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Title :   CRYSTAL STRUCTURE OF GLUTAMATE RACEMASE FROM LISTERIA MONOCYTOGENES IN COMPLEX WITH SUCCINIC ACID

Authors :   K. A. Majorek, M. Chruszcz, T. Skarina, O. Onopriyenko, J. Stam, W. F. An A. Savchenko, J. M. Bujnicki, W. Minor, Center For Structural Geno Infectious Diseases (Csgid)

Date :   27 Aug 09 (Deposition) - 22 Sep 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A  (1x)
Biol. Unit 3: B  (1x)

Keywords :   Glutamate Racemase, Structural Genomics, Cell Wall Biogenesis/Degradation, Isomerase, Peptidoglycan Synthesis, Center For Structural Genomics Of Infectious Diseases, Csgid, Cell Shape (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. A. Majorek, M. Chruszcz, T. Skarina, O. Onopriyenko, J. Stam, W. F. Anderson, A. Savchenko, J. M. Bujnicki, W. Minor, Center For Structural Genomics Of Infectious Diseases (Csgid)
Crystal Structure Of Glutamate Racemase From Listeria Monocytogenes In Complex With Succinic Acid
To Be Published
PubMed: search

Molecule 1 - GLUTAMATE RACEMASE
	Chains	:	A, B
	EC Number	:	5.1.1.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG7
	Expression System Strain	:	BL21 DE3 STAR MAGIC
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	LMO1237, MURI, RACE
	Organism Scientific	:	LISTERIA MONOCYTOGENES
	Organism Taxid	:	169963
	Strain	:	EGD-E

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:	A
Biological Unit 3 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 18)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	MSE	14	Mod. Amino Acid	SELENOMETHIONINE
3	SIN	2	Ligand/Ion	SUCCINIC ACID

Biological Unit 1 (2, 16)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MSE	14	Mod. Amino Acid	SELENOMETHIONINE
3	SIN	2	Ligand/Ion	SUCCINIC ACID

Biological Unit 2 (2, 8)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MSE	7	Mod. Amino Acid	SELENOMETHIONINE
3	SIN	1	Ligand/Ion	SUCCINIC ACID

Biological Unit 3 (2, 8)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MSE	7	Mod. Amino Acid	SELENOMETHIONINE
3	SIN	1	Ligand/Ion	SUCCINIC ACID

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:10 , CYS A:39 , PRO A:40 , TYR A:41 , GLY A:42 , THR A:74 , THR A:116 , THR A:119 , VAL A:147 , CYS A:183 , HOH A:283 , HOH A:358 , HOH A:374	BINDING SITE FOR RESIDUE SIN A 267
2	AC2	SOFTWARE	SER B:10 , PRO B:40 , TYR B:41 , GLY B:42 , CYS B:72 , ASN B:73 , THR B:74 , HOH B:270 , HOH B:358 , HOH B:445 , HOH B:446	BINDING SITE FOR RESIDUE SIN B 267
3	AC3	SOFTWARE	HOH A:273 , ARG B:84 , ILE B:92 , GLY B:93 , HOH B:278 , HOH B:408	BINDING SITE FOR RESIDUE CL B 268
4	AC4	SOFTWARE	GLY A:42 , THR A:116 , LEU A:117 , HOH A:374 , HOH A:520	BINDING SITE FOR RESIDUE CL A 268

(no "SS Bond" information available for 3IST)

Asymmetric Unit

No.	Residues
1	Cys A:39	-	Pro A:40
2	Cys B:39	-	Pro B:40

(no "SAP(SNP)/Variant" information available for 3IST)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ASP_GLU_RACEMASE_1	PS00923	Aspartate and glutamate racemases signature 1.	MURI_LISMO	69-77	2	A:69-77 B:69-77
2	ASP_GLU_RACEMASE_2	PS00924	Aspartate and glutamate racemases signature 2.	MURI_LISMO	179-189	2	A:179-189 B:179-189

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ASP_GLU_RACEMASE_1	PS00923	Aspartate and glutamate racemases signature 1.	MURI_LISMO	69-77	2	A:69-77 B:69-77
2	ASP_GLU_RACEMASE_2	PS00924	Aspartate and glutamate racemases signature 2.	MURI_LISMO	179-189	2	A:179-189 B:179-189

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ASP_GLU_RACEMASE_1	PS00923	Aspartate and glutamate racemases signature 1.	MURI_LISMO	69-77	1	A:69-77 -
2	ASP_GLU_RACEMASE_2	PS00924	Aspartate and glutamate racemases signature 2.	MURI_LISMO	179-189	1	A:179-189 -

Biological Unit 3 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ASP_GLU_RACEMASE_1	PS00923	Aspartate and glutamate racemases signature 1.	MURI_LISMO	69-77	1	- B:69-77
2	ASP_GLU_RACEMASE_2	PS00924	Aspartate and glutamate racemases signature 2.	MURI_LISMO	179-189	1	- B:179-189

(no "Exon" information available for 3IST)

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:268
 aligned with MURI_LISMO | Q8Y7N7 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:268
                               1                                                                                                                                                                                                                                                                        
                               |     7        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        
           MURI_LISMO     - ---MKQAIGFIDSGVGGLTVVREVLKQLPHEQVYYLGDTARCPYGPRDKEEVAKFTWEMTNFLVDRGIKMLVIACNTATAAALYDIREKLDIPVIGVIQPGSRAALKATRNNKIGVLGTLGTVESMAYPTALKGLNRRVEVDSLACPKFVSVVESGEYKSAIAKKVVAESLLPLKSTKIDTVILGCTHYPLLKPIIENFMGDGVAVINSGEETASEVSALLDYHNLLDATDEEIEHRFFTTGSTQIFKDIAKDWLNMPDMTVEHIKLG 265
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3istA01 A:-2-93,A:207-265  [code=3.40.50.1860, no name defined]                                 3istA02 A:94-206  [code=3.40.50.1860, no name defined]                                                           3istA01 A:-2-93,A:207-265                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee....hhhhhhhhhhhh....eeeee.hhhh.....hhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhh...eeehhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhh....hhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhh............eeee..hhhhhhhhhhhhhh.....eee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------ASP_GLU_R-----------------------------------------------------------------------------------------------------ASP_GLU_RAC---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ist A  -2 SNAmKQAIGFIDSGVGGLTVVREVLKQLPHEQVYYLGDTARCPYGPRDKEEVAKFTWEmTNFLVDRGIKmLVIACNTATAAALYDIREKLDIPVIGVIQPGSRAALKATRNNKIGVLGTLGTVESmAYPTALKGLNRRVEVDSLACPKFVSVVESGEYKSAIAKKVVAESLLPLKSTKIDTVILGCTHYPLLKPIIENFmGDGVAVINSGEETASEVSALLDYHNLLDATDEEIEHRFFTTGSTQIFKDIAKDWLNmPDmTVEHIKLG 265
                               |     7        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        
                               |                                                     56-MSE     67-MSE                                                 123-MSE                                                                   197-MSE                                                  254-MSE       
                               1-MSE                                                                                                                                                                                                                                                         257-MSE

Chain B from PDB  Type:PROTEIN  Length:266
 aligned with MURI_LISMO | Q8Y7N7 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:266
                                    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      
           MURI_LISMO     1 MKQAIGFIDSGVGGLTVVREVLKQLPHEQVYYLGDTARCPYGPRDKEEVAKFTWEMTNFLVDRGIKMLVIACNTATAAALYDIREKLDIPVIGVIQPGSRAALKATRNNKIGVLGTLGTVESMAYPTALKGLNRRVEVDSLACPKFVSVVESGEYKSAIAKKVVAESLLPLKSTKIDTVILGCTHYPLLKPIIENFMGDGVAVINSGEETASEVSALLDYHNLLDATDEEIEHRFFTTGSTQIFKDIAKDWLNMPDMTVEHIKLGK 266
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -3istB01 B:2-93,B:207-266  [code=3.40.50.1860, no name defined]                              3istB02 B:94-206  [code=3.40.50.1860, no name defined]                                                           3istB01 B:2-93,B:207-266                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....hhhhhhhhhhhh....eeeee.hhhh.....hhhhhhhhhhhhhhhhhhhheeeeee.hhhhhhhhhhhhhhhh...eeehhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhh....hhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh...eeehhhhhhhhhhhhhhhhh............eeee..hhhhhhhhhhhhh......eee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------ASP_GLU_R-----------------------------------------------------------------------------------------------------ASP_GLU_RAC----------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ist B   1 mKQAIGFIDSGVGGLTVVREVLKQLPHEQVYYLGDTARCPYGPRDKEEVAKFTWEmTNFLVDRGIKmLVIACNTATAAALYDIREKLDIPVIGVIQPGSRAALKATRNNKIGVLGTLGTVESmAYPTALKGLNRRVEVDSLACPKFVSVVESGEYKSAIAKKVVAESLLPLKSTKIDTVILGCTHYPLLKPIIENFmGDGVAVINSGEETASEVSALLDYHNLLDATDEEIEHRFFTTGSTQIFKDIAKDWLNmPDmTVEHIKLGK 266
                            |       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      
                            1-MSE                                                 56-MSE     67-MSE                                                 123-MSE                                                                   197-MSE                                                  254-MSE        
                                                                                                                                                                                                                                                                                          257-MSE

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 3IST)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1860, no name defined] (18)

Listeria monocytogenes. Organism_taxid: 169963. Strain: egd-e. (2)

1a	3istA02	A:94-206
1b	3istB02	B:94-206
1c	3istB01	B:2-93,B:207-266
1d	3istA01	A:-2-93,A:207-265

(no "Pfam Domain" information available for 3IST)

Asymmetric Unit(hide GO term definitions)

Chain A,B (MURI_LISMO | Q8Y7N7)

molecular function
	GO:0008881	glutamate racemase activity	Catalysis of the reaction: L-glutamate = D-glutamate.
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	GO:0036361	racemase activity, acting on amino acids and derivatives	Catalysis of the interconversion of the two enantiomers of a chiral amino acid or amino acid derivative.
	GO:0016855	racemase and epimerase activity, acting on amino acids and derivatives	Catalysis of a reaction that alters the configuration of one or more chiral centers in an amino acid.
biological process
	GO:0071555	cell wall organization	A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
	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.
	GO:0006807	nitrogen compound metabolic process	The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
	GO:0009252	peptidoglycan biosynthetic process	The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
	GO:0008360	regulation of cell shape	Any process that modulates the surface configuration of a cell.

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	MURI_LISMO \| Q8Y7N7	:	3hfr 3isv

3hfr	CRYSTAL STRUCTURE OF GLUTAMATE RACEMASE FROM LISTERIA MONOCYTOGENES RELATED ID: IDP00347 RELATED DB: TARGETDB
3isv	CRYSTAL STRUCTURE OF GLUTAMATE RACEMASE FROM LISTERIA MONOCYTOGENES IN COMPLEX WITH ACETATE ION

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