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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF HELICOBACTER PYLORI GLUTAMATE RACEMASE IN COMPLEX WITH D-GLUTAMATE AND AN INHIBITOR

Authors :   T. Lundqvist

Date :   25 Nov 08 (Deposition) - 09 Dec 08 (Release) - 03 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.87

Chains :   Asym./Biol. Unit : A,B,E,F

Keywords :   Isomerase, Cell Shape, Glutamate Racemase, Cell Wall Biogenesis/Degradation, Peptidoglycan Synthesis, Peptidoglycan Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Geng, G. Basarab, J. Comita-Prevoir, M. Gowravaram, P. Hill, A. Kiely, J. Loch, L. Macpherson, M. Morningstar, G. Mullen, E. Osimboni, A. Satz, C. Eyermann, T. Lundqvist
Potent And Selective Inhibitors Of Helicobacter Pylori Glutamate Racemase (Muri): Pyridodiazepine Amines
Bioorg. Med. Chem. Lett. V. 19 930 2009
PubMed-ID: 19097892 | Reference-DOI: 10.1016/J.BMCL.2008.11.113

Molecule 1 - GLUTAMATE RACEMASE
	Chains	:	A, B, E, F
	EC Number	:	5.1.1.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	HELICOBACTER PYLORI
	Organism Taxid	:	210

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 6)

No.	Name	Count	Type	Full Name
1	DGL	4	Ligand/Ion	D-GLUTAMIC ACID
2	VGA	2	Ligand/Ion	1-[(3S)-5-PHENYL-3-THIOPHEN-2-YL-3H-1,4-BENZODIAZEPIN-2-YL]AZETIDIN-3-OL

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:7 , SER A:8 , PRO A:38 , TYR A:39 , GLY A:40 , CYS A:70 , ASN A:71 , THR A:72 , THR A:116 , CYS A:181 , THR A:182 , HOH A:2007 , HOH A:2294 , HOH A:2393	BINDING SITE FOR RESIDUE DGL A1256
2	AC2	SOFTWARE	ASP B:7 , SER B:8 , PRO B:38 , TYR B:39 , GLY B:40 , CYS B:70 , ASN B:71 , THR B:72 , THR B:116 , CYS B:181 , THR B:182 , HOH B:2007 , HOH B:2264 , HOH B:2328	BINDING SITE FOR RESIDUE DGL B1255
3	AC3	SOFTWARE	ASP E:7 , SER E:8 , PRO E:38 , TYR E:39 , GLY E:40 , CYS E:70 , ASN E:71 , THR E:72 , THR E:116 , CYS E:181 , THR E:182 , HIS E:183 , HOH E:2325 , HOH E:2326	BINDING SITE FOR RESIDUE DGL E1255
4	AC4	SOFTWARE	ASP F:7 , SER F:8 , PRO F:38 , TYR F:39 , GLY F:40 , CYS F:70 , ASN F:71 , THR F:72 , THR F:116 , CYS F:181 , THR F:182 , HOH F:2243 , HOH F:2307	BINDING SITE FOR RESIDUE DGL F1255
5	AC5	SOFTWARE	PRO A:38 , THR A:41 , SER A:143 , VAL A:146 , PRO A:147 , GLU A:150 , GLU A:151 , HOH A:2244 , PRO B:38 , THR B:41 , LYS B:117 , VAL B:146 , PRO B:147 , GLU B:150 , GLU B:151 , HOH B:2214 , HOH B:2329	BINDING SITE FOR RESIDUE VGA B1256
6	AC6	SOFTWARE	THR E:41 , SER E:143 , VAL E:146 , PRO E:147 , GLU E:150 , GLU E:151 , HOH E:2327 , HOH E:2328 , PRO F:38 , VAL F:146 , PRO F:147 , GLU F:150 , GLU F:151	BINDING SITE FOR RESIDUE VGA E1256

(no "SS Bond" information available for 2W4I)

Asymmetric/Biological Unit

No.	Residues
1	Val A:37	-	Pro A:38
2	Val B:37	-	Pro B:38
3	Val E:37	-	Pro E:38
4	Val F:37	-	Pro F:38

(no "SAP(SNP)/Variant" information available for 2W4I)

Asymmetric/Biological Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ASP_GLU_RACEMASE_1	PS00923	Aspartate and glutamate racemases signature 1.	MURI_HELPJ	67-75	4	A:67-75 B:67-75 E:67-75 F:67-75
2	ASP_GLU_RACEMASE_2	PS00924	Aspartate and glutamate racemases signature 2.	MURI_HELPJ	177-187	4	A:177-187 B:177-187 E:177-187 F:177-187

(no "Exon" information available for 2W4I)

Asymmetric/Biological 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:255
 aligned with MURI_HELPJ | Q9ZLT0 from UniProtKB/Swiss-Prot  Length:255

    Alignment length:255
                                    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     
           MURI_HELPJ     1 MKIGVFDSGVGGFSVLKSLLKARLFDEIIYYGDSARVPYGTKDPTTIKQFGLEALDFFKPHEIELLIVACNTASALALEEMQKYSKIPIVGVIEPSILAIKRQVEDKNAPILVLGTKATIQSNAYDNALKQQGYLNISHLATSLFVPLIEESILEGELLETCMHYYFTPLEILPEVIILGCTHFPLIAQKIEGYFMGHFALPTPPLLIHSGDAIVEYLQQKYALKNNACTFPKVEFHASGDVIWLERQAKEWLKL 255
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhh...eeeeee..........hhhhhhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhh....eee.hhhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhhh....eeeee..hhhhhhhh...hhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhhhhhh.....eeeehhhhhhhhhhhhhhhhh......eeeeee..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ASP_GLU_R-----------------------------------------------------------------------------------------------------ASP_GLU_RAC-------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w4i A   1 MKIGVFDSGVGGFSVLKSLLKARLFDEIIYYGDSARVPYGTKDPTTIKQFGLEALDFFKPHEIELLIVACNTASALALEEMQKYSKIPIVGVIEPSILAIKRQVEDKNAPILVLGTKATIQSNAYDNALKQQGYLNISHLATSLFVPLIEESILEGELLETCMHYYFTPLEILPEVIILGCTHFPLIAQKIEGYFMGHFALPTPPLLIHSGDAIVEYLQQKYALKNNACTFPKVEFHASGDVIWLERQAKEWLKL 255
                                    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

Chain B from PDB  Type:PROTEIN  Length:254
 aligned with MURI_HELPJ | Q9ZLT0 from UniProtKB/Swiss-Prot  Length:255

    Alignment length:254
                                    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    
           MURI_HELPJ     1 MKIGVFDSGVGGFSVLKSLLKARLFDEIIYYGDSARVPYGTKDPTTIKQFGLEALDFFKPHEIELLIVACNTASALALEEMQKYSKIPIVGVIEPSILAIKRQVEDKNAPILVLGTKATIQSNAYDNALKQQGYLNISHLATSLFVPLIEESILEGELLETCMHYYFTPLEILPEVIILGCTHFPLIAQKIEGYFMGHFALPTPPLLIHSGDAIVEYLQQKYALKNNACTFPKVEFHASGDVIWLERQAKEWLK 254
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhh...eeeeee..........hhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhh...ee.hhhhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhhh....eeeee..hhhhhhhh...hhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhhhhhh.....eeeehhhhhhhhhhhhh..........eeeeee..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ASP_GLU_R-----------------------------------------------------------------------------------------------------ASP_GLU_RAC------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w4i B   1 MKIGVFDSGVGGFSVLKSLLKARLFDEIIYYGDSARVPYGTKDPTTIKQFGLEALDFFKPHEIELLIVACNTASALALEEMQKYSKIPIVGVIEPSILAIKRQVEDKNAPILVLGTKATIQSNAYDNALKQQGYLNISHLATSLFVPLIEESILEGELLETCMHYYFTPLEILPEVIILGCTHFPLIAQKIEGYFMGHFALPTPPLLIHSGDAIVEYLQQKYALKNNACTFPKVEFHASGDVIWLERQAKEWLK 254
                                    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

Chain E from PDB  Type:PROTEIN  Length:254
 aligned with MURI_HELPJ | Q9ZLT0 from UniProtKB/Swiss-Prot  Length:255

    Alignment length:254
                                    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    
           MURI_HELPJ     1 MKIGVFDSGVGGFSVLKSLLKARLFDEIIYYGDSARVPYGTKDPTTIKQFGLEALDFFKPHEIELLIVACNTASALALEEMQKYSKIPIVGVIEPSILAIKRQVEDKNAPILVLGTKATIQSNAYDNALKQQGYLNISHLATSLFVPLIEESILEGELLETCMHYYFTPLEILPEVIILGCTHFPLIAQKIEGYFMGHFALPTPPLLIHSGDAIVEYLQQKYALKNNACTFPKVEFHASGDVIWLERQAKEWLK 254
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhh...eeeeee..........hhhhhhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhh....eeehhhhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhhh....eeeee..hhhhhhhh...hhhhhhhhhhhhhh.......eeee...hhhhhhhhhhhhhhhhh......eeeehhhhhhhhhhhhh..........eeeeee..hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ASP_GLU_R-----------------------------------------------------------------------------------------------------ASP_GLU_RAC------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w4i E   1 MKIGVFDSGVGGFSVLKSLLKARLFDEIIYYGDSARVPYGTKDPTTIKQFGLEALDFFKPHEIELLIVACNTASALALEEMQKYSKIPIVGVIEPSILAIKRQVEDKNAPILVLGTKATIQSNAYDNALKQQGYLNISHLATSLFVPLIEESILEGELLETCMHYYFTPLEILPEVIILGCTHFPLIAQKIEGYFMGHFALPTPPLLIHSGDAIVEYLQQKYALKNNACTFPKVEFHASGDVIWLERQAKEWLK 254
                                    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

Chain F from PDB  Type:PROTEIN  Length:254
 aligned with MURI_HELPJ | Q9ZLT0 from UniProtKB/Swiss-Prot  Length:255

    Alignment length:254
                                    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    
           MURI_HELPJ     1 MKIGVFDSGVGGFSVLKSLLKARLFDEIIYYGDSARVPYGTKDPTTIKQFGLEALDFFKPHEIELLIVACNTASALALEEMQKYSKIPIVGVIEPSILAIKRQVEDKNAPILVLGTKATIQSNAYDNALKQQGYLNISHLATSLFVPLIEESILEGELLETCMHYYFTPLEILPEVIILGCTHFPLIAQKIEGYFMGHFALPTPPLLIHSGDAIVEYLQQKYALKNNACTFPKVEFHASGDVIWLERQAKEWLK 254
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --Asp_Glu_race-2w4iF01 F:3-219                                                                                                                                                                                             ----------------------------------- Pfam domains (1)
           Pfam domains (2) --Asp_Glu_race-2w4iF02 F:3-219                                                                                                                                                                                             ----------------------------------- Pfam domains (2)
           Pfam domains (3) --Asp_Glu_race-2w4iF03 F:3-219                                                                                                                                                                                             ----------------------------------- Pfam domains (3)
           Pfam domains (4) --Asp_Glu_race-2w4iF04 F:3-219                                                                                                                                                                                             ----------------------------------- Pfam domains (4)
         Sec.struct. author .eeeeee....hhhhhhhhhhh....eeeeee..........hhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhh....ee.hhhhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhhh....eeeee..hhhhhhhh...hhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhhhhh......eeeehhhhhhhhhhhhh..........eeeeee..hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ASP_GLU_R-----------------------------------------------------------------------------------------------------ASP_GLU_RAC------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w4i F   1 MKIGVFDSGVGGFSVLKSLLKARLFDEIIYYGDSARVPYGTKDPTTIKQFGLEALDFFKPHEIELLIVACNTASALALEEMQKYSKIPIVGVIEPSILAIKRQVEDKNAPILVLGTKATIQSNAYDNALKQQGYLNISHLATSLFVPLIEESILEGELLETCMHYYFTPLEILPEVIILGCTHFPLIAQKIEGYFMGHFALPTPPLLIHSGDAIVEYLQQKYALKNNACTFPKVEFHASGDVIWLERQAKEWLK 254
                                    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

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 2W4I)

(no "CATH Domain" information available for 2W4I)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Asp-glut_race (23)

Family: Asp_Glu_race (23)

Helicobacter pylori J99 (Campylobacter pylori J99) (3)

1a	Asp_Glu_race-2w4iF01	F:3-219
1b	Asp_Glu_race-2w4iF02	F:3-219
1c	Asp_Glu_race-2w4iF03	F:3-219
1d	Asp_Glu_race-2w4iF04	F:3-219

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,E,F (MURI_HELPJ | Q9ZLT0)

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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Val A:37 - Pro A:38	[ RasMol ]
		Val B:37 - Pro B:38	[ RasMol ]
		Val E:37 - Pro E:38	[ RasMol ]
		Val F:37 - Pro F:38	[ RasMol ]

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	2w4i
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	MURI_HELPJ \| Q9ZLT0
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	5.1.1.3
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	MURI_HELPJ \| Q9ZLT0	:	2jfx 2jfy 2jfz 4b1f

2jfx	CRYSTAL STRUCTURE OF HELICOBACTER PYLORI GLUTAMATE RACEMASE IN COMPLEX WITH D- GLUTAMATE
2jfy	CRYSTAL STRUCTURE OF HELICOBACTER PYLORI GLUTAMATE RACEMASE IN COMPLEX WITH D- GLUTAMATE
2jfz	CRYSTAL STRUCTURE OF HELICOBACTER PYLORI GLUTAMATE RACEMASE IN COMPLEX WITH D- GLUTAMATE AND AN INHIBITOR

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 8)

Exons (0, 0)

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Pfam Domains (1, 4)

Gene Ontology (9, 9)

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