1XA3 - JenaLib

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Title :   CRYSTAL STRUCTURE OF CAIB, A TYPE III COA TRANSFERASE IN CARNITINE METABOLISM

Authors :   P. Stenmark, D. Gurmu, P. Nordlund, Structural Proteomics In Europe (Spine)

Date :   25 Aug 04 (Deposition) - 16 Nov 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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

Keywords :   Caib, Carnitine, Coa Transferase, Coa, Coenzyme A, Interlocked, Dimer, Bis-Tris, Structural Proteomics In Europe, Spine, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Stenmark, D. Gurmu, P. Nordlund
Crystal Structure Of Caib, A Type-Iii Coa Transferase In Carnitine Metabolism
Biochemistry V. 43 13996 2004
PubMed-ID: 15518548 | Reference-DOI: 10.1021/BI048481C
(for further references see the PDB file header)

Molecule 1
	Chains	:	A, B
	EC Number	:	2.8.3.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PT73.3
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	CAIB
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 36)

No.	Name	Count	Type	Full Name
1	BTB	2	Ligand/Ion	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2	MSE	32	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:96 , LYS A:97 , ARG A:104 , HOH A:1686 , HOH A:1767 , HOH A:1771	BINDING SITE FOR RESIDUE SO4 A 1501
2	AC2	SOFTWARE	LYS B:97 , ALA B:100 , ARG B:103 , ARG B:104	BINDING SITE FOR RESIDUE SO4 B 1502
3	AC3	SOFTWARE	TYR A:210 , ASP A:230 , TYR A:233 , GLU A:249 , HOH A:1657 , HOH A:1658 , HOH A:1829 , GLU B:23 , TYR B:140 , TYR B:166 , HOH B:1621 , HOH B:1861	BINDING SITE FOR RESIDUE BTB A 1601
4	AC4	SOFTWARE	GLU A:23 , TYR A:140 , TYR A:166 , TYR B:210 , ASP B:230 , GLU B:249 , VAL B:251 , HOH B:1606 , HOH B:1638 , HOH B:1721	BINDING SITE FOR RESIDUE BTB B 1602

(no "SS Bond" information available for 1XA3)

Asymmetric/Biological Unit

No.	Residues
1	Phe A:164	-	Pro A:165
2	Mse A:357	-	Pro A:358
3	Phe B:164	-	Pro B:165
4	Mse B:357	-	Pro B:358

Asymmetric/Biological Unit (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_CAIB_ECOLI_001 *	V	187	A	CAIB_ECOLI	---	---	A/B	V	187	A
2	UniProt	VAR_CAIB_ECOLI_002 *	T	302	A	CAIB_ECOLI	---	---	A/B	T	302	A
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 1XA3)

(no "Exon" information available for 1XA3)

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:400
 aligned with CAIB_ECOLI | P31572 from UniProtKB/Swiss-Prot  Length:405

    Alignment length:400
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403
           CAIB_ECOLI     4 LPMPKFGPLAGLRVVFSGIEIAGPFAGQMFAEWGAEVIWIENVAWADTIRVQPNYPQLSRRNLHALSLNIFKDEGREAFLKLMETTDIFIEASKGPAFARRGITDEVLWQHNPKLVIAHLSGFGQYGTEEYTNLPAYNTIAQAFSGYLIQNGDVDQPMPAFPYTADYFSGLTATTAALAALHKVRETGKGESIDIAMYEVMLRMGQYFMMDYFNGGEMCPRMSKGKDPYYAGCGLYKCADGYIVMELVGITQIEECFKDIGLAHLLGTPEIPEGTQLIHRIECPYGPLVEEKLDAWLATHTIAEVKERFAELNIACAKVLTVPELESNPQYVARESITQWQTMDGRTCKGPNIMPKFKNNPGQIWRGMPSHGMDTAAILKNIGYSENDIQELVSKGLAKV 403
               SCOP domains d1xa3a_ A: Crotonobetainyl-CoA:carnitine CoA-transferase, CaiB                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1xa3A01 A:4-226,A:330-403 Crotonobetainyl-coa:carnitine coa-transferase; domain 1                                                                                                                                              1xa3A02 A:227-329 formyl-coa transferase, domain 3                                                     1xa3A01 A:4-226,A:330-403                                                  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.hhhhhhhhhhhhh.eeee..hhhhh..hhhhhhhh.eeeee.....eeeee....ee................hhhhhhhhh..hhhhhhhhhhh..ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A------------------------------------------------------------------------------------------------------------------A----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xa3 A   4 LPmPKFGPLAGLRVVFSGIEIAGPFAGQmFAEWGAEVIWIENVAWADTIRVQPNYPQLSRRNLHALSLNIFKDEGREAFLKLmETTDIFIEASKGPAFARRGITDEVLWQHNPKLVIAHLSGFGQYGTEEYTNLPAYNTIAQAFSGYLIQNGDVDQPmPAFPYTADYFSGLTATTAALAALHKVRETGKGESIDIAmYEVmLRmGQYFmmDYFNGGEmCPRmSKGKDPYYAGCGLYKCADGYIVmELVGITQIEECFKDIGLAHLLGTPEIPEGTQLIHRIECPYGPLVEEKLDAWLATHTIAEVKERFAELNIACAKVLTVPELESNPQYVARESITQWQTmDGRTCKGPNImPKFKNNPGQIWRGmPSHGmDTAAILKNIGYSENDIQELVSKGLAKV 403
                              |     13        23        33        43        53        63        73        83  |     93       103       113       123       133       143       153       163       173       183       193      |203|  |   213       223 |     233       243    |  253       263       273       283       293       303       313       323       333       343  |    353   |   363       373  |    383       393       403
                              |                        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 B from PDB  Type:PROTEIN  Length:400
 aligned with CAIB_ECOLI | P31572 from UniProtKB/Swiss-Prot  Length:405

    Alignment length:400
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403
           CAIB_ECOLI     4 LPMPKFGPLAGLRVVFSGIEIAGPFAGQMFAEWGAEVIWIENVAWADTIRVQPNYPQLSRRNLHALSLNIFKDEGREAFLKLMETTDIFIEASKGPAFARRGITDEVLWQHNPKLVIAHLSGFGQYGTEEYTNLPAYNTIAQAFSGYLIQNGDVDQPMPAFPYTADYFSGLTATTAALAALHKVRETGKGESIDIAMYEVMLRMGQYFMMDYFNGGEMCPRMSKGKDPYYAGCGLYKCADGYIVMELVGITQIEECFKDIGLAHLLGTPEIPEGTQLIHRIECPYGPLVEEKLDAWLATHTIAEVKERFAELNIACAKVLTVPELESNPQYVARESITQWQTMDGRTCKGPNIMPKFKNNPGQIWRGMPSHGMDTAAILKNIGYSENDIQELVSKGLAKV 403
               SCOP domains d1xa3b_ B: Crotonobetainyl-CoA:carnitine CoA-transferase, CaiB                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1xa3B01 B:4-236,B:329-403 Crotonobetainyl-coa:carnitine coa-transferase; domain 1                                                                                                                                                        1xa3B02 B:237-328 formyl-coa transferase, domain 3                                          1xa3B01 B:4-236,B:329-403                                                   CATH domains
           Pfam domains (1) -----------------------------------------------------------------CoA_transf_3-1xa3B01 B:69-258                                                                                                                                                                 ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------CoA_transf_3-1xa3B02 B:69-258                                                                                                                                                                 ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ............eeeee...hhhhhhhhhhhhh..eeeeee.....hhhhhh.hhhhhhh...eeeee...hhhhhhhhhhhhh...eeeee...hhhhhh..hhhhhhhhh...eeeeee...............hhhhhhhhh.hhhh.ee..ee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhh..................eeeeee..eeeeee..hhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhh.hhhhhhhhhhhhh.eeee..hhhhh..hhhhhhhh.eeeee.....eeeee....ee................hhhhhhhhh..hhhhhhhhhhhh.ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A------------------------------------------------------------------------------------------------------------------A----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xa3 B   4 LPmPKFGPLAGLRVVFSGIEIAGPFAGQmFAEWGAEVIWIENVAWADTIRVQPNYPQLSRRNLHALSLNIFKDEGREAFLKLmETTDIFIEASKGPAFARRGITDEVLWQHNPKLVIAHLSGFGQYGTEEYTNLPAYNTIAQAFSGYLIQNGDVDQPmPAFPYTADYFSGLTATTAALAALHKVRETGKGESIDIAmYEVmLRmGQYFmmDYFNGGEmCPRmSKGKDPYYAGCGLYKCADGYIVmELVGITQIEECFKDIGLAHLLGTPEIPEGTQLIHRIECPYGPLVEEKLDAWLATHTIAEVKERFAELNIACAKVLTVPELESNPQYVARESITQWQTmDGRTCKGPNImPKFKNNPGQIWRGmPSHGmDTAAILKNIGYSENDIQELVSKGLAKV 403
                              |     13        23        33        43        53        63        73        83  |     93       103       113       123       133       143       153       163       173       183       193      |203|  |   213       223 |     233       243    |  253       263       273       283       293       303       313       323       333       343  |    353   |   363       373  |    383       393       403
                              6-MSE                    32-MSE                                                86-MSE                                                                    161-MSE                                200-MSE  |    ||     221-MSE                    248-MSE                                                                                           346-MSE    357-MSE       371-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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: CoA-transferase family III (CaiB/BaiF) (35)

Superfamily: CoA-transferase family III (CaiB/BaiF) (35)

Family: CoA-transferase family III (CaiB/BaiF) (35)

Protein domain: Crotonobetainyl-CoA:carnitine CoA-transferase, CaiB (7)

Escherichia coli [TaxId: 562] (7)

1a	d1xa3a_	A:
1b	d1xa3b_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: formyl-coa transferase, domain 3 (26)

Homologous Superfamily: formyl-coa transferase, domain 3 (26)

Escherichia coli. Organism_taxid: 562. (10)

1a	1xa3A02	A:227-329
1b	1xa3B02	B:237-328

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: Crotonobetainyl-coa:carnitine coa-transferase; domain 1 (26)

Escherichia coli. Organism_taxid: 562. (10)

2a	1xa3B01	B:4-236,B:329-403
2b	1xa3A01	A:4-226,A:330-403

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: CoA_transf_3 (25)

Escherichia coli (strain K12) (13)

1a	CoA_transf_3-1xa3B01	B:69-258
1b	CoA_transf_3-1xa3B02	B:69-258

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Mse A:357 - Pro A:358	[ RasMol ]
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		Phe A:164 - Pro A:165	[ RasMol ]
		Phe B:164 - Pro B:165	[ RasMol ]

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	1xa3
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	CAIB_ECOLI \| P31572	:	1xa4 1xk6 1xk7 1xvt 1xvu 1xvv

1xa4	CAIB COMPLEXED WITH COENZYME A
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 36)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 4)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

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