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(-) Description

Title :  CRYSTAL STRUCTURE- C2 FORM- OF ESCHERICHIA COLI CROTONOBETAINYL-COA: CARNITINE COA TRANSFERASE (CAIB)
 
Authors :  E. S. Rangarajan, Y. Li, P. Iannuzzi, M. Cygler, A. Matte, Montreal-Kin Bacterial Structural Genomics Initiative (Bsgi)
Date :  27 Sep 04  (Deposition) - 15 Mar 05  (Release) - 13 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Caib, Coa Transferase, Carnitine, Crotonobetainyl Coa, Montreal- Kingston Bacterial Structural Genomics Initiative, Bsgi, Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. S. Rangarajan, Y. Li, P. Iannuzzi, M. Cygler, A. Matte
Crystal Structure Of Escherichia Coli Crotonobetainyl-Coa: Carnitine Coa-Transferase (Caib) And Its Complexes With Coa And Carnitinyl-Coa.
Biochemistry V. 44 5728 2005
PubMed-ID: 15823031  |  Reference-DOI: 10.1021/BI047656F

(-) Compounds

Molecule 1
    Chains: A, B, C
    EC Number: 2.8.3.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-4T1
    Expression System Strain: E. COLI. DL41 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CAIB
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): A  
Biological Unit 2 (1x):  BC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 51)

Asymmetric Unit (1, 51)
No.NameCountTypeFull Name
1MSE51Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 34)
No.NameCountTypeFull Name
1MSE34Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 34)
No.NameCountTypeFull Name
1MSE34Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1XK7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1XK7)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Phe A:164 -Pro A:165
2Mse A:357 -Pro A:358
3Phe B:164 -Pro B:165
4Mse B:357 -Pro B:358
5Phe C:164 -Pro C:165
6Mse C:357 -Pro C:358

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 6)

Asymmetric Unit (2, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_CAIB_ECOLI_001 *V187ACAIB_ECOLI  ---  ---A/B/CV187A
2UniProtVAR_CAIB_ECOLI_002 *T302ACAIB_ECOLI  ---  ---A/B/CT302A
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_CAIB_ECOLI_001 *V187ACAIB_ECOLI  ---  ---AV187A
2UniProtVAR_CAIB_ECOLI_002 *T302ACAIB_ECOLI  ---  ---AT302A
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_CAIB_ECOLI_001 *V187ACAIB_ECOLI  ---  ---B/CV187A
2UniProtVAR_CAIB_ECOLI_002 *T302ACAIB_ECOLI  ---  ---B/CT302A
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1XK7)

(-) Exons   (0, 0)

(no "Exon" information available for 1XK7)

(-) Sequences/Alignments

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:407
 aligned with CAIB_ECOLI | P31572 from UniProtKB/Swiss-Prot  Length:405

    Alignment length:407
                              1                                                                                                                                                                                                                                                                                                                                                                                                                    
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       
           CAIB_ECOLI     - --MDHLPMPKFGPLAGLRVVFSGIEIAGPFAGQMFAEWGAEVIWIENVAWADTIRVQPNYPQLSRRNLHALSLNIFKDEGREAFLKLMETTDIFIEASKGPAFARRGITDEVLWQHNPKLVIAHLSGFGQYGTEEYTNLPAYNTIAQAFSGYLIQNGDVDQPMPAFPYTADYFSGLTATTAALAALHKVRETGKGESIDIAMYEVMLRMGQYFMMDYFNGGEMCPRMSKGKDPYYAGCGLYKCADGYIVMELVGITQIEECFKDIGLAHLLGTPEIPEGTQLIHRIECPYGPLVEEKLDAWLATHTIAEVKERFAELNIACAKVLTVPELESNPQYVARESITQWQTMDGRTCKGPNIMPKFKNNPGQIWRGMPSHGMDTAAILKNIGYSENDIQELVSKGLAKVED 405
               SCOP domains d1xk7a_ A: Crotonobetainyl-CoA:carnitine CoA-transferase, CaiB                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1xk7A01 A:-1-226,A:330-405 Crotonobetainyl-coa:carnitine coa-transferase; domain 1                                                                                                                                                  1xk7A02 A:227-329 formyl-coa transferase, domain 3                                                     1xk7A01 A:-1-226,A:330-405                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeee...hhhhhhhhhhhhh..eeeeee.....hhhhhh.hhhhhhh...eeeee...hhhhhhhhhhhhh...eeeee...hhhhhh..hhhhhhhhh...eeeeee...............hhhhhhhhh.hhhh.ee..ee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhh..................eeeeee..eeeeee..hhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhh.hhhhhhhhhhhh..eeee..hhhhh..hhhhhhhh.eeeee.....eeeee......................hhhhhhhhh..hhhhhhhhhhh..ee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A------------------------------------------------------------------------------------------------------------------A------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xk7 A  -1 SHmDHLPmPKFGPLAGLRVVFSGIEIAGPFAGQmFAEWGAEVIWIENVAWADTIRVQPNYPQLSRRNLHALSLNIFKDEGREAFLKLmETTDIFIEASKGPAFARRGITDEVLWQHNPKLVIAHLSGFGQYGTEEYTNLPAYNTIAQAFSGYLIQNGDVDQPmPAFPYTADYFSGLTATTAALAALHKVRETGKGESIDIAmYEVmLRmGQYFmmDYFNGGEmCPRmSKGKDPYYAGCGLYKCADGYIVmELVGITQIEECFKDIGLAHLLGTPEIPEGTQLIHRIECPYGPLVEEKLDAWLATHTIAEVKERFAELNIACAKVLTVPELESNPQYVARESITQWQTmDGRTCKGPNImPKFKNNPGQIWRGmPSHGmDTAAILKNIGYSENDIQELVSKGLAKVED 405
                              |    | 8        18        28   |    38        48        58        68        78       |88        98       108       118       128       138       148       158  |    168       178       188       198 |   | 208   ||  218  |   |228       238       248       258       268       278       288       298       308       318       328       338       348       358       368  |    378       388       398       
                              |    |                        32-MSE                                                86-MSE                                                                    161-MSE                                200-MSE  |    ||     221-MSE                    248-MSE                                                                                           346-MSE    357-MSE       371-MSE|                             
                              1-MSE|                                                                                                                                                                                                   204-MSE   ||         225-MSE                                                                                                                                                376-MSE                         
                                   6-MSE                                                                                                                                                                                                  207-MSE||                                                                                                                                                                                                
                                                                                                                                                                                                                                               212-MSE                                                                                                                                                                                             
                                                                                                                                                                                                                                                213-MSE                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:407
 aligned with CAIB_ECOLI | P31572 from UniProtKB/Swiss-Prot  Length:405

    Alignment length:407
                              1                                                                                                                                                                                                                                                                                                                                                                                                                    
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       
           CAIB_ECOLI     - --MDHLPMPKFGPLAGLRVVFSGIEIAGPFAGQMFAEWGAEVIWIENVAWADTIRVQPNYPQLSRRNLHALSLNIFKDEGREAFLKLMETTDIFIEASKGPAFARRGITDEVLWQHNPKLVIAHLSGFGQYGTEEYTNLPAYNTIAQAFSGYLIQNGDVDQPMPAFPYTADYFSGLTATTAALAALHKVRETGKGESIDIAMYEVMLRMGQYFMMDYFNGGEMCPRMSKGKDPYYAGCGLYKCADGYIVMELVGITQIEECFKDIGLAHLLGTPEIPEGTQLIHRIECPYGPLVEEKLDAWLATHTIAEVKERFAELNIACAKVLTVPELESNPQYVARESITQWQTMDGRTCKGPNIMPKFKNNPGQIWRGMPSHGMDTAAILKNIGYSENDIQELVSKGLAKVED 405
               SCOP domains d1xk7b_ B: Crotonobetainyl-CoA:carnitine CoA-transferase, CaiB                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1xk7B01 B:-1-226,B:330-405 Crotonobetainyl-coa:carnitine coa-transferase; domain 1                                                                                                                                                  1xk7B02 B:227-329 formyl-coa transferase, domain 3                                                     1xk7B01 B:-1-226,B:330-405                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeee...hhhhhhhhhhhhh..eeeeee.....hhhhhh.hhhhhhh...eeeee...hhhhhhhhhhhhh...eeeee...hhhhhh..hhhhhhhhh...eeeeee...............hhhhhhhhh.hhhh.ee..ee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhh..................eeeee....eeeee..hhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhh.hhhhhhhhhhhhh.eeee..hhhhh..hhhhhhhh.eeeee.....eeeee....ee................hhhhhhhhh..hhhhhhhhhhh..ee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A------------------------------------------------------------------------------------------------------------------A------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xk7 B  -1 SHmDHLPmPKFGPLAGLRVVFSGIEIAGPFAGQmFAEWGAEVIWIENVAWADTIRVQPNYPQLSRRNLHALSLNIFKDEGREAFLKLmETTDIFIEASKGPAFARRGITDEVLWQHNPKLVIAHLSGFGQYGTEEYTNLPAYNTIAQAFSGYLIQNGDVDQPmPAFPYTADYFSGLTATTAALAALHKVRETGKGESIDIAmYEVmLRmGQYFmmDYFNGGEmCPRmSKGKDPYYAGCGLYKCADGYIVmELVGITQIEECFKDIGLAHLLGTPEIPEGTQLIHRIECPYGPLVEEKLDAWLATHTIAEVKERFAELNIACAKVLTVPELESNPQYVARESITQWQTmDGRTCKGPNImPKFKNNPGQIWRGmPSHGmDTAAILKNIGYSENDIQELVSKGLAKVED 405
                              |    | 8        18        28   |    38        48        58        68        78       |88        98       108       118       128       138       148       158  |    168       178       188       198 |   | 208   ||  218  |   |228       238       248       258       268       278       288       298       308       318       328       338       348       358       368  |    378       388       398       
                              1-MSE|                        32-MSE                                                86-MSE                                                                    161-MSE                                200-MSE  |    ||     221-MSE                    248-MSE                                                                                           346-MSE    357-MSE       371-MSE|                             
                                   6-MSE                                                                                                                                                                                               204-MSE   ||         225-MSE                                                                                                                                                376-MSE                         
                                                                                                                                                                                                                                          207-MSE||                                                                                                                                                                                                
                                                                                                                                                                                                                                               212-MSE                                                                                                                                                                                             
                                                                                                                                                                                                                                                213-MSE                                                                                                                                                                                            


Chain C from PDB  Type:PROTEIN  Length:407
 aligned with CAIB_ECOLI | P31572 from UniProtKB/Swiss-Prot  Length:405

    Alignment length:407
                              1                                                                                                                                                                                                                                                                                                                                                                                                                    
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       
           CAIB_ECOLI     - --MDHLPMPKFGPLAGLRVVFSGIEIAGPFAGQMFAEWGAEVIWIENVAWADTIRVQPNYPQLSRRNLHALSLNIFKDEGREAFLKLMETTDIFIEASKGPAFARRGITDEVLWQHNPKLVIAHLSGFGQYGTEEYTNLPAYNTIAQAFSGYLIQNGDVDQPMPAFPYTADYFSGLTATTAALAALHKVRETGKGESIDIAMYEVMLRMGQYFMMDYFNGGEMCPRMSKGKDPYYAGCGLYKCADGYIVMELVGITQIEECFKDIGLAHLLGTPEIPEGTQLIHRIECPYGPLVEEKLDAWLATHTIAEVKERFAELNIACAKVLTVPELESNPQYVARESITQWQTMDGRTCKGPNIMPKFKNNPGQIWRGMPSHGMDTAAILKNIGYSENDIQELVSKGLAKVED 405
               SCOP domains d1xk7c_ C: Crotonobetainyl-CoA:carnitine CoA-transferase, CaiB                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1xk7C01 C:-1-226,C:330-405 Crotonobetainyl-coa:carnitine coa-transferase; domain 1                                                                                                                                                  1xk7C02 C:227-329 formyl-coa transferase, domain 3                                                     1xk7C01 C:-1-226,C:330-405                                                   CATH domains
           Pfam domains (1) ----------------------------------------------------------------------CoA_transf_3-1xk7C01 C:69-258                                                                                                                                                                 --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------CoA_transf_3-1xk7C02 C:69-258                                                                                                                                                                 --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ----------------------------------------------------------------------CoA_transf_3-1xk7C03 C:69-258                                                                                                                                                                 --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (3)
         Sec.struct. author .................eeeee...hhhhhhhhhhhhh..eeeeee.....hhhhhh.hhhhhhh...eeeee...hhhhhhhhhhhhh...eeeee...hhhhhh..hhhhhhhhh...eeeeee...............hhhhhhhhhhhhhhhee..ee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhh..................eeeee....eeeee..hhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee..hhhhh..hhhhhhhh.eeeee.....eeeee....ee................hhhhhhhhh..hhhhhhhhhhh..ee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A------------------------------------------------------------------------------------------------------------------A------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xk7 C  -1 SHmDHLPmPKFGPLAGLRVVFSGIEIAGPFAGQmFAEWGAEVIWIENVAWADTIRVQPNYPQLSRRNLHALSLNIFKDEGREAFLKLmETTDIFIEASKGPAFARRGITDEVLWQHNPKLVIAHLSGFGQYGTEEYTNLPAYNTIAQAFSGYLIQNGDVDQPmPAFPYTADYFSGLTATTAALAALHKVRETGKGESIDIAmYEVmLRmGQYFmmDYFNGGEmCPRmSKGKDPYYAGCGLYKCADGYIVmELVGITQIEECFKDIGLAHLLGTPEIPEGTQLIHRIECPYGPLVEEKLDAWLATHTIAEVKERFAELNIACAKVLTVPELESNPQYVARESITQWQTmDGRTCKGPNImPKFKNNPGQIWRGmPSHGmDTAAILKNIGYSENDIQELVSKGLAKVED 405
                              |    | 8        18        28   |    38        48        58        68        78       |88        98       108       118       128       138       148       158  |    168       178       188       198 |   | 208   ||  218  |   |228       238       248       258       268       278       288       298       308       318       328       338       348       358       368  |    378       388       398       
                              1-MSE|                        32-MSE                                                86-MSE                                                                    161-MSE                                200-MSE  |    ||     221-MSE                    248-MSE                                                                                           346-MSE    357-MSE       371-MSE|                             
                                   6-MSE                                                                                                                                                                                               204-MSE   ||         225-MSE                                                                                                                                                376-MSE                         
                                                                                                                                                                                                                                          207-MSE||                                                                                                                                                                                                
                                                                                                                                                                                                                                               212-MSE                                                                                                                                                                                             
                                                                                                                                                                                                                                                213-MSE
   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, 3)

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

(-) CATH Domains  (2, 6)

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

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: no clan defined [family: CoA_transf_3] (25)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (CAIB_ECOLI | P31572)
molecular function
    GO:0008410    CoA-transferase activity    Catalysis of the transfer of a coenzyme A (CoA) group from one compound (donor) to another (acceptor).
    GO:0008735    carnitine dehydratase activity    Catalysis of the reaction: (R)-carnitine = crotono-betaine + H(2)O.
    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: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:0016782    transferase activity, transferring sulfur-containing groups    Catalysis of the transfer of a sulfur-containing group from one compound (donor) to another (acceptor).
biological process
    GO:0042413    carnitine catabolic process    The chemical reactions and pathways resulting in the breakdown of carnitine (hydroxy-trimethyl aminobutyric acid), a compound that participates in the transfer of acyl groups across the inner mitochondrial membrane.
    GO:0009437    carnitine metabolic process    The chemical reactions and pathways involving carnitine (hydroxy-trimethyl aminobutyric acid), a compound that participates in the transfer of acyl groups across the inner mitochondrial membrane.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  1xk7
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  CAIB_ECOLI | P31572
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  2.8.3.-
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CAIB_ECOLI | P31572: 1xa3 1xa4 1xk6 1xvt 1xvu 1xvv

(-) Related Entries Specified in the PDB File

1xk6 RELATED ID: CAIB_ECOLI RELATED DB: TARGETDB