3C8Z - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   THE 1.6 A CRYSTAL STRUCTURE OF MSHC: THE RATE LIMITING ENZYME IN THE MYCOTHIOL BIOSYNTHETIC PATHWAY

Authors :   L. W. Tremblay, F. Fan, M. W. Vetting, J. S. Blanchard

Date :   14 Feb 08 (Deposition) - 30 Dec 08 (Release) - 30 Dec 08 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Cysteine Ligase, Rossmann Fold, Cys-Sa Inhibitor, Zinc Binding, Atp-Binding, Aminoacyl-Trna Synthetase, Nucleotide- Binding, Protein Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. W. Tremblay, F. Fan, M. W. Vetting, J. S. Blanchard
The 1. 6 A Crystal Structure Of Mycobacterium Smegmatis Mshc: The Penultimate Enzyme In The Mycothiol Biosynthetic Pathway.
Biochemistry V. 47 13326 2008
PubMed-ID: 19053270 | Reference-DOI: 10.1021/BI801708F
(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 Plasmid	:	PET28A
	Expression System Strain	:	ROSETTA2BL21(DE3)
	Expression System Vector Type	:	PLASMID
	Gene	:	CYSS
	Organism Scientific	:	MYCOBACTERIUM SMEGMATIS

		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 (5, 12)

No.	Name	Count	Type	Full Name
1	1PE	1	Ligand/Ion	PENTAETHYLENE GLYCOL
2	5CA	2	Ligand/Ion	5'-O-(N-(L-CYSTEINYL)-SULFAMOYL)ADENOSINE
3	EPE	1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4	SO4	6	Ligand/Ion	SULFATE ION
5	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	1PE	1	Ligand/Ion	PENTAETHYLENE GLYCOL
2	5CA	1	Ligand/Ion	5'-O-(N-(L-CYSTEINYL)-SULFAMOYL)ADENOSINE
3	EPE	-1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4	SO4	4	Ligand/Ion	SULFATE ION
5	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (3, 4)

No.	Name	Count	Type	Full Name
1	1PE	-1	Ligand/Ion	PENTAETHYLENE GLYCOL
2	5CA	1	Ligand/Ion	5'-O-(N-(L-CYSTEINYL)-SULFAMOYL)ADENOSINE
3	EPE	1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4	SO4	2	Ligand/Ion	SULFATE ION
5	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CYS A:43 , CYS A:231 , HIS A:256	BINDING SITE FOR RESIDUE ZN A 413
02	AC2	SOFTWARE	CYS B:43 , CYS B:231 , HIS B:256	BINDING SITE FOR RESIDUE ZN B 413
03	AC3	SOFTWARE	HOH A:589 , ARG B:15 , ALA B:18 , LEU B:19 , PRO B:34 , HIS B:74 , HOH B:444 , HOH B:504 , HOH B:525 , HOH B:618	BINDING SITE FOR RESIDUE SO4 B 414
04	AC4	SOFTWARE	ARG A:207 , ARG A:210	BINDING SITE FOR RESIDUE SO4 A 414
05	AC5	SOFTWARE	PRO A:7 , ALA A:8 , ARG A:119 , HOH A:511 , HOH A:569	BINDING SITE FOR RESIDUE SO4 A 415
06	AC6	SOFTWARE	PRO B:7 , ALA B:8 , ARG B:119	BINDING SITE FOR RESIDUE SO4 B 415
07	AC7	SOFTWARE	SER A:215 , PRO A:217 , ARG A:222 , HOH A:506 , HIS B:-1	BINDING SITE FOR RESIDUE SO4 A 416
08	AC8	SOFTWARE	PRO A:353 , ASP A:354 , GLY A:391 , HIS A:392 , ASP A:393	BINDING SITE FOR RESIDUE SO4 A 417
09	AC9	SOFTWARE	CYS B:43 , GLY B:44 , ILE B:45 , THR B:46 , HIS B:52 , GLY B:54 , HIS B:55 , THR B:58 , TYR B:59 , ASN B:81 , THR B:83 , TRP B:227 , CYS B:231 , GLY B:248 , GLY B:249 , ASP B:251 , LEU B:252 , HIS B:256 , GLY B:281 , MET B:282 , ILE B:283 , HOH B:459 , HOH B:494 , HOH B:502 , HOH B:512 , HOH B:810 , HOH B:827	BINDING SITE FOR RESIDUE 5CA B 416
10	BC1	SOFTWARE	CYS A:43 , GLY A:44 , ILE A:45 , THR A:46 , GLY A:54 , HIS A:55 , THR A:58 , TYR A:59 , ASN A:81 , THR A:83 , TRP A:227 , CYS A:231 , GLY A:248 , GLY A:249 , ASP A:251 , LEU A:252 , GLY A:281 , MET A:282 , ILE A:283 , HOH A:433 , HOH A:479 , HOH A:579	BINDING SITE FOR RESIDUE 5CA A 418
11	BC2	SOFTWARE	TYR A:157 , GLU A:209 , HOH A:436 , HOH A:477 , PRO B:122 , HIS B:124	BINDING SITE FOR RESIDUE 1PE A 419
12	BC3	SOFTWARE	HOH A:465 , MET B:1 , ASP B:84 , ARG B:101 , ASP B:105 , THR B:108 , ALA B:128 , THR B:130 , TRP B:216	BINDING SITE FOR RESIDUE EPE B 417

(no "SS Bond" information available for 3C8Z)

Asymmetric Unit

No.	Residues
1	Phe A:254	-	Pro A:255
2	Ala B:50	-	Thr B:51
3	Phe B:254	-	Pro B:255

(no "SAP(SNP)/Variant" information available for 3C8Z)

(no "PROSITE Motif" information available for 3C8Z)

(no "Exon" information available for 3C8Z)

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:399
 aligned with MSHC_MYCS2 | A0QZY0 from UniProtKB/Swiss-Prot  Length:412

    Alignment length:412
                                    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  
           MSHC_MYCS2     1 MQSWSAPAIPVVPGRGPALRLFDSADRQVRPVTPGPTATMYVCGITPYDATHLGHAATYLTFDLVHRLWLDAGHTVQYVQNVTDVDDPLFERAERDGIDWRTLGDRETQLFREDMAALRVLPPHDYVAATDAIAEVVEMVEKLLASGAAYIVEDAEYPDVYFRADATAQFGYESGYDRDTMLTLFAERGGDPDRPGKSDQLDALLWRAERPGEPSWPSPFGRGRPGWHVECSAIALTRIGTGLDIQGGGSDLIFPHHEYSAAHAESVTGERRFARHYVHTGMIGWDGHKMSKSRGNLVLVSQLRAQGVDPSAIRLGLFSGHYREDRFWSNEVLDEANARLARWRSATALPEAPDATDVIARVRQYLADDLDTPKALAALDGWCTDALSYGGHDTESPRLVATTVDALLGVDL 412
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................eeee....eeee.....eeeeee.........hhhhhhhhhhhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh......eeee...hhhhhhhhhhhhhhh..eee........eee..............hhhhhhhhhhhh..............eeeeee..............eeehhhhhhhhhhhhhh...eeeeeee.hhh.hhhhhhhhhhhhhhh....eeeeeee..ee-------------.hhhhhhhh..hhhhhhhhhhh......ee.hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c8z A   1 MQSWSAPAIPVVPGRGPALRLFDSADRQVRPVTPGPTATMYVCGITPYDATHLGHAATYLTFDLVHRLWLDAGHTVQYVQNVTDVDDPLFERAERDGIDWRTLGDRETQLFREDMAALRVLPPHDYVAATDAIAEVVEMVEKLLASGAAYIVEDAEYPDVYFRADATAQFGYESGYDRDTMLTLFAERGGDPDRPGKSDQLDALLWRAERPGEPSWPSPFGRGRPGWHVECSAIALTRIGTGLDIQGGGSDLIFPHHEYSAAHAESVTGERRFARHYVHTGMIG-------------VLVSQLRAQGVDPSAIRLGLFSGHYREDRFWSNEVLDEANARLARWRSATALPEAPDATDVIARVRQYLADDLDTPKALAALDGWCTDALSYGGHDTESPRLVATTVDALLGVDL 412
                                    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   |     -       300       310       320       330       340       350       360       370       380       390       400       410  
                                                                                                                                                                                                                                                                                                                     284           298

Chain B from PDB  Type:PROTEIN  Length:401
 aligned with MSHC_MYCS2 | A0QZY0 from UniProtKB/Swiss-Prot  Length:412

    Alignment length:414
                              1                                                                                                                                                                                                                                                                                                                                                                                                                           
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408    
           MSHC_MYCS2     - --MQSWSAPAIPVVPGRGPALRLFDSADRQVRPVTPGPTATMYVCGITPYDATHLGHAATYLTFDLVHRLWLDAGHTVQYVQNVTDVDDPLFERAERDGIDWRTLGDRETQLFREDMAALRVLPPHDYVAATDAIAEVVEMVEKLLASGAAYIVEDAEYPDVYFRADATAQFGYESGYDRDTMLTLFAERGGDPDRPGKSDQLDALLWRAERPGEPSWPSPFGRGRPGWHVECSAIALTRIGTGLDIQGGGSDLIFPHHEYSAAHAESVTGERRFARHYVHTGMIGWDGHKMSKSRGNLVLVSQLRAQGVDPSAIRLGLFSGHYREDRFWSNEVLDEANARLARWRSATALPEAPDATDVIARVRQYLADDLDTPKALAALDGWCTDALSYGGHDTESPRLVATTVDALLGVDL 412
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....................eeee....eeee......eeeee.........hhhhhhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh......eeee...hhhhhhhhhhhhhhh..eee........eee..............hhhhhhhhhhhh..............eeeeee..............eeehhhhhhhhhhhhhh.....eeeee.hhh.hhhhhhhhhhhhhhh......eeeee..ee-------------.hhhhhhhh..hhhhhhhhhhh......ee.hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3c8z B  -1 HMMQSWSAPAIPVVPGRGPALRLFDSADRQVRPVTPGPTATMYVCGITPYDATHLGHAATYLTFDLVHRLWLDAGHTVQYVQNVTDVDDPLFERAERDGIDWRTLGDRETQLFREDMAALRVLPPHDYVAATDAIAEVVEMVEKLLASGAAYIVEDAEYPDVYFRADATAQFGYESGYDRDTMLTLFAERGGDPDRPGKSDQLDALLWRAERPGEPSWPSPFGRGRPGWHVECSAIALTRIGTGLDIQGGGSDLIFPHHEYSAAHAESVTGERRFARHYVHTGMIG-------------VLVSQLRAQGVDPSAIRLGLFSGHYREDRFWSNEVLDEANARLARWRSATALPEAPDATDVIARVRQYLADDLDTPKALAALDGWCTDALSYGGHDTESPRLVATTVDALLGVDL 412
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278     |   -       298       308       318       328       338       348       358       368       378       388       398       408    
                                                                                                                                                                                                                                                                                                                       284           298

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 3C8Z)

(no "CATH Domain" information available for 3C8Z)

(no "Pfam Domain" information available for 3C8Z)

Asymmetric Unit(hide GO term definitions)

Chain A,B (MSHC_MYCS2 | A0QZY0)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0035446	cysteine-glucosaminylinositol ligase activity	Catalysis of the reaction: 1-(2-amino-2-deoxy-alpha-D-glucopyranoside)-1D-myo-inositol + L-cysteine + ATP = 1-D-myo-inosityl-2-L-cysteinylamido-2-deoxy-alpha-D-glucopyranoside + AMP + diphosphate + 2 H+. 1-(2-amino-2-deoxy-alpha-D-glucopyranoside)-1D-myo-inositol is also known as glucosaminyl-inositol or GlcN-Ins, and 1-D-myo-inosityl-2-L-cysteinylamido-2-deoxy-alpha-D-glucopyranoside as desacetylmycothiol or Cys-GlcN-Ins.
	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:0010125	mycothiol biosynthetic process	The chemical reactions and pathways resulting in the formation of mycothiol, which consists of N-acetyl-L-cysteine linked to a pseudodisaccharide, D-glucosamine and myo-inositol. Mycothiol is produced in actinomycetes like mycobacteria and serves similar functions to glutathione.

Asymmetric Unit
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	Cis Peptide Bonds
		Ala B:50 - Thr B:51	[ RasMol ]
		Phe A:254 - Pro A:255	[ RasMol ]
		Phe B:254 - Pro B:255	[ RasMol ]

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	3c8z
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1li5	CYSTEINYL-TRNA SYNTHASE
1u0b	CYSTEINYL-TRNA SYNTHASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 12)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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Gene Ontology (7, 7)

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