2GSH - JenaLib

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Title :   CRYSTAL STRUCTURE OF L-RHAMNONATE DEHYDRATASE FROM SALMONELLA TYPHIMURIUM

Authors :   Y. Patskovsky, V. N. Malashkevich, J. M. Sauder, M. Dickey, J. M. Adams, S. R. Wasserman, J. Gerlt, S. C. Almo, S. K. Burley, New York Sgx Rese Center For Structural Genomics (Nysgxrc)

Date :   26 Apr 06 (Deposition) - 09 May 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.39

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (4x)

Keywords :   Enolase, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Patskovsky, V. N. Malashkevich, J. M. Sauder, M. Dickey, S. Ozyurt, S. R. Wasserman, J. Gerlt, S. C. Almo
Crystal Structure Of L-Rhamnonate Dehydratase From Salmonella Typhimurium Lt2
To Be Published
PubMed: search

Molecule 1 - L-RHAMNONATE DEHYDRATASE
	Chains	:	A, B
	EC Number	:	4.2.1.90
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	STM2291
	Organism Scientific	:	SALMONELLA TYPHIMURIUM
	Organism Taxid	:	99287
	Strain	:	LT2

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (4x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 8)

No.	Name	Count	Type	Full Name
1	GOL	8	Ligand/Ion	GLYCEROL
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP B:226 , GLU B:252 , GLU B:280 , HOH B:419 , HOH B:481	BINDING SITE FOR RESIDUE MG B 414
2	AC2	SOFTWARE	ASP A:226 , GLU A:252 , GLU A:280 , HOH A:418 , HOH A:480	BINDING SITE FOR RESIDUE MG A 414
3	AC3	SOFTWARE	ASP A:232 , VAL A:233 , ASN A:234 , ASP B:297 , GLY B:323 , LEU B:325	BINDING SITE FOR RESIDUE GOL A 415
4	AC4	SOFTWARE	ASP A:297 , GLN A:324 , LEU A:325 , ASP B:232 , VAL B:233 , ASN B:234	BINDING SITE FOR RESIDUE GOL A 416

(no "SS Bond" information available for 2GSH)

Asymmetric Unit

No.	Residues
1	Asp A:365	-	Pro A:366
2	Asp B:365	-	Pro B:366

(no "SAP(SNP)/Variant" information available for 2GSH)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MR_MLE_1	PS00908	Mandelate racemase / muconate lactonizing enzyme family signature 1.	RHMD_SALTY	136-161	2	A:136-161 B:136-161

Biological Unit 1 (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MR_MLE_1	PS00908	Mandelate racemase / muconate lactonizing enzyme family signature 1.	RHMD_SALTY	136-161	8	A:136-161 B:136-161

(no "Exon" information available for 2GSH)

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:403
 aligned with RHMD_SALTY | Q8ZNF9 from UniProtKB/Swiss-Prot  Length:405

    Alignment length:403
                                    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   
           RHMD_SALTY     3 NIMTLPKIKHVRAWFIGGATAEKGAGGGDYHDQGGNHWIDDHIATPMSKYRDYEQSRQSFGINVLGTLIVEVEAENRQTGFAVSTAGEMGCFIVEKHLNRFIEGKCVSDIKLIHDQMLGATMYYSGSGGLVMNTISCVDLALWDLFGKVVGLPVYKLLGGAVRDEIQFYATGARPDLAKEMGFIGGKMPTHWGPHDGDAGIRKDAAMVADMREKCGPDFWLMLDCWMSQDVNYATKLAHACAPFNLKWIEECLPPQQYEGYRELKRNAPAGMMVTSGEHHGTLQSFRTLAETGIDIMQPDVGWCGGLTTLVEIAALAKSRGQLVVPHGSSVYSHHAVITFTNTPFSEFLMTSPDCSTLRPQFDPILLDEPVPVNGRIHKSVLDKPGFGVELNRDCHLKRPYSH 405
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeehhhhh...............hhhhh.........................eeeeeeee....eeeeeee.hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh......eeeeeee..hhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhh..eee......hhhhhhhhhhh.....eeee.....hhhhhhhhhh....ee........hhhhhhhhhhhhhhh..ee....hhhhhhhhhh.......eeee................ee....hhh.eeehhhhh......ee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------MR_MLE_1  PDB: A:136-161  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gsh A   3 NIMTLPKIKHVRAWFIGGATAEKGAGGGDYHDQGGNHWIDDHIATPMSKYRDYEQSRQSFGINVLGTLIVEVEAENRQTGFAVSTAGEMGCFIVEKHLNRFIEGKCVSDIKLIHDQMLGATMYYSGSGGLVMNTISCVDLALWDLFGKVVGLPVYKLLGGAVRDEIQFYATGARPDLAKEMGFIGGKMPTHWGPHDGDAGIRKDAAMVADMREKCGPDFWLMLDCWMSQDVNYATKLAHACAPFNLKWIEECLPPQQYEGYRELKRNAPAGMMVTSGEHHGTLQSFRTLAETGIDIMQPDVGWCGGLTTLVEIAALAKSRGQLVVPHGSSVYSHHAVITFTNTPFSEFLMTSPDCSTLRPQFDPILLDEPVPVNGRIHKSVLDKPGFGVELNRDCHLKRPYSH 405
                                    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

Chain B from PDB  Type:PROTEIN  Length:403
 aligned with RHMD_SALTY | Q8ZNF9 from UniProtKB/Swiss-Prot  Length:405

    Alignment length:403
                                    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   
           RHMD_SALTY     3 NIMTLPKIKHVRAWFIGGATAEKGAGGGDYHDQGGNHWIDDHIATPMSKYRDYEQSRQSFGINVLGTLIVEVEAENRQTGFAVSTAGEMGCFIVEKHLNRFIEGKCVSDIKLIHDQMLGATMYYSGSGGLVMNTISCVDLALWDLFGKVVGLPVYKLLGGAVRDEIQFYATGARPDLAKEMGFIGGKMPTHWGPHDGDAGIRKDAAMVADMREKCGPDFWLMLDCWMSQDVNYATKLAHACAPFNLKWIEECLPPQQYEGYRELKRNAPAGMMVTSGEHHGTLQSFRTLAETGIDIMQPDVGWCGGLTTLVEIAALAKSRGQLVVPHGSSVYSHHAVITFTNTPFSEFLMTSPDCSTLRPQFDPILLDEPVPVNGRIHKSVLDKPGFGVELNRDCHLKRPYSH 405
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeehhhhh...............hhhhh.........................eeeeeeee....eeeeeee.hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh......eeeeeee..hhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhh..eee......hhhhhhhhhhh.....eeee.....hhhhhhhhhh....ee........hhhhhhhhhhhhhhh..ee....hhhhhhhhhh.......eeee................ee....hhh.eeehhhhh......ee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------MR_MLE_1  PDB: B:136-161  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gsh B   3 NIMTLPKIKHVRAWFIGGATAEKGAGGGDYHDQGGNHWIDDHIATPMSKYRDYEQSRQSFGINVLGTLIVEVEAENRQTGFAVSTAGEMGCFIVEKHLNRFIEGKCVSDIKLIHDQMLGATMYYSGSGGLVMNTISCVDLALWDLFGKVVGLPVYKLLGGAVRDEIQFYATGARPDLAKEMGFIGGKMPTHWGPHDGDAGIRKDAAMVADMREKCGPDFWLMLDCWMSQDVNYATKLAHACAPFNLKWIEECLPPQQYEGYRELKRNAPAGMMVTSGEHHGTLQSFRTLAETGIDIMQPDVGWCGGLTTLVEIAALAKSRGQLVVPHGSSVYSHHAVITFTNTPFSEFLMTSPDCSTLRPQFDPILLDEPVPVNGRIHKSVLDKPGFGVELNRDCHLKRPYSH 405
                                    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

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 '\|'

(no "SCOP Domain" information available for 2GSH)

(no "CATH Domain" information available for 2GSH)

(no "Pfam Domain" information available for 2GSH)

Asymmetric Unit(hide GO term definitions)

Chain A,B (RHMD_SALTY | Q8ZNF9)

molecular function
	GO:0050032	L-rhamnonate dehydratase activity	Catalysis of the reaction: L-rhamnonate = 2-dehydro-3-deoxy-L-rhamnonate + 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: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:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0009063	cellular amino acid catabolic process	The chemical reactions and pathways resulting in the breakdown of amino acids, organic acids containing one or more amino substituents.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

Asymmetric Unit
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	Cis Peptide Bonds
		Asp A:365 - Pro A:366	[ RasMol ]
		Asp B:365 - Pro B:366	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	2gsh
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Description

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Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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Exons (0, 0)

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