2P3Z - JenaLib

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

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

Date :   10 Mar 07 (Deposition) - 20 Mar 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

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

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

Molecule 1 - L-RHAMNONATE DEHYDRATASE
	Atcc	:	700720
	Chains	:	A, B
	EC Number	:	4.2.1.90
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	BC-BSGX3(BC)
	Expression System Strain	:	BL21(DE3)-CODON+RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	YFAW, STM2291
	Organism Scientific	:	SALMONELLA TYPHIMURIUM LT2
	Organism Taxid	:	99287
	Strain	:	LT2, SGSC1412

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	NA	2	Ligand/Ion	SODIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:226 , GLU A:252 , GLU A:280 , HOH A:557 , HOH A:732	BINDING SITE FOR RESIDUE NA A 501
2	AC2	SOFTWARE	LYS B:189 , ASP B:226 , GLU B:252 , GLU B:280 , HOH B:579 , HOH B:715	BINDING SITE FOR RESIDUE NA B 501

(no "SS Bond" information available for 2P3Z)

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 2P3Z)

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 2P3Z)

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

    Alignment length:405
                                                                                                                                                                                                                                                                                                                                                                                                                                             405 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401   | 
           RHMD_SALTY     2 ENIMTLPKIKHVRAWFIGGATAEKGAGGGDYHDQGGNHWIDDHIATPMSKYRDYEQSRQSFGINVLGTLIVEVEAENRQTGFAVSTAGEMGCFIVEKHLNRFIEGKCVSDIKLIHDQMLGATMYYSGSGGLVMNTISCVDLALWDLFGKVVGLPVYKLLGGAVRDEIQFYATGARPDLAKEMGFIGGKMPTHWGPHDGDAGIRKDAAMVADMREKCGPDFWLMLDCWMSQDVNYATKLAHACAPFNLKWIEECLPPQQYEGYRELKRNAPAGMMVTSGEHHGTLQSFRTLAETGIDIMQPDVGWCGGLTTLVEIAALAKSRGQLVVPHGSSVYSHHAVITFTNTPFSEFLMTSPDCSTLRPQFDPILLDEPVPVNGRIHKSVLDKPGFGVELNRDCHLKRPYSH-   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeee....................hhhh.........hhhhh..hhhhh.....eeeeeeee....eeeeeeehhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.......eeeeeee..hhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhh..eee.....hhhhhhhhhhhhh...eeeee.....hhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhh.......eeee................e.........eee.hhhh......ee............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------MR_MLE_1  PDB: A:136-161  ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p3z A   2 ENIMTLPKIKHVRAWFIGGATAEKGAGGGDYHDQGGNHWIDDHIATPMSKYRDYEQSRQSFGINVLGTLIVEVEAENRQTGFAVSTAGEMGCFIVEKHLNRFIEGKCVSDIKLIHDQMLGATMYYSGSGGLVMNTISCVDLALWDLFGKVVGLPVYKLLGGAVRDEIQFYATGARPDLAKEMGFIGGKMPTHWGPHDGDAGIRKDAAMVADMREKCGPDFWLMLDCWMSQDVNYATKLAHACAPFNLKWIEECLPPQQYEGYRELKRNAPAGMMVTSGEHHGTLQSFRTLAETGIDIMQPDVGWCGGLTTLVEIAALAKSRGQLVVPHGSSVYSHHAVITFTNTPFSEFLMTSPDCSTLRPQFDPILLDEPVPVNGRIHKSVLDKPGFGVELNRDCHLKRPYSHE 406
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401

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

    Alignment length:405
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400     
           RHMD_SALTY     1 MENIMTLPKIKHVRAWFIGGATAEKGAGGGDYHDQGGNHWIDDHIATPMSKYRDYEQSRQSFGINVLGTLIVEVEAENRQTGFAVSTAGEMGCFIVEKHLNRFIEGKCVSDIKLIHDQMLGATMYYSGSGGLVMNTISCVDLALWDLFGKVVGLPVYKLLGGAVRDEIQFYATGARPDLAKEMGFIGGKMPTHWGPHDGDAGIRKDAAMVADMREKCGPDFWLMLDCWMSQDVNYATKLAHACAPFNLKWIEECLPPQQYEGYRELKRNAPAGMMVTSGEHHGTLQSFRTLAETGIDIMQPDVGWCGGLTTLVEIAALAKSRGQLVVPHGSSVYSHHAVITFTNTPFSEFLMTSPDCSTLRPQFDPILLDEPVPVNGRIHKSVLDKPGFGVELNRDCHLKRPYSH 405
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------------------------------MR_MLE_N-2p3zB01 B:69-161                                                                    -----------------------------------------------MR_MLE-2p3zB03 B:209-278                                              MR_MLE_C-2p3zB05 B:279-392                                                                                        ------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------MR_MLE_N-2p3zB02 B:69-161                                                                    -----------------------------------------------MR_MLE-2p3zB04 B:209-278                                              MR_MLE_C-2p3zB06 B:279-392                                                                                        ------------- Pfam domains (2)
         Sec.struct. author .........eeeeeeeee....................hhhhh........hhhhh.hhhhhh.....eeeeeeee....eeeeeeehhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh......eeeeeee..hhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhh....eeee.....hhhhhhhhhh....ee........hhhhhhhhhhhhhhh..ee.....hhhhhhhhh.......eeee................ee........eee...........ee............ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------MR_MLE_1  PDB: B:136-161  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p3z B   1 LENIMTLPKIKHVRAWFIGGATAEKGAGGGDYHDQGGNHWIDDHIATPMSKYRDYEQSRQSFGINVLGTLIVEVEAENRQTGFAVSTAGEMGCFIVEKHLNRFIEGKCVSDIKLIHDQMLGATMYYSGSGGLVMNTISCVDLALWDLFGKVVGLPVYKLLGGAVRDEIQFYATGARPDLAKEMGFIGGKMPTHWGPHDGDAGIRKDAAMVADMREKCGPDFWLMLDCWMSQDVNYATKLAHACAPFNLKWIEECLPPQQYEGYRELKRNAPAGMMVTSGEHHGTLQSFRTLAETGIDIMQPDVGWCGGLTTLVEIAALAKSRGQLVVPHGSSVYSHHAVITFTNTPFSEFLMTSPDCSTLRPQFDPILLDEPVPVNGRIHKSVLDKPGFGVELNRDCHLKRPYSH 405
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400

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 2P3Z)

(no "CATH Domain" information available for 2P3Z)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Enolase_N (69)

Family: MR_MLE_N (47)

Salmonella typhimurium (1)

1a	MR_MLE_N-2p3zB01	B:69-161
1b	MR_MLE_N-2p3zB02	B:69-161

Clan: Enolase_TIM (82)

Family: MR_MLE (48)

Salmonella typhimurium (1)

2a	MR_MLE-2p3zB03	B:209-278
2b	MR_MLE-2p3zB04	B:209-278

Family: MR_MLE_C (29)

Salmonella typhimurium (1)

3a	MR_MLE_C-2p3zB05	B:279-392
3b	MR_MLE_C-2p3zB06	B:279-392

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.

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

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2gsh	CRYSTAL STRUCTURE OF L-RHAMNONATE DEHYDRATASE FROM SALMONELLA TYPHIMURIUM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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