1RR2 - JenaLib

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Title :   PROPIONIBACTERIUM SHERMANII TRANSCARBOXYLASE 5S SUBUNIT BOUND TO 2-KETOBUTYRIC ACID

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

Date :   08 Dec 03 (Deposition) - 07 Sep 04 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Tim-Barrel, Carbamylated Lysine, Transcarboxylase, Cobalt, 2- Ketobutyric Acid, 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
	Other Details	:	RESIDUE 184 EXISTS IN TWO ALTERNATE CONFORMATIONS: KCX AND LYS

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 3)

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

Biological Unit 1 (2, 4)

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

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:23 , KCX A:184 , HIS A:215 , HIS A:217 , HOH A:655	BINDING SITE FOR RESIDUE CO A 529
2	AC2	SOFTWARE	ARG A:22 , GLN A:26 , GLY A:58 , ALA A:59 , LEU A:91 , KCX A:184 , MET A:186 , HOH A:655	BINDING SITE FOR RESIDUE 2KT A 530

(no "SS Bond" information available for 1RR2)

Asymmetric Unit

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

(no "SAP(SNP)/Variant" information available for 1RR2)

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 1RR2)

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:473
 aligned with 5S_PROFR | Q70AC7 from UniProtKB/Swiss-Prot  Length:505

    Alignment length:473
                                                                                                                                                                                                                 185                                                                                                                                                                                                                                                                                                 
                                                                                                                                                                                                               184 |                                                                                                                                                                                                                                                                                                 
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182 | |   191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471   
             5S_PROFR     3 PREIEVSEPREVGITELVLRDAHQSLMATRMAMEDMVGACADIDAAGYWSVECWGGATYDSCIRFLNEDPWERLRTFRKLMPNSRLQMLLRGQNLLGYRHYNDEVVDRFVDKSAENGMDVFRVFDAMNDPRNMAHAMAAVKKAGKHAQGTICYTISPVHTVEGYVKLAGQLLDMGADSIALK-DMAALLKPQPAYDIIKAIKDTYGQKTQINLHCHSTTGVTEVSLMKAIEAGVDVVDTAISSMSLGPGHNPTESVAEMLEGTGYTTNLDYDRLHKIRDHFKAIRPKYKKFESKTLVDTSIFKSQIPGGMLSNMESQLRAQGAEDKMDEVMAEVPRVRKAAGFPPLVTPSSQIVGTQAVFNVMMGEYKRMTGEFADIMLGYYGASPADRDPKVVKLAEEQSGKKPITQRPADLLPPEWEKQSKEAATLKGFNGTDEDVLTYALFPQVAPVFFEHRAEGPHSVALTDAQLKAEA 474
               SCOP domains -d1rr2a2 A:4-306 Transcarboxylase 5S subunit, N-terminal domain                                                                                                                                                                                                                                                  d1rr2a1 A:307-474 Transcarboxylase 5S subunit, C-terminal domain                                                                                                         SCOP domains
               CATH domains --------1rr2A01 A:11-294 Aldolase class I                                                                                                                                                                                                                                                            ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........ee.eeee...hhhhhhhhh...hhhhhhhhhhhhhh....eeeeee.hhhhhhhhh...hhhhhhhhhhhhh....eeeeehhhhh......hhhhhhhhhhhhhhh...eeee......hhhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhhhhhh...eeeeeee.....hhhhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhh...eeee.hhhhh......hhhhhhhh.....ee...hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh.......hhhhhhhh.....hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh.......hhhhhhhhh..........hhhhhhhhhhhhh......hhhhh...hhhhhhhhhh.......hhhhhhhhhhh..hhhhhhhhhhhh......hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------PYR_CT  PDB: A:14-276 UniProt: 14-276                                                                                                                                                                                                                                   ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rr2 A   3 PREIEVSEPREVGITELVLRDAHQSLMATRMAMEDMVGACADIDAAGYWSVECWGGATYDSCIRFLNEDPWERLRTFRKLMPNSRLQMLLRGQNLLGYRHYNDEVVDRFVDKSAENGMDVFRVFDAMNDPRNMAHAMAAVKKAGKHAQGTICYTISPVHTVEGYVKLAGQLLDMGADSIALkKDMAALLKPQPAYDIIKAIKDTYGQKTQINLHCHSTTGVTEVSLMKAIEAGVDVVDTAISSMSLGPGHNPTESVAEMLEGTGYTTNLDYDRLHKIRDHFKAIRPKYKKFESKTLVDTSIFKSQIPGGMLSNMESQLRAQGAEDKMDEVMAEVPRVRKAAGFPPLVTPSSQIVGTQAVFNVMMGEYKRMTGEFADIMLGYYGASPADRDPKVVKLAEEQSGKKPITQRPADLLPPEWEKQSKEAATLKGFNGTDEDVLTYALFPQVAPVFFEHRAEGPHSVALTDAQLKAEA 474
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182 |     191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471   
                                                                                                                                                                                                               184-KCX

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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)

1rr2A01

A:11-294

(no "Pfam Domain" information available for 1RR2)

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

1rqb	PROPIONIBACTERIUM SHERMANII TRANSCARBOXYLASE 5S SUBUNIT
1rqe	PROPIONIBACTERIUM SHERMANII TRANSCARBOXYLASE 5S SUBUNIT BOUND TO OXALOACETATE
1rqh	PROPIONIBACTERIUM SHERMANII TRANSCARBOXYLASE 5S SUBUNIT BOUND TO PYRUVATE
1s27	PROPIONIBACTERIUM SHERMANII TRANSCARBOXYLASE 5S SUBUNIT (M186I)
1s3h	PROPIONIBACTERIUM SHERMANII TRANSCARBOXYLASE 5S SUBUNIT A59T

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