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Asym./Biol. Unit (Jmol Viewer)

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

Title :   STRUCTURE OF THE MYCOBACTERIUM TUBERCULOSIS APS KINASE CYSC IN COMPLEX WITH ADP AND APS

Authors :   O. Poyraz, B. Lohkamp, R. Schnell, G. Schneider

Date :   29 Jul 13 (Deposition) - 13 Aug 14 (Release) - 08 Apr 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Transferase, Sulfur Assimilation, Adp (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   O. Poyraz, K. Brunner, B. Lohkamp, H. Axelsson, L. G. J. Hammarstrom, R. Schnell, G. Schneider
Crystal Structures Of The Kinase Domain Of The Sulfate- Activating Complex In Mycobacterium Tuberculosis.
Plos One V. 10 21494 2015
PubMed-ID: 25807013 | Reference-DOI: 10.1371/JOURNAL.PONE.0121494

Molecule 1 - BIFUNCTIONAL ENZYME CYSN/CYSC
	Chains	:	A, B
	EC Number	:	2.7.7.4, 2.7.1.25
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET28APLUS
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 440-612
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	1773
	Synonym	:	CYSC, SULFATE ADENYLYLTRANSFERASE SUBUNIT 1, ATP-SULFURYLASE LARGE SUBUNIT, SULFATE ADENYLATE TRANSFERASE, SAT, ADENYLYL-SULFATE KINASE, APS KINASE, ATP ADENOSINE-5'-PHOSPHOSULFATE 3'-PHOSPHOTRANSFERASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 8)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	ADX	2	Ligand/Ion	ADENOSINE-5'-PHOSPHOSULFATE
3	CIT	2	Ligand/Ion	CITRIC ACID
4	EDO	2	Ligand/Ion	1,2-ETHANEDIOL

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:480 , ARG A:483 , PHE A:492 , ARG A:497 , ASN A:500 , LEU A:501 , ALA A:522 , ILE A:523 , SER A:524 , PRO A:525 , LYS A:562 , LEU A:564 , HIS A:575 , PHE A:576 , THR A:577 , EDO A:1616 , HOH A:2005 , HOH A:2025	BINDING SITE FOR RESIDUE ADX A1613
2	AC2	SOFTWARE	LEU A:451 , GLY A:453 , SER A:454 , GLY A:455 , LYS A:456 , SER A:457 , SER A:458 , ARG A:559 , PRO A:561 , ARG A:597 , ILE A:599 , GLN A:602 , EDO A:1616 , HOH A:2005 , ADP B:1614	BINDING SITE FOR RESIDUE ADP A1614
3	AC3	SOFTWARE	ALA A:527 , ARG A:530 , ALA A:531 , ARG A:534 , GLU A:546 , PRO A:586 , LYS A:587 , ASN A:588 , PRO A:589	BINDING SITE FOR RESIDUE CIT A1615
4	AC4	SOFTWARE	SER A:457 , ASP A:478 , ASP A:480 , PRO A:521 , ADX A:1613 , ADP A:1614 , HOH A:2005	BINDING SITE FOR RESIDUE EDO A1616
5	AC5	SOFTWARE	GLY B:479 , ARG B:483 , PHE B:492 , ARG B:497 , ASN B:500 , LEU B:501 , ALA B:522 , ILE B:523 , SER B:524 , PRO B:525 , LYS B:562 , LEU B:564 , HIS B:575 , PHE B:576 , THR B:577 , EDO B:1616 , HOH B:2004	BINDING SITE FOR RESIDUE ADX B1613
6	AC6	SOFTWARE	ARG A:558 , ADP A:1614 , LEU B:451 , SER B:452 , GLY B:453 , SER B:454 , GLY B:455 , LYS B:456 , SER B:457 , SER B:458 , ARG B:559 , ARG B:597 , ILE B:599 , GLN B:602 , EDO B:1616 , HOH B:2004	BINDING SITE FOR RESIDUE ADP B1614
7	AC7	SOFTWARE	ALA B:527 , ARG B:530 , ALA B:531 , ARG B:534 , GLU B:546 , LYS B:587 , ASN B:588	BINDING SITE FOR RESIDUE CIT B1615
8	AC8	SOFTWARE	ASP B:478 , PRO B:521 , ADX B:1613 , ADP B:1614 , HOH B:2004	BINDING SITE FOR RESIDUE EDO B1616

(no "SS Bond" information available for 4BZQ)

(no "Cis Peptide Bond" information available for 4BZQ)

(no "SAP(SNP)/Variant" information available for 4BZQ)

(no "PROSITE Motif" information available for 4BZQ)

(no "Exon" information available for 4BZQ)

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:173
 aligned with CYSNC_MYCTO | P9WNM4 from UniProtKB/Swiss-Prot  Length:614

    Alignment length:173
                                   449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609   
          CYSNC_MYCTO   440 PPRGKTVWFTGLSGSGKSSVAMLVERKLLEKGISAYVLDGDNLRHGLNADLGFSMADRAENLRRLSHVATLLADCGHLVLVPAISPLAEHRALARKVHADAGIDFFEVFCDTPLQDCERRDPKGLYAKARAGEITHFTGIDSPYQRPKNPDLRLTPDRSIDEQAQEVIDLLES 612
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.....hhhhhhhhhhhhhhhh...eee.hhhhhh.........hhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhh..hhhhhhhh....................eee....hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bzq A 440 PPRGKTVWFTGLSGSGKSSVAMLVERKLLEKGISAYVLDGDNLRHGLNADLGFSMADRAENLRRLSHVATLLADCGHLVLVPAISPLAEHRALARKVHADAGIDFFEVFCDTPLQDCERRDPKGLYAKARAGEITHFTGIDSPYQRPKNPDLRLTPDRSIDEQAQEVIDLLES 612
                                   449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609

Chain A from PDB  Type:PROTEIN  Length:173
 aligned with CYSNC_MYCTU | P9WNM5 from UniProtKB/Swiss-Prot  Length:614

    Alignment length:173
                                   449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609   
          CYSNC_MYCTU   440 PPRGKTVWFTGLSGSGKSSVAMLVERKLLEKGISAYVLDGDNLRHGLNADLGFSMADRAENLRRLSHVATLLADCGHLVLVPAISPLAEHRALARKVHADAGIDFFEVFCDTPLQDCERRDPKGLYAKARAGEITHFTGIDSPYQRPKNPDLRLTPDRSIDEQAQEVIDLLES 612
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.....hhhhhhhhhhhhhhhh...eee.hhhhhh.........hhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhh..hhhhhhhh....................eee....hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bzq A 440 PPRGKTVWFTGLSGSGKSSVAMLVERKLLEKGISAYVLDGDNLRHGLNADLGFSMADRAENLRRLSHVATLLADCGHLVLVPAISPLAEHRALARKVHADAGIDFFEVFCDTPLQDCERRDPKGLYAKARAGEITHFTGIDSPYQRPKNPDLRLTPDRSIDEQAQEVIDLLES 612
                                   449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609

Chain B from PDB  Type:PROTEIN  Length:173
 aligned with CYSNC_MYCTO | P9WNM4 from UniProtKB/Swiss-Prot  Length:614

    Alignment length:173
                                   449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609   
          CYSNC_MYCTO   440 PPRGKTVWFTGLSGSGKSSVAMLVERKLLEKGISAYVLDGDNLRHGLNADLGFSMADRAENLRRLSHVATLLADCGHLVLVPAISPLAEHRALARKVHADAGIDFFEVFCDTPLQDCERRDPKGLYAKARAGEITHFTGIDSPYQRPKNPDLRLTPDRSIDEQAQEVIDLLES 612
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.....hhhhhhhhhhhhhhhh...eee.hhhhhh.........hhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhh..hhhhhhhh....................eee....hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bzq B 440 PPRGKTVWFTGLSGSGKSSVAMLVERKLLEKGISAYVLDGDNLRHGLNADLGFSMADRAENLRRLSHVATLLADCGHLVLVPAISPLAEHRALARKVHADAGIDFFEVFCDTPLQDCERRDPKGLYAKARAGEITHFTGIDSPYQRPKNPDLRLTPDRSIDEQAQEVIDLLES 612
                                   449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609

Chain B from PDB  Type:PROTEIN  Length:173
 aligned with CYSNC_MYCTU | P9WNM5 from UniProtKB/Swiss-Prot  Length:614

    Alignment length:173
                                   449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609   
          CYSNC_MYCTU   440 PPRGKTVWFTGLSGSGKSSVAMLVERKLLEKGISAYVLDGDNLRHGLNADLGFSMADRAENLRRLSHVATLLADCGHLVLVPAISPLAEHRALARKVHADAGIDFFEVFCDTPLQDCERRDPKGLYAKARAGEITHFTGIDSPYQRPKNPDLRLTPDRSIDEQAQEVIDLLES 612
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.....hhhhhhhhhhhhhhhh...eee.hhhhhh.........hhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhh..hhhhhhhh....................eee....hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bzq B 440 PPRGKTVWFTGLSGSGKSSVAMLVERKLLEKGISAYVLDGDNLRHGLNADLGFSMADRAENLRRLSHVATLLADCGHLVLVPAISPLAEHRALARKVHADAGIDFFEVFCDTPLQDCERRDPKGLYAKARAGEITHFTGIDSPYQRPKNPDLRLTPDRSIDEQAQEVIDLLES 612
                                   449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609

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 4BZQ)

(no "CATH Domain" information available for 4BZQ)

(no "Pfam Domain" information available for 4BZQ)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (CYSNC_MYCTU | P9WNM5)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	GO:0003924	GTPase activity	Catalysis of the reaction: GTP + H2O = GDP + phosphate.
	GO:0004020	adenylylsulfate kinase activity	Catalysis of the reaction: ATP + adenylylsulfate = ADP + 3'-phosphoadenosine 5'-phosphosulfate.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	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:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	GO:0004781	sulfate adenylyltransferase (ATP) activity	Catalysis of the reaction: ATP + sulfate = diphosphate + adenylylsulfate.
	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:0034599	cellular response to oxidative stress	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
	GO:0010438	cellular response to sulfur starvation	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of sulfur.
	GO:0040007	growth	The increase in size or mass of an entire organism, a part of an organism or a cell.
	GO:0070814	hydrogen sulfide biosynthetic process	The chemical reactions and pathways resulting in the formation of hydrogen sulfide, H2S.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	GO:0000103	sulfate assimilation	The pathways by which inorganic sulfate is processed and incorporated into sulfated compounds.
	GO:0010134	sulfate assimilation via adenylyl sulfate reduction	The pathway by which inorganic sulfate is activated, reduced and incorporated into sulfated compounds, where the activated sulfate, adenylyl-sulfate, is reduced to sulfite by the activity of adenylyl-sulfate reductase.
	GO:0006790	sulfur compound metabolic process	The chemical reactions and pathways involving the nonmetallic element sulfur or compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione.
cellular component
	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:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0009336	sulfate adenylyltransferase complex (ATP)	An enzyme complex that catalyzes the formation adenylylsulfate from sulfate and ATP.

Chain A,B (CYSNC_MYCTO | P9WNM4)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	GO:0003924	GTPase activity	Catalysis of the reaction: GTP + H2O = GDP + phosphate.
	GO:0004020	adenylylsulfate kinase activity	Catalysis of the reaction: ATP + adenylylsulfate = ADP + 3'-phosphoadenosine 5'-phosphosulfate.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	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:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	GO:0004781	sulfate adenylyltransferase (ATP) activity	Catalysis of the reaction: ATP + sulfate = diphosphate + adenylylsulfate.
	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:0070814	hydrogen sulfide biosynthetic process	The chemical reactions and pathways resulting in the formation of hydrogen sulfide, H2S.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	GO:0000103	sulfate assimilation	The pathways by which inorganic sulfate is processed and incorporated into sulfated compounds.
	GO:0006790	sulfur compound metabolic process	The chemical reactions and pathways involving the nonmetallic element sulfur or compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4bzq)

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	CYSNC_MYCTO \| P9WNM4	:	4bzp 4bzx
	CYSNC_MYCTU \| P9WNM5	:	4bzp 4bzx 4rfv

4bzp	STRUCTURE OF THE MYCOBACTERIUM TUBERCULOSIS APS KINASE CYSC IN COMPLEX WITH ADP
4bzx	STRUCTURE OF THE MYCOBACTERIUM TUBERCULOSIS APS KINASE CYSC IN COMPLEX WITH AMPPNP AND APS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (0, 0)

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Pfam Domains (0, 0)

Gene Ontology (22, 37)

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