1RQB - JenaLib

Asymmetric Unit (Jmol Viewer)

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   PROPIONIBACTERIUM SHERMANII TRANSCARBOXYLASE 5S SUBUNIT

Authors :   P. R. Hall, R. Zheng, L. Antony, M. Pusztai-Carey, P. R. Carey, V. C. Yee

Date :   04 Dec 03 (Deposition) - 07 Sep 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Tim-Barrel, Carbamylated Lysine, Transcarboxylase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. R. Hall, R. Zheng, L. Antony, M. Pusztai-Carey, P. R. Carey, V. C. Yee
Transcarboxylase 5S Structures: Assembly And Catalytic Mechanism Of A Multienzyme Complex Subunit.
Embo J. V. 23 3621 2004
PubMed-ID: 15329673 | Reference-DOI: 10.1038/SJ.EMBOJ.7600373
(for further references see the PDB file header)

Molecule 1 - TRANSCARBOXYLASE 5S SUBUNIT
	Chains	:	A
	EC Number	:	2.1.3.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PETBLUE-2
	Expression System Strain	:	TUNER(DE3)PLACI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	5S
	Organism Scientific	:	PROPIONIBACTERIUM FREUDENREICHII SUBSP. SHERMANII
	Organism Taxid	:	1752
	Strain	:	SUBSP. SHERMANII

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 25)

No.	Name	Count	Type	Full Name
1	CO	1	Ligand/Ion	COBALT (II) ION
2	KCX	1	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
3	MSE	23	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 48)

No.	Name	Count	Type	Full Name
1	CO	-1	Ligand/Ion	COBALT (II) ION
2	KCX	2	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
3	MSE	46	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:23 , KCX A:184 , HIS A:215 , HIS A:217 , HOH A:885	BINDING SITE FOR RESIDUE CO A 529

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

Asymmetric Unit

No.	Residues
1	Thr A:349	-	Pro A:350

(no "SAP(SNP)/Variant" information available for 1RQB)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PYR_CT	PS50991	Pyruvate carboxyltransferase domain.	5S_PROFR	14-276	1	A:14-276

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PYR_CT	PS50991	Pyruvate carboxyltransferase domain.	5S_PROFR	14-276	2	A:14-276

(no "Exon" information available for 1RQB)

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:472
 aligned with 5S_PROFR | Q70AC7 from UniProtKB/Swiss-Prot  Length:505

    Alignment length:472
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472  
             5S_PROFR     3 PREIEVSEPREVGITELVLRDAHQSLMATRMAMEDMVGACADIDAAGYWSVECWGGATYDSCIRFLNEDPWERLRTFRKLMPNSRLQMLLRGQNLLGYRHYNDEVVDRFVDKSAENGMDVFRVFDAMNDPRNMAHAMAAVKKAGKHAQGTICYTISPVHTVEGYVKLAGQLLDMGADSIALKDMAALLKPQPAYDIIKAIKDTYGQKTQINLHCHSTTGVTEVSLMKAIEAGVDVVDTAISSMSLGPGHNPTESVAEMLEGTGYTTNLDYDRLHKIRDHFKAIRPKYKKFESKTLVDTSIFKSQIPGGMLSNMESQLRAQGAEDKMDEVMAEVPRVRKAAGFPPLVTPSSQIVGTQAVFNVMMGEYKRMTGEFADIMLGYYGASPADRDPKVVKLAEEQSGKKPITQRPADLLPPEWEKQSKEAATLKGFNGTDEDVLTYALFPQVAPVFFEHRAEGPHSVALTDAQLKAEA 474
               SCOP domains -d1rqba2 A:4-306 Transcarboxylase 5S subunit, N-terminal domain                                                                                                                                                                                                                                                 d1rqba1 A:307-474 Transcarboxylase 5S subunit, C-terminal domain                                                                                                         SCOP domains
               CATH domains --------1rqbA01 A:11-294 Aldolase class I                                                                                                                                                                                                                                                           ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -------------------HMGL-like-1rqbA01 A:22-265                                                                                                                                                                                                                          ------------------------------------PYC_OADA-1rqbA02 A:302-474                                                                                                                                                    Pfam domains
         Sec.struct. author .........ee.eeee...hhhhhhhh....hhhhhhhhhhhhhhh...eeeeee.hhhhhhhhh...hhhhhhhhhhhhh....eeeeehhhhh......hhhhhhhhhhhhhhh...eeee......hhhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhh...eeee.hhhhh......hhhhhhhhh....ee...hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.....hhhhhhhhh..........hhhhhhhhhhhhh......hhhhhh..hhhhhhhhhh.......hhhhhhhhhhh..hhhhhhhhhhhh......hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------PYR_CT  PDB: A:14-276 UniProt: 14-276                                                                                                                                                                                                                                  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rqb A   3 PREIEVSEPREVGITELVLRDAHQSLmATRmAmEDmVGACADIDAAGYWSVECWGGATYDSCIRFLNEDPWERLRTFRKLmPNSRLQmLLRGQNLLGYRHYNDEVVDRFVDKSAENGmDVFRVFDAmNDPRNmAHAmAAVKKAGKHAQGTICYTISPVHTVEGYVKLAGQLLDmGADSIALkDmAALLKPQPAYDIIKAIKDTYGQKTQINLHCHSTTGVTEVSLmKAIEAGVDVVDTAISSmSLGPGHNPTESVAEmLEGTGYTTNLDYDRLHKIRDHFKAIRPKYKKFESKTLVDTSIFKSQIPGGmLSNmESQLRAQGAEDKmDEVmAEVPRVRKAAGFPPLVTPSSQIVGTQAVFNVmmGEYKRmTGEFADImLGYYGASPADRDPKVVKLAEEQSGKKPITQRPADLLPPEWEKQSKEAATLKGFNGTDEDVLTYALFPQVAPVFFEHRAEGPHSVALTDAQLKAEA 474
                                    12        22      | 32| |  |  42        52        62        72        82|      |92       102       112       122      |132  |   |142       152       162       172   |   182 | |   192       202       212       222     | 232       242  |    252       262       272       282       292       302       312  |    322     | 332       342       352       362 ||    372      |382       392       402       412       422       432       442       452       462       472  
                                                     29-MSE |  |                                           83-MSE 90-MSE                       120-MSE  129-MSE |   |                                  176-MSE 184-KCX                                     228-MSE          245-MSE        260-MSE                                            311-MSE          328-MSE                             364-MSE  |     379-MSE                                                                                           
                                                         33-MSE|                                                                                              135-MSE                                            186-MSE                                                                                                                          315-MSE          332-MSE                          365-MSE |                                                                                                       
                                                           35-MSE                                                                                                 139-MSE                                                                                                                                                                                                                                 371-MSE                                                                                                   
                                                              38-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 Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Aldolase class I (887)

Shermanii (Propionibacterium freudenreichii subsp) (6)

1rqbA01

A:11-294

Asymmetric Unit(hide GO term definitions)

Chain A (5S_PROFR | Q70AC7)


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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
GO:0047154	methylmalonyl-CoA carboxytransferase activity	Catalysis of the reaction: pyruvate + D-methylmalonyl-CoA = oxaloacetic acid + propionyl-CoA.
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.

Asymmetric Unit
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		Thr A:349 - Pro A:350	[ RasMol ]

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	2.1.3.1
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	5S_PROFR \| Q70AC7	:	1rqe 1rqh 1rr2 1s3h 1u5j

1rqe	PROPIONIBACTERIUM SHERMANII TRANSCARBOXYLASE 5S SUBUNIT BOUND TO OXALOACETATE
1rqh	PROPIONIBACTERIUM SHERMANII TRANSCARBOXYLASE 5S SUBUNIT BOUND TO PYRUVATE
1rr2	PROPIONIBACTERIUM SHERMANII TRANSCARBOXYLASE 5S SUBUNIT BOUND TO 2-KETOBUTYRIC ACID

Description

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Ligands, Modified Residues, Ions (3, 25)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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