1LKC - JenaLib

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Title :   CRYSTAL STRUCTURE OF L-THREONINE-O-3-PHOSPHATE DECARBOXYLASE FROM SALMONELLA ENTERICA

Authors :   C. G. Cheong, C. B. Bauer, K. R. Brushaber, J. C. Escalante-Semerena, I.

Date :   24 Apr 02 (Deposition) - 01 May 02 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Cobd, L-Threonine-O-3-Phosphate, 1-Amino-2-Propanol-Phosphate, Plp, Decarboxylase, Cobalamin, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. G. Cheong, C. B. Bauer, K. R. Brushaber, J. C. Escalante-Semerena, I. Rayment
Three-Dimensional Structure Of The L-Threonine-O-3-Phosphat Decarboxylase (Cobd) Enzyme From Salmonella Enterica.
Biochemistry V. 41 4798 2002
PubMed-ID: 11939774 | Reference-DOI: 10.1021/BI012111W

Molecule 1 - L-THREONINE-O-3-PHOSPHATE DECARBOXYLASE
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	COBD
	Organism Scientific	:	SALMONELLA ENTERICA
	Organism Taxid	:	28901
	Synonym	:	COBD

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 4)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	PLP	1	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE
3	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (3, 8)

No.	Name	Count	Type	Full Name
1	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
2	PLP	2	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE
3	PO4	2	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:8 , GLY A:9 , ASN A:157 , ARG A:323 , TYR A:328 , ARG A:337 , HOH A:858 , HOH A:917	BINDING SITE FOR RESIDUE PO4 A 700
2	AC2	SOFTWARE	TYR A:56 , GLY A:84 , GLU A:85 , THR A:86 , PHE A:108 , CYS A:153 , ASN A:157 , ASP A:185 , ALA A:187 , PHE A:188 , SER A:213 , THR A:215 , LYS A:216 , ARG A:224	BINDING SITE FOR RESIDUE PLP A 800
3	AC3	SOFTWARE	ASP A:190 , ARG A:212 , SER A:213 , TYR A:227 , HOH A:820 , HOH A:822	BINDING SITE FOR RESIDUE EDO A 701
4	AC4	SOFTWARE	LEU A:152 , CYS A:153 , ASN A:156 , PRO A:163 , HOH A:809 , HOH A:1201	BINDING SITE FOR RESIDUE EDO A 702

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

Asymmetric Unit

No.	Residues
1	Thr A:105	-	Pro A:106
2	Thr A:154	-	Pro A:155
3	Asn A:157	-	Pro A:158

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AA_TRANSFER_CLASS_1	PS00105	Aminotransferases class-I pyridoxal-phosphate attachment site.	COBD_SALTY	213-226	1	A:213-226

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AA_TRANSFER_CLASS_1	PS00105	Aminotransferases class-I pyridoxal-phosphate attachment site.	COBD_SALTY	213-226	2	A:213-226

(no "Exon" information available for 1LKC)

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:355
 aligned with COBD_SALTY | P97084 from UniProtKB/Swiss-Prot  Length:364

    Alignment length:355
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357     
           COBD_SALTY     8 HGGNIREAATVLGISPDQLLDFSANINPLGMPVSVKRALIDNLDCIERYPDADYFHLHQALARHHQVPASWILAGNGETESIFTVASGLKPRRAMIVTPGFAEYGRALAQSGCEIRRWSLREADGWQLTDAILEALTPDLDCLFLCTPNNPTGLLPERPLLQAIADRCKSLNINLILDEAFIDFIPHETGFIPALKDNPHIWVLRSLTKFYAIPGLRLGYLVNSDDAAMARMRRQQMPWSVNALAALAGEVALQDSAWQQATWHWLREEGARFYQALCQLPLLTVYPGRANYLLLRCEREDIDLQRRLLTQRILIRSCANYPGLDSRYYRVAIRSAAQNERLLAALRNVLTGIAP 362
               SCOP domains d1lkca_ A: L-threonine-O-3-phosphate decarboxylase CobD                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1lkcA01 A:8-37,A:263-362      1lkcA02 A:38-262 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                             1lkcA01 A:8-37,A:263-362 Aspartate Aminotransferase, domain 1                                        CATH domains
               Pfam domains ----------------Aminotran_1_2-1lkcA01 A:24-353                                                                                                                                                                                                                                                                                                            --------- Pfam domains
         Sec.struct. author ....hhhhhhhhh.hhhhhee..........hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhh.eeee.hhhhhhhhhhhhhh..eeeeee...hhhhhhhhhh..eeeeee.hhhhh....hhhhhhh.....eeeee..........hhhhhhhhhhhhhhh..eeeee..hhhhh.....hhhhh.....eeeeee............eeee..hhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..eee......eeeeee.....hhhhhhhhh.ee.ee..........eeeee..hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CL---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lkc A   8 HGGNIREPATVLGISPDQLLDFSANINPLGMPVSVKRALIDNLDCIERYPDADYFHLHQALARHHQVPASWILAGNGETESIFTVASGLKPRRAMIVTPGFAEYGRALAQSGCEIRRWSLREADGWQLTDAILEALTPDLDCLFLCTPNNPTGLLPERPLLQAIADRCKSLNINLILDEAFIDFIPHETGFIPALKDNPHIWVLRSLTKFYAIPGLRLGYLVNSDDAAMARMRRQQMPWSVNALAALAGEVALQDSAWQQATWHWLREEGARFYQALCQLPLLTVYPGRANYLLLRCEREDIDLQRRLLTQRILIRSCANYPGLDSRYYRVAIRSAAQNERLLAALRNVLTGIAP 362
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: PLP-dependent transferase-like (627)

Superfamily: PLP-dependent transferases (625)

Family: AAT-like (184)

Protein domain: L-threonine-O-3-phosphate decarboxylase CobD (4)

Salmonella enterica [TaxId: 28901] (4)

d1lkca_

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PLP_aminotran (240)

Family: Aminotran_1_2 (77)

Salmonella typhimurium (4)

Aminotran_1_2-1lkcA01

A:24-353

Asymmetric Unit(hide GO term definitions)

Chain A (COBD_SALTY | P97084)

molecular function
	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:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0030170	pyridoxal phosphate binding	Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
	GO:0048472	threonine-phosphate decarboxylase activity	Catalysis of the reaction: O-phospho-L-threonine + H(+) = (R)-1-aminopropan-2-yl phosphate + CO(2).
biological process
	GO:0009058	biosynthetic process	The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
	GO:0009236	cobalamin biosynthetic process	The chemical reactions and pathways resulting in the formation of cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.

Asymmetric Unit
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	Cis Peptide Bonds
		Asn A:157 - Pro A:158	[ RasMol ]
		Thr A:105 - Pro A:106	[ RasMol ]
		Thr A:154 - Pro A:155	[ RasMol ]

Biological Unit
	Complete Structure
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	1lkc
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	COBD_SALTY \| P97084	:	1lc5 1lc7 1lc8

1kus	THIS IS MORE REFINED STRUCTURE OF 1KUS

Description

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Ligands, Modified Residues, Ions (3, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

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