 , THR C:292 , SER C:415 , LYS C:418 , GLY C:421 , VAL C:423 , THR C:424 , ASP C:433 , LYS C:496 , HOH C:2014	BINDING SITE FOR RESIDUE VRT C1542
06	AC6	SOFTWARE	PHE B:407 , GLU B:455 , GLU C:462 , ARG C:511 , EDO C:1544	BINDING SITE FOR RESIDUE EDO C1543
07	AC7	SOFTWARE	GLU B:455 , LEU B:458 , TYR C:294 , PRO C:402 , ARG C:511 , EDO C:1543	BINDING SITE FOR RESIDUE EDO C1544
08	AC8	SOFTWARE	ALA C:398 , THR C:401 , TYR C:403 , HOH C:2046 , HOH C:2049	BINDING SITE FOR RESIDUE K C1545
09	AC9	SOFTWARE	ALA D:286 , THR D:287 , LEU D:288 , THR D:292 , SER D:415 , LYS D:418 , GLY D:421 , VAL D:423 , THR D:424 , ASP D:433 , LYS D:496 , HOH D:2007 , HOH D:2008 , HOH D:2052 , HOH D:2108	BINDING SITE FOR RESIDUE VRT D1542
10	BC1	SOFTWARE	ALA D:398 , THR D:401 , TYR D:403 , HOH D:2034 , HOH D:2035 , HOH D:2038	BINDING SITE FOR RESIDUE K D1543

(no "SS Bond" information available for 5FOG)

(no "Cis Peptide Bond" information available for 5FOG)

(no "SAP(SNP)/Variant" information available for 5FOG)

(no "PROSITE Motif" information available for 5FOG)

(no "Exon" information available for 5FOG)

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
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Chain A from PDB  Type:PROTEIN  Length:279
                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee...hhhhhhhhh..eeeeeeee.hhhhhhhh.eeee....eeeeeee.......hhhhh......ee.hhhhhh....eeeeehhhhhhhhhh.....ee....ee.eeeeee.hhhh..eee.......eeeeee...........eeee....hhhhhhhhhhhhhhhhhhhhh..hhhhh......ee......hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhhh..eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fog A 254 GPQEYTLIKLKIHLIPEFLGSIVKGREVFVVCATLRPETMYGQTNCWILPDGEYDLVLAFDQVIPYDAKTSDGVLCKIFDKYEDTMKECNTVYICSERSAYNMAYQGIVPLIHGLPRIVSLGKVYGEQLIGTPLSAPMTPYSLIFILPMFSISMEKGTGIVTSVPSDSPDDYAALRDIKTKPLLREKYSIKDEWILDPLEIIEVPGFGFMTAELLCNQYKIQSQNDSAKLKQAKEEIYKKEFYEGILIRGKYSGMKICDAKELIRESLIKDGYALIYLE 541
                                   263       273       283       293       303       313       323       333       343       353       363   ||  382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532         
                                                                                                                                           367|                                                                                                                                                                    
                                                                                                                                            377

Chain B from PDB  Type:PROTEIN  Length:281
                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee...hhhhhhhhh..eeeeeeee.hhhhhhhh.eeee....eeeeeee...........ee.hhhhhh....eeeeehhhhhhhhhh.....eeeee.......eeeee.eeeeee.hhhh..eee.......eeeeee...........eeee....hhhhhhhhhhhhhhhhhhhhh..hhhhh......ee......hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhhh..eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fog B 254 GPQEYTLIKLKIHLIPEFLGSIVKGREVFVVCATLRPETMYGQTNCWILPDGEYDLVLAFDQVIPGVLCKIFDKYEDTMKECNTVYICSERSAYNMAYQGIVPLIHGREQGVSDKLLPRIVSLGKVYGEQLIGTPLSAPMTPYSLIFILPMFSISMEKGTGIVTSVPSDSPDDYAALRDIKTKPLLREKYSIKDEWILDPLEIIEVPGFGFMTAELLCNQYKIQSQNDSAKLKQAKEEIYKKEFYEGILIRGKYSGMKICDAKELIRESLIKDGYALIYLE 541
                                   263       273       283       293       303       313    || 330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540 
                                                                                          318|                                                                                                                                                                                                                       
                                                                                           326

Chain C from PDB  Type:PROTEIN  Length:274
                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee...hhhhhhhhh..eeeeeeee.hhhhhhhh.eeee....eeeeeee..............ee.hhhhhhhh..eeeeehhhhhhhhhh.....ee...ee.eeeeee.hhhh..eee........eeeee...........eeee....hhhhhhhhhhhhhhhhhhhhh..hhhhh......ee......hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhhh..eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fog C 254 GPQEYTLIKLKIHLIPEFLGSIVKGREVFVVCATLRPETMYGQTNCWILPDGEYDLVLAFDQVIPTSDGVLCKIFDKYEDTMKECNTVYICSERSAYNMAYQGIVPLIHLPRIVSLGKVYGEQLIGTPLSAPMTPYSLIFILPMFSISMEKGTGIVTSVPSDSPDDYAALRDIKTKPLLREKYSIKDEWILDPLEIIEVPGFGFMTAELLCNQYKIQSQNDSAKLKQAKEEIYKKEFYEGILIRGKYSGMKICDAKELIRESLIKDGYALIYLE 541
                                   263       273       283       293       303       313    || 327       337       347       357       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537    
                                                                                          318|                                        366|                                                                                                                                                                    
                                                                                           323                                         377

Chain D from PDB  Type:PROTEIN  Length:284
                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee...hhhhh......eeeeeeee.hhhhhhhh.eeee....eeeeeee..............ee.hhhhhh....eeeeehhhhhhhhhh.....ee.............ee.eeeeee.hhhh..eee........eeeee...........eeee....hhhhhhhhhhhhhhhhhhhhh..hhhhh......ee......hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhhh..eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fog D 254 GPQEYTLIKLKIHLIPEFLGSIVKGREVFVVCATLRPETMYGQTNCWILPDGEYDLVLAFDQVIPTSDGVLCKIFDKYEDTMKECNTVYICSERSAYNMAYQGIVPLIHGREQGVSDKLLPRIVSLGKVYGEQLIGTPLSAPMTPYSLIFILPMFSISMEKGTGIVTSVPSDSPDDYAALRDIKTKPLLREKYSIKDEWILDPLEIIEVPGFGFMTAELLCNQYKIQSQNDSAKLKQAKEEIYKKEFYEGILIRGKYSGMKICDAKELIRESLIKDGYALIYLE 541
                                   263       273       283       293       303       313    || 327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537    
                                                                                          318|                                                                                                                                                                                                                          
                                                                                           323

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

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Ligands, Modified Residues, Ions (3, 10)

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