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(-) Description

Title :  CRYSTAL STRUCTURE OF MYCOBACTERIUM SMEGMATIS ALPHA-KETOGLUTARATE DECARBOXYLASE HOMODIMER (ORTHORHOMBIC FORM)
 
Authors :  T. Wagner, M. Bellinzoni, A. M. Wehenkel, H. M. O'Hare, P. M. Alzari
Date :  05 Oct 10  (Deposition) - 15 Jun 11  (Release) - 12 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.74
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Lyase, Kdh, Kgd (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Wagner, M. Bellinzoni, A. M. Wehenkel, H. M. O'Hare, P. M. Alzari
Functional Plasticity And Allosteric Regulation Of Alpha-Ketoglutarate Decarboxylase In Central Mycobacterial Metabolism.
Chem. Biol. V. 18 1011 2011
PubMed-ID: 21867916  |  Reference-DOI: 10.1016/J.CHEMBIOL.2011.06.004

(-) Compounds

Molecule 1 - 2-OXOGLUTARATE DECARBOXYLASE
    Chains: A, B
    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 116-1227
    Organism Scientific: MYCOBACTERIUM SMEGMATIS
    Organism Taxid: 246196
    Strain: MC2 155
    Synonym: ALPHA-KETOGLUTARATE DECARBOXYLASE, 2-OXOGLUTARATE CARBOXY- LYASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2MG2Ligand/IonMAGNESIUM ION
3TPP2Ligand/IonTHIAMINE DIPHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:540 , SER A:604 , HIS A:605 , LEU A:606 , GLY A:644 , ASP A:645 , ALA A:646 , ALA A:647 , ASN A:678 , ILE A:680 , GLY A:681 , HIS A:747 , MG A:2002 , HOH A:3017 , HOH A:3054 , HOH A:3055 , GLN B:901 , LEU B:950 , GLU B:952 , GLN B:976 , PHE B:980BINDING SITE FOR RESIDUE TPP A2001
2AC2SOFTWAREASP A:645 , ASN A:678 , ILE A:680 , TPP A:2001 , HOH A:3017BINDING SITE FOR RESIDUE MG A2002
3AC3SOFTWAREASP A:1004 , HIS A:1055 , ASP A:1058 , ILE A:1060 , HOH A:3043BINDING SITE FOR RESIDUE CA A2003
4AC4SOFTWAREGLN A:901 , LEU A:950 , GLU A:952 , GLN A:976 , PHE A:980 , ARG B:540 , SER B:604 , HIS B:605 , LEU B:606 , GLY B:644 , ASP B:645 , ALA B:646 , ALA B:647 , ASN B:678 , ILE B:680 , GLY B:681 , HIS B:747 , MG B:2002 , HOH B:3021 , HOH B:3060 , HOH B:3062 , HOH B:3063BINDING SITE FOR RESIDUE TPP B2001
5AC5SOFTWAREASP B:645 , ASN B:678 , ILE B:680 , TPP B:2001 , HOH B:3062BINDING SITE FOR RESIDUE MG B2002
6AC6SOFTWAREASP B:1004 , HIS B:1055 , ASP B:1058 , ILE B:1060 , HOH B:3051BINDING SITE FOR RESIDUE CA B2003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2XT6)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:1144 -Pro A:1145
2Ala B:1144 -Pro B:1145

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2XT6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2XT6)

(-) Exons   (0, 0)

(no "Exon" information available for 2XT6)

(-) Sequences/Alignments

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:1055
 aligned with KGD_MYCS2 | A0R2B1 from UniProtKB/Swiss-Prot  Length:1227

    Alignment length:1107
                                   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       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    121 EVPTATSVRAIPAKLMIDNRVVINNHLKRTRGGKISFTHLLGYAIVQAVKKFPNMNRHFAVVDGKPTAITPAHTNLGLAIDLQGKDGNRSLVVAAIKRCETMRFGQFIAAYEDIVRRARDGKLTAEDFSGVTISLTNPGTLGTVHSVPRLMQGQGAIIGAGAMEYPAEFQGASEERIADLGIGKLITLTSTYDHRIIQGAESGDFLRTIHQLLLDDDFFDEIFRELGIPYEPVRWRTDNPDSIEDKNARVIELIAAYRNRGHLMADIDPLRLDNTRFRSHPDLDVNSHGLTLWDLDREFKVDGFAGVQRKKLRDILSVLRDAYCRHVGVEYTHILEPEQQRWIQERVETKHDKPTVAEQKYILSKLNAAEAFETFLQTKYVGQKRFSLEGAETVIPMMDAVIDQCAEHGLDEVVIAMPHRGRLNVLANIVGKPYSQIFSEFEGNLNPSQAHGSGDVKYHLGATGTYIQMFGDNDIEVSLTANPSHLEAVDPVLEGLVRAKQDLLDTGEEGSDNRFSVVPLMLHGDAAFAGQGVVAETLNLALLRGYRTGGTIHIVVNNQIGFTTAPTDSRSSEYCTDVAKMIGAPIFHVNGDDPEACAWVARLAVDFRQAFKKDVVIDMLCYRRRGHNEGDDPSMTQPYMYDVIDTKRGSRKAYTEALIGRGDISMKEAEDALRDYQGQLERVFNEVRELEKHEIEPSESVEADQQIPSKLATAVDKAMLQRIGDAHLALPEGFTVHPRVRPVLEKRREMAYEGRIDWAFAELLALGSLIAEGKLVRLSGQDTQRGTFTQRHAVIVDRKTGEEFTPLQLLATNPDGTPTGGKFLVYNSALSEFAAVGFEYGYSVGNPDAMVLWEAQFGDFVNGAQSIIDEFISSGEAKWGQLSDVVLLLPHGHEGQGPDHTSGRIERFLQLWAEGSMTIAMPSTPANYFHLLRRHGKDGIQRPLIVFTPKSMLRNKAAVSDIRDFTESKFRSVLEEPMYTDGEGDRNKVTRLLLTSGKIYYELAARKAKENREDVAIVRIEQLAPLPRRRLAETLDRYPNVKEKFWVQEEPANQGAWPSFGLTLPEILPDHFTGLKRISRRAMSAPSSGSSKVHAVEQQEILDTAFG 1227
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeehhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhheeee....eeee......eeee.-----------.eeee.hhhhhhhhhhhhhhhhhhhhhh....hhhhh....eeee..------------.....eeeee............hhhhhhhhh...eeeeeeeee....hhhhhhhhhhhhhhhh.hhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhh........hhhhhh......hhhhh.hhhhh..eeee......eeeehhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhh...hhhhhh...-------------hhhhh..eeeeee......eeeeee.........hhhhhhhhhhhhhhhh............eeeeeeeehhhhhhhhhhhhhhh............eeeeee.......hhhhhh.....hhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhh..eeeeee...........hhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh----------------.....hhhhhhhhhhhh............hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..eeeeee..............ee......eehhhhhhh..........eeeeee....hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhh..hhhhhhh.....eeeee.............hhhhhhhhh.....eee...hhhhhhhhhhhhhhh.....eeeee.hhhhh......hhhhhhh.....ee.hhhhhh.........eeeee..hhhhhhhhhhhhhh...eeeeee.eee..hhhhhhhhhh......eeeeeeeee....hhhhhhhhhhhhhhhhhh..eeeee.........hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2xt6 A  121 EVPTATSVRAIPAKLMIDNRVVINNHLKRTRGGKISFTHLLGYAIVQAVKKFPNMNRHFAVVDGKPTAITPAHTNLGLAI-----------VVAAIKRCETMRFGQFIAAYEDIVRRARDGKLTAEDFSGVTISLTNP------------MQGQGAIIGAGAMEYPAEFQGASEERIADLGIGKLITLTSTYDHRIIQGAESGDFLRTIHQLLLDDDFFDEIFRELGIPYEPVRWRTDNPDSIEDKNARVIELIAAYRNRGHLMADIDPLRLDNTRFRSHPDLDVNSHGLTLWDLDREFKVDGFAGVQRKKLRDILSVLRDAYCRHVGVEYTHILEPEQQRWIQERVETKHDKPTVAEQKYILSKLNAAEAFETFLQTKYVGQKRFSLEGAETVIPMMDAVIDQCAEHGLDEVVIAMPHRGRLNVLANIVGKPYSQIFSEF-------------DVKYHLGATGTYIQMFGDNDIEVSLTANPSHLEAVDPVLEGLVRAKQDLLDTGEEGSDNRFSVVPLMLHGDAAFAGQGVVAETLNLALLRGYRTGGTIHIVVNNQIGFTTAPTDSRSSEYCTDVAKMIGAPIFHVNGDDPEACAWVARLAVDFRQAFKKDVVIDMLCYRRRGHNEGDDPSMTQPYMYDVIDTKRGSRKAYTEALIGRGDISMKEAEDALRDYQGQLERVFNEVRELEKHE----------------LATAVDKAMLQRIGDAHLALPEGFTVHPRVRPVLEKRREMAYEGRIDWAFAELLALGSLIAEGKLVRLSGQDTQRGTFTQRHAVIVDRKTGEEFTPLQLLATNPDGTPTGGKFLVYNSALSEFAAVGFEYGYSVGNPDAMVLWEAQFGDFVNGAQSIIDEFISSGEAKWGQLSDVVLLLPHGHEGQGPDHTSGRIERFLQLWAEGSMTIAMPSTPANYFHLLRRHGKDGIQRPLIVFTPKSMLRNKAAVSDIRDFTESKFRSVLEEPMYTDGEGDRNKVTRLLLTSGKIYYELAARKAKENREDVAIVRIEQLAPLPRRRLAETLDRYPNVKEKFWVQEEPANQGAWPSFGLTLPEILPDHFTGLKRISRRAMSAPSSGSSKVHAVEQQEILDTAFG 1227
                                   130       140       150       160       170       180       190       200         - |     220       230       240       250       | -         -|      280       290       300       310       320       330       340       350       360       370       380       390       400       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       
                                                                                                         200         212                                           258          271                                                                                                                                                                                                                                                                                               561           575                                                                                                                                                                                                                                            814              831                                                                                                                                                                                                                                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:989
 aligned with KGD_MYCS2 | A0R2B1 from UniProtKB/Swiss-Prot  Length:1227

    Alignment length:1100
                                   137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877       887       897       907       917       927       937       947       957       967       977       987       997      1007      1017      1027      1037      1047      1057      1067      1077      1087      1097      1107      1117      1127      1137      1147      1157      1167      1177      1187      1197      1207      1217      1227
           KGD_MYCS2    128 VRAIPAKLMIDNRVVINNHLKRTRGGKISFTHLLGYAIVQAVKKFPNMNRHFAVVDGKPTAITPAHTNLGLAIDLQGKDGNRSLVVAAIKRCETMRFGQFIAAYEDIVRRARDGKLTAEDFSGVTISLTNPGTLGTVHSVPRLMQGQGAIIGAGAMEYPAEFQGASEERIADLGIGKLITLTSTYDHRIIQGAESGDFLRTIHQLLLDDDFFDEIFRELGIPYEPVRWRTDNPDSIEDKNARVIELIAAYRNRGHLMADIDPLRLDNTRFRSHPDLDVNSHGLTLWDLDREFKVDGFAGVQRKKLRDILSVLRDAYCRHVGVEYTHILEPEQQRWIQERVETKHDKPTVAEQKYILSKLNAAEAFETFLQTKYVGQKRFSLEGAETVIPMMDAVIDQCAEHGLDEVVIAMPHRGRLNVLANIVGKPYSQIFSEFEGNLNPSQAHGSGDVKYHLGATGTYIQMFGDNDIEVSLTANPSHLEAVDPVLEGLVRAKQDLLDTGEEGSDNRFSVVPLMLHGDAAFAGQGVVAETLNLALLRGYRTGGTIHIVVNNQIGFTTAPTDSRSSEYCTDVAKMIGAPIFHVNGDDPEACAWVARLAVDFRQAFKKDVVIDMLCYRRRGHNEGDDPSMTQPYMYDVIDTKRGSRKAYTEALIGRGDISMKEAEDALRDYQGQLERVFNEVRELEKHEIEPSESVEADQQIPSKLATAVDKAMLQRIGDAHLALPEGFTVHPRVRPVLEKRREMAYEGRIDWAFAELLALGSLIAEGKLVRLSGQDTQRGTFTQRHAVIVDRKTGEEFTPLQLLATNPDGTPTGGKFLVYNSALSEFAAVGFEYGYSVGNPDAMVLWEAQFGDFVNGAQSIIDEFISSGEAKWGQLSDVVLLLPHGHEGQGPDHTSGRIERFLQLWAEGSMTIAMPSTPANYFHLLRRHGKDGIQRPLIVFTPKSMLRNKAAVSDIRDFTESKFRSVLEEPMYTDGEGDRNKVTRLLLTSGKIYYELAARKAKENREDVAIVRIEQLAPLPRRRLAETLDRYPNVKEKFWVQEEPANQGAWPSFGLTLPEILPDHFTGLKRISRRAMSAPSSGSSKVHAVEQQEILDTAFG 1227
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) 2-oxoacid_dh-2xt6B01 B:128-338                                                                                                                                                                                     -------------------------------------------------------------------------------------------------------------------------------------------------E1_dh-2xt6B03 B:484-810                                                                                                                                                                                                                                                                                                                                     ------------------------------------------Transket_pyr-2xt6B05 B:874-1076                                                                                                                                                                            ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) 2-oxoacid_dh-2xt6B02 B:128-338                                                                                                                                                                                     -------------------------------------------------------------------------------------------------------------------------------------------------E1_dh-2xt6B04 B:484-810                                                                                                                                                                                                                                                                                                                                     ------------------------------------------Transket_pyr-2xt6B06 B:874-1076                                                                                                                                                                            ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .eeeehhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh--------------------------..eee.------------..eee.hhhhhhhhhhhhhhhhhhhhhh....hhhhh....eee.---------------------.......--------..hhhhhhh...eeee..--------hhhhhhhhhhhhhhh.hhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh......hhhhh.hhhhh..eeee......eeeehhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhh...hhhhhh.---------------hhhhh..eeeeee......eeeeee.........hhhhhhhhhhhhhhhh............eeeeeeeehhhhhhhhhhhhhhh............eeeeee.......hhhhhh.....hhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhh..eeeeee...........hhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh---------------------....hhhhhhhhhhhh............hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..eeeeee..............ee......eehhhhhhh..........eeeeee....hhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh..hhhhhhh.....eeeee.............hhhhhhhhh.....eee...hhhhhhhhhhhhhhh.....eeeee.hhhhh......hhhhhhh.....ee.hhhhhh.........eeeee..hhhhhhhhhhhhhh...eeeeee.eee..hhhhhhhhhh......eeeeeeeee....hhhhhhhhhhhhhhhhhh..eeeee.........hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2xt6 B  128 VRAIPAKLMIDNRVVINNHLKRTRGGKISFTHLLGYAIVQ--------------------------TNLGLA------------VVAAIKRCETMRFGQFIAAYEDIVRRARDGKLTAEDFSGVTISLT---------------------IGAGAME--------SEERIADLGIGKLITLTS--------GAESGDFLRTIHQLLLDDDFFDEIFRELGIPYEPVRWRTDNPDSIEDKNARVIELIAAYRNRGHLMADIDPLRLDNTRFRSHPDLDVNSHGLTLWDLDREFKVDGFAGVQRKKLRDILSVLRDAYCRHVGVEYTHILEPEQQRWIQERVETKHDKPTVAEQKYILSKLNAAEAFETFLQTKYVGQKRFSLEGAETVIPMMDAVIDQCAEHGLDEVVIAMPHRGRLNVLANIVGKPYSQIFS---------------DVKYHLGATGTYIQMFGDNDIEVSLTANPSHLEAVDPVLEGLVRAKQDLLDTGEEGSDNRFSVVPLMLHGDAAFAGQGVVAETLNLALLRGYRTGGTIHIVVNNQIGFTTAPTDSRSSEYCTDVAKMIGAPIFHVNGDDPEACAWVARLAVDFRQAFKKDVVIDMLCYRRRGHNEGDDPSMTQPYMYDVIDTKRGSRKAYTEALIGRGDISMKEAEDALRDYQGQLERVFNEVREL---------------------ATAVDKAMLQRIGDAHLALPEGFTVHPRVRPVLEKRREMAYEGRIDWAFAELLALGSLIAEGKLVRLSGQDTQRGTFTQRHAVIVDRKTGEEFTPLQLLATNPDGTPTGGKFLVYNSALSEFAAVGFEYGYSVGNPDAMVLWEAQFGDFVNGAQSIIDEFISSGEAKWGQLSDVVLLLPHGHEGQGPDHTSGRIERFLQLWAEGSMTIAMPSTPANYFHLLRRHGKDGIQRPLIVFTPKSMLRNKAAVSDIRDFTESKFRSVLEEPMYTDGEGDRNKVTRLLLTSGKIYYELAARKAKENREDVAIVRIEQLAPLPRRRLAETLDRYPNVKEKFWVQEEPANQGAWPSFGLTLPEILPDHFTGLKRISRRAMSAPSSGSSKVHAVEQQEILDTAFG 1227
                                   137       147       157       167         -         -      |197 |       -    |  217       227       237       247        |-         -         -|     |  -     | 297       307  |      - |     327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557 |       -       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807  |      -         -    |  837       847       857       867       877       887       897       907       917       927       937       947       957       967       977       987       997      1007      1017      1027      1037      1047      1057      1067      1077      1087      1097      1107      1117      1127      1137      1147      1157      1167      1177      1187      1197      1207      1217      1227
                                                                 167                        194  199          212                                         256                   278   284      293              310      319                                                                                                                                                                                                                                             559             575                                                                                                                                                                                                                                        810                   832
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2XT6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XT6)

(-) Pfam Domains  (3, 6)

Asymmetric/Biological Unit
(-)
Clan: CoA-acyltrans (22)
(-)
Clan: THDP-binding (106)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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.

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        KGD_MYCS2 | A0R2B1: 2xt9 2xta 2y0p 2yic 2yid 3zhq 3zhr 3zhs 3zht 3zhu 3zhv

(-) Related Entries Specified in the PDB File

2xt5 CRYSTAL STRUCTURE OF THE SUCA DOMAIN OF MYCOBACTERIUM SMEGMATIS ALPHA-KETOGLUTARATE DECARBOXYLASE (TRICLINIC FORM)
2xt7 CRYSTAL STRUCTURE OF THE SUCA DOMAIN OF MYCOBACTERIUM SMEGMATIS ALPHA-KETOGLUTARATE DECARBOXYLASE IN COMPLEX WITH THE ENAMINE- THDP INTERMEDIATE
2xt8 CRYSTAL STRUCTURE OF MYCOBACTERIUM SMEGMATIS ALPHA-KETOGLUTARATE DECARBOXYLASE HOMOHEXAMER IN COMPLEX WITH GARA (MONOCLINIC FORM)
2xt9 CRYSTAL STRUCTURE OF MYCOBACTERIUM SMEGMATIS ALPHA-KETOGLUTARATE DECARBOXYLASE IN COMPLEX WITH GARA
2xta CRYSTAL STRUCTURE OF THE SUCA DOMAIN OF MYCOBACTERIUM SMEGMATIS ALPHA-KETOGLUTARATE DECARBOXYLASE IN COMPLEX WITH ACETYL-COA ( TRICLINIC FORM)