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Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS CYSM, THE CYSTEINE SYNTHASE B

Authors :   C. T. Jurgenson, K. E. Burns, T. P. Begley, S. E. Ealick

Date :   22 Jul 08 (Deposition) - 23 Sep 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.81

Chains :   Asym./Biol. Unit : A,B

Keywords :   Cysteine Synthase, Amino-Acid Biosynthesis, Cysteine Biosynthesis, Pyridoxal Phosphate, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. T. Jurgenson, K. E. Burns, T. P. Begley, S. E. Ealick
Crystal Structure Of A Sulfur Carrier Protein Complex Found In The Cysteine Biosynthetic Pathway Of Mycobacterium Tuberculosis.
Biochemistry V. 47 10354 2008
PubMed-ID: 18771296 | Reference-DOI: 10.1021/BI800915J

Molecule 1 - CYSTEINE SYNTHASE B
	Atcc	:	25618
	Chains	:	A, B
	EC Number	:	2.5.1.47
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET16B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CYSM, RV1336, MT1377, MTCY130.21
	Mutation	:	YES
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	83332
	Strain	:	H37RV
	Synonym	:	O-ACETYLSERINE SULFHYDRYLASE B, O-ACETYLSERINE(THIOL)-LYASE B, CSASE B

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 5)

No.	Name	Count	Type	Full Name
1	PLP	2	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE
2	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:240 , SER A:241 , ASP A:246 , HIS A:271	BINDING SITE FOR RESIDUE SO4 A 324
2	AC2	SOFTWARE	THR B:78 , SER B:79 , GLY B:80 , GLN B:151 , TYR B:152 , HOH B:494 , HOH B:499	BINDING SITE FOR RESIDUE SO4 B 324
3	AC3	SOFTWARE	ARG B:286 , HOH B:481 , HOH B:493	BINDING SITE FOR RESIDUE SO4 B 325
4	AC4	SOFTWARE	LYS A:51 , ASN A:81 , GLY A:182 , LEU A:183 , GLY A:184 , THR A:185 , THR A:186 , GLY A:187 , THR A:188 , SER A:265 , ALA A:294 , ASP A:295 , HOH A:425	BINDING SITE FOR RESIDUE PLP A 401
5	AC5	SOFTWARE	LYS B:51 , ASN B:81 , GLY B:182 , GLY B:184 , THR B:185 , THR B:186 , GLY B:187 , THR B:188 , ALA B:218 , LEU B:219 , SER B:265 , ALA B:294 , ASP B:295 , HOH B:441	BINDING SITE FOR RESIDUE PLP B 401

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

(no "Cis Peptide Bond" information available for 3DWI)

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYS_SYNTHASE	PS00901	Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site.	CYSM_MYCTO	40-58	2	A:40-58 B:40-58
1	CYS_SYNTHASE	PS00901		CYSM_MYCTU	40-58	2	A:40-58 B:40-58

(no "Exon" information available for 3DWI)

Asymmetric/Biological 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:297
 aligned with CYSM_MYCTO | P9WP52 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:314
                                    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    
           CYSM_MYCTO     1 MTRYDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAAEGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLPEITHFVAGLGTTGTLMGTGRFLREHVANVKIVAAEPRYGEGVYALRNMDEGFVPELYDPEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKYLSTGAYAGSLDDAE 314
               SCOP domains d3dwia_ A: automated matches                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.hhhhhh....eee................eeeeeee.hhh.....hhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhh..eeeee.--.hhhhhhhhhhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh...eeeeee..---------------...........eeee.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------------------------CYS_SYNTHASE       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dwi A   1 MTRYDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSA--GGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLPEITHFVAGLGTTGTLMGTGRFLREHVANVAIVAAEPR---------------VPELYDPEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKYLSTGAYAGSLDDAE 314
                                    10        20        30        40        50        60        70        80        90       100       110       120   |  |130       140       150       160       170       180       190       200       210|        -      |230       240       250       260       270       280       290       300       310    
                                                                                                                                                     124  |                                                                                 211             227                                                                                       
                                                                                                                                                        127

Chain A from PDB  Type:PROTEIN  Length:297
 aligned with CYSM_MYCTU | P9WP53 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:314
                                    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    
           CYSM_MYCTU     1 MTRYDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAAEGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLPEITHFVAGLGTTGTLMGTGRFLREHVANVKIVAAEPRYGEGVYALRNMDEGFVPELYDPEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKYLSTGAYAGSLDDAE 314
               SCOP domains d3dwia_ A: automated matches                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.hhhhhh....eee................eeeeeee.hhh.....hhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhh..eeeee.--.hhhhhhhhhhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh...eeeeee..---------------...........eeee.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------CYS_SYNTHASE       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dwi A   1 MTRYDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSA--GGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLPEITHFVAGLGTTGTLMGTGRFLREHVANVAIVAAEPR---------------VPELYDPEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKYLSTGAYAGSLDDAE 314
                                    10        20        30        40        50        60        70        80        90       100       110       120   |  |130       140       150       160       170       180       190       200       210|        -      |230       240       250       260       270       280       290       300       310    
                                                                                                                                                     124  |                                                                                 211             227                                                                                       
                                                                                                                                                        127

Chain B from PDB  Type:PROTEIN  Length:309
 aligned with CYSM_MYCTO | P9WP52 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:312
                                    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  
           CYSM_MYCTO     1 MTRYDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAAEGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLPEITHFVAGLGTTGTLMGTGRFLREHVANVKIVAAEPRYGEGVYALRNMDEGFVPELYDPEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKYLSTGAYAGSLDD 312
               SCOP domains d3dwib_ B: automated matches                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee.hhhhh.....eee................eeeeeee.hhh.....hhhhhhhhhhhhhhh.......eeee...hhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhh.eeee...---hhhhhhhhhhhhh....eee.....hhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh...eeeeeee.....................hhhhh.eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) ---------------------------------------CYS_SYNTHASE       -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3dwi B   1 MTRYDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAA---SNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLPEITHFVAGLGTTGTLMGTGRFLREHVANVAIVAAEPRYGEGVYALRNMDEGFVPELYDPEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKYLSTGAYAGSLDD 312
                                    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  
                                                                                                                                                      125 129

Chain B from PDB  Type:PROTEIN  Length:309
 aligned with CYSM_MYCTU | P9WP53 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:312
                                    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  
           CYSM_MYCTU     1 MTRYDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAAEGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLPEITHFVAGLGTTGTLMGTGRFLREHVANVKIVAAEPRYGEGVYALRNMDEGFVPELYDPEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKYLSTGAYAGSLDD 312
               SCOP domains d3dwib_ B: automated matches                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee.hhhhh.....eee................eeeeeee.hhh.....hhhhhhhhhhhhhhh.......eeee...hhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhh.eeee...---hhhhhhhhhhhhh....eee.....hhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh...eeeeeee.....................hhhhh.eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------CYS_SYNTHASE       -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3dwi B   1 MTRYDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAA---SNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLPEITHFVAGLGTTGTLMGTGRFLREHVANVAIVAAEPRYGEGVYALRNMDEGFVPELYDPEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKYLSTGAYAGSLDD 312
                                    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  
                                                                                                                                                      125 129

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Tryptophan synthase beta subunit-like PLP-dependent enzymes (165)

Superfamily: Tryptophan synthase beta subunit-like PLP-dependent enzymes (165)

Family: automated matches (45)

Protein domain: automated matches (45)

Mycobacterium tuberculosis [TaxId: 83332] (2)

1a	d3dwia_	A:
1b	d3dwib_	B:

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (CYSM_MYCTO | P9WP52)

molecular function
	GO:0004124	cysteine synthase activity	Catalysis of the reaction: O3-acetyl-L-serine + hydrogen sulfide = L-cysteine + acetate.
	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:0008652	cellular amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
	GO:0019344	cysteine biosynthetic process	The chemical reactions and pathways resulting in the formation of cysteine, 2-amino-3-mercaptopropanoic acid.
	GO:0006535	cysteine biosynthetic process from serine	The chemical reactions and pathways resulting in the formation of cysteine from other compounds, including serine.

Chain A,B (CYSM_MYCTU | P9WP53)

molecular function
	GO:0033847	O-phosphoserine sulfhydrylase activity	Catalysis of the reaction: O-phospho-L-serine + hydrogen sulfide = L-cysteine + phosphate.
	GO:0004124	cysteine synthase activity	Catalysis of the reaction: O3-acetyl-L-serine + hydrogen sulfide = L-cysteine + acetate.
	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:0030170	pyridoxal phosphate binding	Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
	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:0008652	cellular amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
	GO:0019344	cysteine biosynthetic process	The chemical reactions and pathways resulting in the formation of cysteine, 2-amino-3-mercaptopropanoic acid.
	GO:0006535	cysteine biosynthetic process from serine	The chemical reactions and pathways resulting in the formation of cysteine from other compounds, including serine.
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:0043234	protein complex	A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3dwi)

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	3dwi
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	CYSM_MYCTO \| P9WP52
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	CYSM_MYCTU \| P9WP53
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	2.5.1.47
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UniProtKB/Swiss-Prot
	CYSM_MYCTO \| P9WP52	:	3dki 3dwg 3fgp 5i7a
	CYSM_MYCTU \| P9WP53	:	3dki 3dwg 3fgp 5i6d 5i7a 5i7h 5i7o 5i7r 5iw8 5iwc

3dwg	CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS CYSM-CYSO COMPLEX, A CYSTEINE SYNTHASE B - ANTIGEN COMPLEX
3dwm	CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS CYSO, AN ANTIGEN CFP10A

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (11, 16)

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