2XT9 - JenaLib

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Asym. Unit - sites (Jmol Viewer)

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF MYCOBACTERIUM SMEGMATIS ALPHA-KETOGLUTARATE DECARBOXYLASE IN COMPLEX WITH GARA

Authors :   T. Wagner, M. Bellinzoni, A. M. Wehenkel, H. M. O'Hare, P. M. Alzari

Date :   05 Oct 10 (Deposition) - 12 Oct 11 (Release) - 12 Oct 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Lyase-Signaling Protein Complex, Kdh, Kgd (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Wagner, M. Bellinzoni, A. M. Wehenkel, H. M. O'Hare, P. M. Alzari
Dynamic Allosteric Control Of Multifunctional Alpha-Ketoglutarate Decarboxylase In Mycobacteria
To Be Published
PubMed: search

Molecule 1 - 2-OXOGLUTARATE DECARBOXYLASE
	Chains	:	A
	EC Number	:	4.1.1.71
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-28A
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 361-1227
	Organism Scientific	:	MYCOBACTERIUM SMEGMATIS
	Organism Taxid	:	246196
	Strain	:	MC2 155
	Synonym	:	ALPHA-KETOGLUTARATE DECARBOXYLASE, 2-OXOGLUTARATE CARBOXY-LYASE

Molecule 2 - PUTATIVE SIGNAL TRANSDUCTION PROTEIN GARA
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-28A
	Expression System Strain	:	BL21AI
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	FHA DOMAIN, RESIDUES 45-158
	Organism Scientific	:	MYCOBACTERIUM SMEGMATIS
	Organism Taxid	:	246196
	Strain	:	MC2 155
	Synonym	:	FHA PROTEIN GARA

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	MG	1	Ligand/Ion	MAGNESIUM ION
3	TPP	1	Ligand/Ion	THIAMINE DIPHOSPHATE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	TPP	2	Ligand/Ion	THIAMINE DIPHOSPHATE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:540 , SER A:604 , HIS A:605 , LEU A:606 , GLY A:644 , ASP A:645 , ALA A:646 , ALA A:647 , GLN A:651 , ASN A:678 , ILE A:680 , GLY A:681 , HIS A:747 , GLN A:901 , LEU A:950 , GLU A:952 , GLN A:976 , PHE A:980 , MG A:2002 , HOH A:3119 , HOH A:3332 , HOH A:3333 , HOH A:3334	BINDING SITE FOR RESIDUE TPP A2001
2	AC2	SOFTWARE	ASP A:645 , ASN A:678 , ILE A:680 , TPP A:2001 , HOH A:3119	BINDING SITE FOR RESIDUE MG A2002
3	AC3	SOFTWARE	ASP A:1004 , HIS A:1055 , ASP A:1058 , ILE A:1060 , HOH A:3278 , HOH A:3279	BINDING SITE FOR RESIDUE CA A2003

(no "SS Bond" information available for 2XT9)

Asymmetric Unit

No.	Residues
1	Ala A:1144	-	Pro A:1145

(no "SAP(SNP)/Variant" information available for 2XT9)

(no "PROSITE Motif" information available for 2XT9)

(no "Exon" information available for 2XT9)

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:824
 aligned with KGD_MYCS2 | A0R2B1 from UniProtKB/Swiss-Prot  Length:1227

    Alignment length:867
                                   370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920       930       940       950       960       970       980       990      1000      1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210      1220       
           KGD_MYCS2    361 DSIEDKNARVIELIAAYRNRGHLMADIDPLRLDNTRFRSHPDLDVNSHGLTLWDLDREFKVDGFAGVQRKKLRDILSVLRDAYCRHVGVEYTHILEPEQQRWIQERVETKHDKPTVAEQKYILSKLNAAEAFETFLQTKYVGQKRFSLEGAETVIPMMDAVIDQCAEHGLDEVVIAMPHRGRLNVLANIVGKPYSQIFSEFEGNLNPSQAHGSGDVKYHLGATGTYIQMFGDNDIEVSLTANPSHLEAVDPVLEGLVRAKQDLLDTGEEGSDNRFSVVPLMLHGDAAFAGQGVVAETLNLALLRGYRTGGTIHIVVNNQIGFTTAPTDSRSSEYCTDVAKMIGAPIFHVNGDDPEACAWVARLAVDFRQAFKKDVVIDMLCYRRRGHNEGDDPSMTQPYMYDVIDTKRGSRKAYTEALIGRGDISMKEAEDALRDYQGQLERVFNEVRELEKHEIEPSESVEADQQIPSKLATAVDKAMLQRIGDAHLALPEGFTVHPRVRPVLEKRREMAYEGRIDWAFAELLALGSLIAEGKLVRLSGQDTQRGTFTQRHAVIVDRKTGEEFTPLQLLATNPDGTPTGGKFLVYNSALSEFAAVGFEYGYSVGNPDAMVLWEAQFGDFVNGAQSIIDEFISSGEAKWGQLSDVVLLLPHGHEGQGPDHTSGRIERFLQLWAEGSMTIAMPSTPANYFHLLRRHGKDGIQRPLIVFTPKSMLRNKAAVSDIRDFTESKFRSVLEEPMYTDGEGDRNKVTRLLLTSGKIYYELAARKAKENREDVAIVRIEQLAPLPRRRLAETLDRYPNVKEKFWVQEEPANQGAWPSFGLTLPEILPDHFTGLKRISRRAMSAPSSGSSKVHAVEQQEILDTAFG 1227
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh........hhhhh---------....hhhhh..eee.-----..eeehhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhh...hhhhhh...------------.hhhhh..eeeeee......eeeeee.........hhhhhhhhhhhhhhhh............eeeeeeeehhhhhhhhhhhhhhh............eeeeee.......hhhhh......hhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhh..eeeeee...........hhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.-----------------.....hhhhhhhhhhhh............hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..eeeeee..............ee......eehhhhhhh..........eeeeee....hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhh..hhhhhhh.....eeeee.............hhhhhhhhh.....eee...hhhhhhhhhhhhhhh.....eeeee.hhhhhh......hhhhhh.....ee.hhhhhh...hhhhh.eeeee..hhhhhhhhhhhhhh...eeeeee.eee..hhhhhhhhhh......eeeeeeeee....hhhhhhhhhhhhhhhhhh..eeeee.........hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2xt9 A  361 DSIEDKNARVIELIAAYRNRGHLMADIDPLRLDNTRF---------SHGLTLWDLDREFKV-----VQRKKLRDILSVLRDAYCRHVGVEYTHILEPEQQRWIQERVETKHDKPTVAEQKYILSKLNAAEAFETFLQTKYVGQKRFSLEGAETVIPMMDAVIDQCAEHGLDEVVIAMPHRGRLNVLANIVGKPYSQIFSEF------------GDVKYHLGATGTYIQMFGDNDIEVSLTANPSHLEAVDPVLEGLVRAKQDLLDTGEEGSDNRFSVVPLMLHGDAAFAGQGVVAETLNLALLRGYRTGGTIHIVVNNQIGFTTAPTDSRSSEYCTDVAKMIGAPIFHVNGDDPEACAWVARLAVDFRQAFKKDVVIDMLCYRRRGHNEGDDPSMTQPYMYDVIDTKRGSRKAYTEALIGRGDISMKEAEDALRDYQGQLERVFNEVRELEKH-----------------LATAVDKAMLQRIGDAHLALPEGFTVHPRVRPVLEKRREMAYEGRIDWAFAELLALGSLIAEGKLVRLSGQDTQRGTFTQRHAVIVDRKTGEEFTPLQLLATNPDGTPTGGKFLVYNSALSEFAAVGFEYGYSVGNPDAMVLWEAQFGDFVNGAQSIIDEFISSGEAKWGQLSDVVLLLPHGHEGQGPDHTSGRIERFLQLWAEGSMTIAMPSTPANYFHLLRRHGKDGIQRPLIVFTPKSMLRNKAAVSDIRDFTESKFRSVLEEPMYTDGEGDRNKVTRLLLTSGKIYYELAARKAKENREDVAIVRIEQLAPLPRRRLAETLDRYPNVKEKFWVQEEPANQGAWPSFGLTLPEILPDHFTGLKRISRRAMSAPSSGSSKVHAVEQQEILDTAFG 1227
                                   370       380       390      |  -      |410       420|     |430       440       450       460       470       480       490       500       510       520       530       540       550       560|        -   |   580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810  |      -         -|      840       850       860       870       880       890       900       910       920       930       940       950       960       970       980       990      1000      1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210      1220       
                                                              397       407           421   427                                                                                                                                   561          574                                                                                                                                                                                                                                            813               831

Chain B from PDB  Type:PROTEIN  Length:97
 aligned with Q9RP36_MYCSM | Q9RP36 from UniProtKB/TrEMBL  Length:158

    Alignment length:97
                                    60        70        80        90       100       110       120       130       140       
        Q9RP36_MYCSM     51 PSGSALLVVKRGPNAGSRFLLDQPTTSAGRHPDSDIFLDDVTVSRRHAEFRLEGGEFQVVDVGSLNGTYVNREPVDSAVLANGDEVQIGKFRLVFLT  147
               SCOP domains d2xt9b_ B: automated matches                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee......eeee...eeeee......ee..........eeeeee..eeeeee......eee..ee..eeee....eeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                2xt9 B   51 PSGSALLVVKRGPNAGSRFLLDQPTTSAGRHPDSDIFLDDVTVSRRHAEFRLEGGEFQVVDVGSLNGTYVNREPVDSAVLANGDEVQIGKFRLVFLT  147
                                    60        70        80        90       100       110       120       130       140

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: SMAD/FHA domain (62)

Superfamily: SMAD/FHA domain (62)

Family: automated matches (9)

Protein domain: automated matches (9)

Mycobacterium smegmatis [TaxId: 246196] (1)

d2xt9b_

(no "CATH Domain" information available for 2XT9)

(no "Pfam Domain" information available for 2XT9)

Asymmetric Unit(hide GO term definitions)

Chain A (KGD_MYCS2 | A0R2B1)

molecular function
	GO:0050439	2-hydroxy-3-oxoadipate synthase activity	Catalysis of the reaction: 2-oxoglutarate + glyoxylate + H(+) = 2-hydroxy-3-oxoadipate + CO(2).
	GO:0008683	2-oxoglutarate decarboxylase activity	Catalysis of the reaction: 2-oxoglutarate + H(+) = CO(2) + succinate semialdehyde.
	GO:0016831	carboxy-lyase activity	Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
	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:0004149	dihydrolipoyllysine-residue succinyltransferase activity	Catalysis of the reaction: succinyl-CoA + dihydrolipoamide = CoA + S-succinyldihydrolipoamide.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016624	oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces a disulfide.
	GO:0004591	oxoglutarate dehydrogenase (succinyl-transferring) activity	Catalysis of the reaction: 2-oxoglutarate + lipoamide = S-succinyldihydrolipoamide + CO2.
	GO:0030976	thiamine pyrophosphate binding	Interacting selectively and non-covalently with thiamine pyrophosphate, the diphosphoric ester of thiamine. Acts as a coenzyme of several (de)carboxylases, transketolases, and alpha-oxoacid dehydrogenases.
	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.
	GO:0016746	transferase activity, transferring acyl groups	Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
biological process
	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:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0006099	tricarboxylic acid cycle	A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.

Chain B (Q9RP36_MYCSM | Q9RP36)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		TPP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ala A:1144 - Pro A:1145	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	2xt9
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		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
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	KGD_MYCS2 \| A0R2B1
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	Q9RP36_MYCSM \| Q9RP36
		Comparative Protein Structure Models	:	ModBase
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Access by Enzyme Classificator (EC Number)
	4.1.1.71
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

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		Disease Information	:	OMIM

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		Interatomic Contacts of Structural Units	:	CSU
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	Q9RP36_MYCSM \| Q9RP36
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	KGD_MYCS2 \| A0R2B1	:	2xt6 2xta 2y0p 2yic 2yid 3zhq 3zhr 3zhs 3zht 3zhu 3zhv

2xt6	CRYSTAL STRUCTURE OF MYCOBACTERIUM SMEGMATIS ALPHA- KETOGLUTARATE DECARBOXYLASE HOMODIMER (ORTHORHOMBIC FORM)
2xta	CRYSTAL STRUCTURE OF THE SUCA DOMAIN OF MYCOBACTERIUM SMEGMATIS ALPHA-KETOGLUTARATE DECARBOXYLASE IN COMPLEX WITH ACETYL-COA (TRICLINIC FORM)
2y0p	CRYSTAL STRUCTURE OF THE SUCA DOMAIN OF MYCOBACTERIUM SMEGMATIS ALPHA-KETOGLUTARATE DECARBOXYLASE IN COMPLEX WITH THE ENAMINE-THDP INTERMEDIATE AND ACETYL-COA
2yic	CRYSTAL STRUCTURE OF THE SUCA DOMAIN OF MYCOBACTERIUM SMEGMATIS ALPHA-KETOGLUTARATE DECARBOXYLASE(TRICLINIC FORM)
2yid	CRYSTAL STRUCTURE OF THE SUCA DOMAIN OF MYCOBACTERIUM SMEGMATIS ALPHA-KETOGLUTARATE DECARBOXYLASE IN COMPLEX WITH THE ENAMINE-THDP INTERMEDIATE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (16, 16)

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