1U5J - JenaLib

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Title :   PROPIONIBACTERIUM SHERMANII TRANSCARBOXYLASE 5S SUBUNIT, MET186ILE

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

Date :   27 Jul 04 (Deposition) - 07 Sep 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Tim-Barrel, Carbamylated Lysine, Transcarboxylase, Cobalt, 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
	Mutation	:	YES
	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 (2, 2)

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

Biological Unit 1 (1, 2)

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

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:557	BINDING SITE FOR RESIDUE CO A 529

(no "SS Bond" information available for 1U5J)

Asymmetric Unit

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

(no "SAP(SNP)/Variant" information available for 1U5J)

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 1U5J)

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
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Chain A from PDB  Type:PROTEIN  Length:471
 aligned with 5S_PROFR | Q70AC7 from UniProtKB/Swiss-Prot  Length:505

    Alignment length:471
                                    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       413       423       433       443       453       463       473 
             5S_PROFR     4 REIEVSEPREVGITELVLRDAHQSLMATRMAMEDMVGACADIDAAGYWSVECWGGATYDSCIRFLNEDPWERLRTFRKLMPNSRLQMLLRGQNLLGYRHYNDEVVDRFVDKSAENGMDVFRVFDAMNDPRNMAHAMAAVKKAGKHAQGTICYTISPVHTVEGYVKLAGQLLDMGADSIALKDMAALLKPQPAYDIIKAIKDTYGQKTQINLHCHSTTGVTEVSLMKAIEAGVDVVDTAISSMSLGPGHNPTESVAEMLEGTGYTTNLDYDRLHKIRDHFKAIRPKYKKFESKTLVDTSIFKSQIPGGMLSNMESQLRAQGAEDKMDEVMAEVPRVRKAAGFPPLVTPSSQIVGTQAVFNVMMGEYKRMTGEFADIMLGYYGASPADRDPKVVKLAEEQSGKKPITQRPADLLPPEWEKQSKEAATLKGFNGTDEDVLTYALFPQVAPVFFEHRAEGPHSVALTDAQLKAEA 474
               SCOP domains d1u5ja2 A:4-306 Transcarboxylase 5S subunit, N-terminal domain                                                                                                                                                                                                                                                 d1u5ja1 A:307-474 Transcarboxylase 5S subunit, C-terminal domain                                                                                                         SCOP domains
               CATH domains -------1u5jA01 A:11-294 Aldolase class I                                                                                                                                                                                                                                                           ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------HMGL-like-1u5jA01 A:22-265                                                                                                                                                                                                                          ------------------------------------PYC_OADA-1u5jA02 A:302-474                                                                                                                                                    Pfam domains
         Sec.struct. author ........ee.eeee...hhhhhhhh.....hhhhhhhhhhhhhhh..eeeeee.hhhhhhhhh...hhhhhhhhhhhhh....eeeeehhhhh......hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhh...eeee.hhhhh......hhhhhhhhh....ee...hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.....hhhhhhhhh..........hhhhhhhhhhhh...............hhhhhhhhhh.......hhhhhhhhhhh..hhhhhhhhhhhh......hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------PYR_CT  PDB: A:14-276 UniProt: 14-276                                                                                                                                                                                                                                  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u5j A   4 REIEVSEPREVGITELVLRDAHQSLMATRMAMEDMVGACADIDAAGYWSVECWGGATYDSCIRFLNEDPWERLRTFRKLMPNSRLQMLLRGQNLLGYRHYNDEVVDRFVDKSAENGMDVFRVFDAMNDPRNMAHAMAAVKKAGKHAQGTICYTISPVHTVEGYVKLAGQLLDMGADSIALkDIAALLKPQPAYDIIKAIKDTYGQKTQINLHCHSTTGVTEVSLMKAIEAGVDVVDTAISSMSLGPGHNPTESVAEMLEGTGYTTNLDYDRLHKIRDHFKAIRPKYKKFESKTLVDTSIFKSQIPGGMLSNMESQLRAQGAEDKMDEVMAEVPRVRKAAGFPPLVTPSSQIVGTQAVFNVMMGEYKRMTGEFADIMLGYYGASPADRDPKVVKLAEEQSGKKPITQRPADLLPPEWEKQSKEAATLKGFNGTDEDVLTYALFPQVAPVFFEHRAEGPHSVALTDAQLKAEA 474
                                    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       413       423       433       443       453       463       473 
                                                                                                                                                                                                              184-KCX

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(

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Architectures( (-)

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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)

1u5jA01

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.

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

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	5S_PROFR \| Q70AC7	:	1rqb 1rqe 1rqh 1rr2 1s3h

1rqb	PROPIONIBACTERIUM SHERMANII TRANSCARBOXYLASE 5S SUBUNIT
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-KETOBUTYRATE
1sh3	PROPIONIBACTERIUM SHERMANII TRANSCARBOXYLASE 5S SUBUNIT, ALA59THR

Description

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Ligands, Modified Residues, Ions (2, 2)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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