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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CO-EXPRESSED SUCCINYL-COA TRANSFERASE A AND B COMPLEX FROM BACILLUS SUBTILIS
 
Authors :  Y. Kim, M. Zhou, L. Stols, W. Eschenfeldt, M. Donnelly, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  27 Feb 08  (Deposition) - 18 Mar 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.59
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Co-Expressed Complex, Hetero-Tetramer, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, M. Zhou, L. Stols, W. Eschenfeldt, M. Donnelly, A. Joachimiak
Crystal Structure Of The Co-Expressed Succinyl-Coa Transferase A And B Complex From Bacillus Subtilis.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SUCCINYL-COA:3-KETOACID-COENZYME A TRANSFERASE SUBUNIT A
    Chains: A, C
    EC Number: 2.8.3.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMCSG17
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: SCOA, YXJD, BSU38990, N15K
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Strain: 168
 
Molecule 2 - SUCCINYL-COA:3-KETOACID-COENZYME A TRANSFERASE SUBUNIT B
    Chains: B, D
    EC Number: 2.8.3.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMCSG21
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: SCOB, YXJE, BSU38980, N15L
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Strain: 168

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3CDK)

(-) Sites  (0, 0)

(no "Site" information available for 3CDK)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1COA_TRANSF_1PS01273 Coenzyme A transferases signature 1.SCOA_BACSU17-32
 		  2A:19-34
C:19-34
2COA_TRANSF_2PS01274 Coenzyme A transferases signature 2.SCOB_BACSU44-52
 		  2B:44-52
D:44-52

(-) Exons   (0, 0)

(no "Exon" information available for 3CDK)

(-) 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:229
 aligned with SCOA_BACSU | P42315 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:229
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221         
           SCOA_BACSU     2 GKVLSSSKEAAKLIHDGDTLIAGGFGLCGIPEQLILSIRDQGVKDLTVVSNNCGVDDWGLGLLLANKQIKKMIASYVGENKIFERQFLSGELEVELVPQGTLAERIRAGGAGIPGFYTATGVGTSIAEGKEHKTFGGRTYVLERGITGDVAIVKAWKADTMGNLIFRKTARNFNPIAAMAGKITIAEAEEIVEAGELDPDHIHTPGIYVQHVVLGASQEKRIEKRTVQQ 230
               SCOP domains d3cdka_ A: automated matches                                                                                                                                                                                                          SCOP domains
               CATH domains 3cdkA01 A:4-228 Glutaconate Coenzyme A-transferase                                                                                                                                                                               ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhh......eeee........hhhhhhhhhhhh...eeeee.........hhhhhhh..eeeeee.....hhhhhhhhh....eeee.hhhhhhhhhhhhhhh..eeee.....hhhhh...eeee..eeeeeee...eeeeeeeeeeee....ee.hhhhh.hhhhhhhheeeeeeeeeeee............hhhhh.eeee............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------COA_TRANSF_1    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cdk A   4 GKVLSSSKEAAKLIHDGDTLIAGGFGLCGIPEQLILSIRDQGVKDLTVVSNNCGVDDWGLGLLLANKQIKKMIASYVGENKIFERQFLSGELEVELVPQGTLAERIRAGGAGIPGFYTATGVGTSIAEGKEHKTFGGRTYVLERGITGDVAIVKAWKADTMGNLIFRKTARNFNPIAAMAGKITIAEAEEIVEAGELDPDHIHTPGIYVQHVVLGASQEKRIEKRTVQQ 232
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223         


Chain B from PDB  Type:PROTEIN  Length:212
 aligned with SCOB_BACSU | P42316 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   
           SCOB_BACSU     1 MKEARKRMVKRAVQEIKDGMNVNLGIGMPTLVANEIPDGVHVMLQSENGLLGIGPYPLEGTEDADLINAGKETITEVTGASYFDSAESFAMIRGGHIDLAILGGMEVSEQGDLANWMIPGKMVKGMGGAMDLVNGAKRIVVIMEHVNKHGESKVKKTCSLPLTGQKVVHRLITDLAVFDFVNGRMTLTELQDGVTIEEVYEKTEADFAVSQSV 213
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3cdkB00 B:1-213 Glutaconate Coenzyme A-transferase; Chain B                                                                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh......eeee..hhhhhhhh........eeee...eeeee....................eeeeeeee.hhhhhhhhhhh....eeee...eee....ee.......-.....hhhhhhhhh.eeeee...........ee..............eee...eeeeee..eeeeeee....hhhhhhhh.....ee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------COA_TRANS----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cdk B   1 MKEARKRMVKRAVQEIKDGMNVNLGIGMPTLVANEIPDGVHVMLQSENGLLGIGPYPLEGTEDADLINAGKETITEVTGASYFDSAESFAMIRGGHIDLAILGGMEVSEQGDLANWMIPGK-VKGMGGAMDLVNGAKRIVVIMEHVNKHGESKVKKTCSLPLTGQKVVHRLITDLAVFDFVNGRMTLTELQDGVTIEEVYEKTEADFAVSQSV 213
                                    10        20        30        40        50        60        70        80        90       100       110       120| |    130       140       150       160       170       180       190       200       210   
                                                                                                                                                  121 |                                                                                          
                                                                                                                                                    123                                                                                          


Chain C from PDB  Type:PROTEIN  Length:229
 aligned with SCOA_BACSU | P42315 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:229
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220         
           SCOA_BACSU     1 MGKVLSSSKEAAKLIHDGDTLIAGGFGLCGIPEQLILSIRDQGVKDLTVVSNNCGVDDWGLGLLLANKQIKKMIASYVGENKIFERQFLSGELEVELVPQGTLAERIRAGGAGIPGFYTATGVGTSIAEGKEHKTFGGRTYVLERGITGDVAIVKAWKADTMGNLIFRKTARNFNPIAAMAGKITIAEAEEIVEAGELDPDHIHTPGIYVQHVVLGASQEKRIEKRTVQ 229
               SCOP domains d3cdkc_ C: automated matches                                                                                                                                                                                                          SCOP domains
               CATH domains 3cdkC01 C:3-228 Glutaconate Coenzyme A-transferase                                                                                                                                                                                --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhh......eeee........hhhhhhhhhhhh...eeee..........hhhhhhh..eeeeee.....hhhhhhhhhh...eeee.hhhhhhhhhhhhhhh..eeee.....hhhhh...eeee..eeeeeee...eeeeeeeeeeee....ee.hhhhh.hhhhhhhheeeeeeeeeeee............hhhhh.eeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------COA_TRANSF_1    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cdk C   3 MGKVLSSSKEAAKLIHDGDTLIAGGFGLCGIPEQLILSIRDQGVKDLTVVSNNCGVDDWGLGLLLANKQIKKMIASYVGENKIFERQFLSGELEVELVPQGTLAERIRAGGAGIPGFYTATGVGTSIAEGKEHKTFGGRTYVLERGITGDVAIVKAWKADTMGNLIFRKTARNFNPIAAMAGKITIAEAEEIVEAGELDPDHIHTPGIYVQHVVLGASQEKRIEKRTVQ 231
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222         


Chain D from PDB  Type:PROTEIN  Length:200
 aligned with SCOB_BACSU | P42316 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:209
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201         
           SCOB_BACSU     2 KEARKRMVKRAVQEIKDGMNVNLGIGMPTLVANEIPDGVHVMLQSENGLLGIGPYPLEGTEDADLINAGKETITEVTGASYFDSAESFAMIRGGHIDLAILGGMEVSEQGDLANWMIPGKMVKGMGGAMDLVNGAKRIVVIMEHVNKHGESKVKKTCSLPLTGQKVVHRLITDLAVFDFVNGRMTLTELQDGVTIEEVYEKTEADFAVS 210
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3cdkD00 D:2-210 Glutaconate Coenzyme A-transferase; Chain B                                                                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh......eeee..hhhhhhhhhh......eeee...eeeee....................eeeeeeee.hhhhhhhhhhh....eeee...ee.....ee......-......hhhhhhhhh..eeee.....----..................eee....eeeee..eeeeee.----..hhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------COA_TRANS-------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cdk D   2 KEARKRMVKRAVQEIKDGMNVNLGIGMPTLVANEIPDGVHVMLQSENGLLGIGPYPLEGTEDADLINAGKETITEVTGASYFDSAESFAMIRGGHIDLAILGGMEVSEQGDLANWMIPG-MVKGMGGAMDLVNGAKRIVVIMEHVN----SKVKKTCSLPLTGQKVVHRLITDLAVFDFVNGRMTLTEL----TIEEVYEKTEADFAVS 210
                                    11        21        31        41        51        61        71        81        91       101       111        |-|      131       141     |   -|      161       171       181        |-   |   201         
                                                                                                                                                120 |                      147  152                                   190  195               
                                                                                                                                                  122
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,C   (SCOA_BACSU | P42315)
molecular function
    GO:0008260    3-oxoacid CoA-transferase activity    Catalysis of the reaction: succinyl-CoA + a 3-oxo acid = succinate + a 3-oxo-acyl-CoA.
    GO:0008410    CoA-transferase activity    Catalysis of the transfer of a coenzyme A (CoA) group from one compound (donor) to another (acceptor).
    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: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.

Chain B,D   (SCOB_BACSU | P42316)
molecular function
    GO:0008260    3-oxoacid CoA-transferase activity    Catalysis of the reaction: succinyl-CoA + a 3-oxo acid = succinate + a 3-oxo-acyl-CoA.
    GO:0008410    CoA-transferase activity    Catalysis of the transfer of a coenzyme A (CoA) group from one compound (donor) to another (acceptor).
    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: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.

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