1EJD - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF UNLIGANDED MURA (TYPE1)

Authors :   S. Eschenburg, E. Schonbrunn

Date :   02 Mar 00 (Deposition) - 25 Oct 00 (Release) - 27 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.55

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A (2x),B (2x)
Biol. Unit 4: A (1x),B (1x)
Biol. Unit 5: B  (2x)

Keywords :   Inside-Out Alpha/Beta Barrel, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Eschenburg, E. Schonbrunn
Comparative X-Ray Analysis Of The Un-Liganded Fosfomycin-Target Mura.
Proteins V. 40 290 2000
PubMed-ID: 10842342 | Reference-DOI: 10.1002/(SICI)1097-0134(20000801)40:2<290::AID-PROT 90>3.0.CO;2-0
(for further references see the PDB file header)

Molecule 1 - UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYLTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.5.1.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	ENTEROBACTER CLOACAE
	Organism Taxid	:	550
	Synonym	:	MURA, EPT

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (2x)	:	A (2x)	B (2x)
Biological Unit 4 (1x)	:	A (1x)	B (1x)
Biological Unit 5 (2x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 22)

No.	Name	Count	Type	Full Name
1	HAI	5	Ligand/Ion	CYCLOHEXYLAMMONIUM ION
2	IAS	2	Mod. Amino Acid	BETA-L-ASPARTIC ACID
3	PO4	15	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (3, 10)

No.	Name	Count	Type	Full Name
1	HAI	2	Ligand/Ion	CYCLOHEXYLAMMONIUM ION
2	IAS	1	Mod. Amino Acid	BETA-L-ASPARTIC ACID
3	PO4	7	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (3, 12)

No.	Name	Count	Type	Full Name
1	HAI	3	Ligand/Ion	CYCLOHEXYLAMMONIUM ION
2	IAS	1	Mod. Amino Acid	BETA-L-ASPARTIC ACID
3	PO4	8	Ligand/Ion	PHOSPHATE ION

Biological Unit 3 (3, 24)

No.	Name	Count	Type	Full Name
1	HAI	6	Ligand/Ion	CYCLOHEXYLAMMONIUM ION
2	IAS	2	Mod. Amino Acid	BETA-L-ASPARTIC ACID
3	PO4	16	Ligand/Ion	PHOSPHATE ION

Biological Unit 4 (3, 12)

No.	Name	Count	Type	Full Name
1	HAI	3	Ligand/Ion	CYCLOHEXYLAMMONIUM ION
2	IAS	1	Mod. Amino Acid	BETA-L-ASPARTIC ACID
3	PO4	8	Ligand/Ion	PHOSPHATE ION

Biological Unit 5 (3, 24)

No.	Name	Count	Type	Full Name
1	HAI	6	Ligand/Ion	CYCLOHEXYLAMMONIUM ION
2	IAS	2	Mod. Amino Acid	BETA-L-ASPARTIC ACID
3	PO4	16	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (19, 19)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN B:23 , ASP B:305 , ARG B:371 , HOH B:423 , HOH B:741 , HOH B:808 , HOH B:832	BINDING SITE FOR RESIDUE PO4 B 2422
02	AC2	SOFTWARE	SER B:162 , VAL B:163 , GLY B:164 , HOH B:425 , HOH B:428 , HOH B:480 , HOH B:838 , PO4 B:2427	BINDING SITE FOR RESIDUE PO4 B 2424
03	AC3	SOFTWARE	HIS B:155 , GLY B:319 , THR B:320 , HOH B:596 , HOH B:729 , PO4 B:2428	BINDING SITE FOR RESIDUE PO4 B 2425
04	AC4	SOFTWARE	ALA B:119 , ASP B:159 , HOH B:825	BINDING SITE FOR RESIDUE PO4 B 2426
05	AC5	SOFTWARE	PRO B:121 , SER B:162 , HOH B:425 , HOH B:917 , PO4 B:2424	BINDING SITE FOR RESIDUE PO4 B 2427
06	AC6	SOFTWARE	GLY B:319 , THR B:320 , HIS B:355 , HOH B:588 , PO4 B:2425	BINDING SITE FOR RESIDUE PO4 B 2428
07	AC7	SOFTWARE	ARG B:401 , GLU B:403 , ARG B:407 , ARG B:415 , HOH B:692	BINDING SITE FOR RESIDUE PO4 B 2429
08	AC8	SOFTWARE	GLU A:274 , HOH A:715 , GLY B:14 , GLU B:15 , HAI B:1422	BINDING SITE FOR RESIDUE PO4 A 2430
09	AC9	SOFTWARE	GLU A:188 , ARG A:232 , HIS A:299 , PRO A:303 , HOH A:444 , HOH A:552 , HOH A:590 , HOH A:815	BINDING SITE FOR RESIDUE PO4 A 2431
10	BC1	SOFTWARE	GLU A:135 , LYS A:137 , HOH A:421 , HOH A:426 , HOH A:435 , HOH A:919 , HAI A:1424	BINDING SITE FOR RESIDUE PO4 A 2432
11	BC2	SOFTWARE	ARG A:252 , ASP A:278 , ARG B:252 , ASN B:253 , HAI B:1420	BINDING SITE FOR RESIDUE PO4 A 2433
12	BC3	SOFTWARE	ARG A:401 , GLU A:403 , ASP A:404 , ARG A:407 , ARG A:415 , HOH A:728 , HOH A:748	BINDING SITE FOR RESIDUE PO4 A 2434
13	BC4	SOFTWARE	HIS A:394 , ARG A:397 , HOH A:592 , HOH A:633 , HOH A:648 , HOH A:895	BINDING SITE FOR RESIDUE PO4 A 2436
14	BC5	SOFTWARE	SER A:162 , VAL A:163 , GLY A:164 , HOH A:423 , HOH A:428 , HOH A:431 , HOH A:764 , HOH A:912	BINDING SITE FOR RESIDUE PO4 A 2437
15	BC6	SOFTWARE	ASP B:193 , ASN B:196 , TYR B:226 , GLN B:255 , HOH B:420 , HOH B:549 , HOH B:551 , HOH B:564	BINDING SITE FOR RESIDUE PO4 B 2439
16	BC7	SOFTWARE	VAL A:250 , TRP A:279 , PO4 A:2433 , VAL B:250 , TRP B:279 , HOH B:427	BINDING SITE FOR RESIDUE HAI B 1420
17	BC8	SOFTWARE	GLU B:65	BINDING SITE FOR RESIDUE HAI B 1421
18	BC9	SOFTWARE	VAL A:250 , GLU A:274 , PO4 A:2430 , VAL B:250 , GLU B:274	BINDING SITE FOR RESIDUE HAI B 1422
19	CC1	SOFTWARE	PHE A:80 , GLN A:108 , GLU A:135 , ASN A:148 , PO4 A:2432	BINDING SITE FOR RESIDUE HAI A 1424

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

Asymmetric Unit

No.	Residues
1	Gly A:8	-	Pro A:9
2	His A:299	-	Pro A:300
3	Gly B:8	-	Pro B:9
4	His B:299	-	Pro B:300

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

(no "PROSITE Motif" information available for 1EJD)

(no "Exon" information available for 1EJD)

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:419
 aligned with MURA_ENTCC | P33038 from UniProtKB/Swiss-Prot  Length:419

    Alignment length:419
                                    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       410         
           MURA_ENTCC     1 MDKFRVQGPTRLQGEVTISGAKNAALPILFAALLAEEPVEIQNVPKLKDIDTTMKLLTQLGTKVERNGSVWIDASNVNNFSAPYDLVKTMRASIWALGPLVARFGQGQVSLPGGCAIGARPVDLHIFGLEKLGAEIKLEEGYVKASVNGRLKGAHIVMDKVSVGATVTIMSAATLAEGTTIIENAAREPEIVDTANFLVALGAKISGQGTDRITIEGVERLGGGVYRVLPDRIETGTFLVAAAISGGKIVCRNAQPDTLDAVLAKLREAGADIETGEDWISLDMHGKRPKAVTVRTAPHPAFPTDMQAQFTLLNLVAEGTGVITETIFENRFMHVPELIRMGAHAEIESNTVICHGVEKLSGAQVMATDLRASASLVLAGCIAEGTTVVDRIYHIDRGYERIEDKLRALGANIERVKGE 419
               SCOP domains d1ejda_ A: UDP-N-acetylglucosamine enolpyruvyl transferase (EPT, MurA, MurZ)                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1ejdA01           --1ejdA02 A:21-228  [code=3.65.10.10, no name defined]                                                                                                                                                            -1ejdA01 A:1-18,A:230-418  [code=3.65.10.10, no name defined]                                                                                                                                 - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....eeeee...hhhhhhhhhhhh......eeee....hhhhhhhhhhhhhh..eee....eeee.......eehhhhhh.hhhhhhhhhhhhhhhheeeee...........hhhhhhhhhhh..eeeee..eeeee........eee....hhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhh..eee.....eeeee.......eeee...hhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhh..eeee...eeeee..........ee.......hhhhhhhhhhhhhh...eeeee........hhhhhhhhh..eeeee..eeeee........ee...hhhhhhhhhhhhhhh.eeeee..hhhhhhhh.hhhhhhhh...eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ejd A   1 MDKFRVQGPTRLQGEVTISGAKNAALPILFAALLAEEPVEIQNVPKLKDIDTTMKLLTQLGTKVERxGSVWIDASNVNNFSAPYDLVKTMRASIWALGPLVARFGQGQVSLPGGCAIGARPVDLHIFGLEKLGAEIKLEEGYVKASVNGRLKGAHIVMDKVSVGATVTIMSAATLAEGTTIIENAAREPEIVDTANFLVALGAKISGQGTDRITIEGVERLGGGVYRVLPDRIETGTFLVAAAISGGKIVCRNAQPDTLDAVLAKLREAGADIETGEDWISLDMHGKRPKAVTVRTAPHPAFPTDMQAQFTLLNLVAEGTGVITETIFENRFMHVPELIRMGAHAEIESNTVICHGVEKLSGAQVMATDLRASASLVLAGCIAEGTTVVDRIYHIDRGYERIEDKLRALGANIERVKGE 419
                                    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       410         
                                                                                             67-IAS

Chain B from PDB  Type:PROTEIN  Length:419
 aligned with MURA_ENTCC | P33038 from UniProtKB/Swiss-Prot  Length:419

    Alignment length:419
                                    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       410         
           MURA_ENTCC     1 MDKFRVQGPTRLQGEVTISGAKNAALPILFAALLAEEPVEIQNVPKLKDIDTTMKLLTQLGTKVERNGSVWIDASNVNNFSAPYDLVKTMRASIWALGPLVARFGQGQVSLPGGCAIGARPVDLHIFGLEKLGAEIKLEEGYVKASVNGRLKGAHIVMDKVSVGATVTIMSAATLAEGTTIIENAAREPEIVDTANFLVALGAKISGQGTDRITIEGVERLGGGVYRVLPDRIETGTFLVAAAISGGKIVCRNAQPDTLDAVLAKLREAGADIETGEDWISLDMHGKRPKAVTVRTAPHPAFPTDMQAQFTLLNLVAEGTGVITETIFENRFMHVPELIRMGAHAEIESNTVICHGVEKLSGAQVMATDLRASASLVLAGCIAEGTTVVDRIYHIDRGYERIEDKLRALGANIERVKGE 419
               SCOP domains d1ejdb_ B: UDP-N-acetylglucosamine enolpyruvyl transferase (EPT, MurA, MurZ)                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1ejdB01           --1ejdB02 B:21-228  [code=3.65.10.10, no name defined]                                                                                                                                                            -1ejdB01 B:1-18,B:230-418  [code=3.65.10.10, no name defined]                                                                                                                                 - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeeee...hhhhhhhhhhhh......eeee....hhhhhhhhhhhhhh..eee....eeee.......eehhhhhh.hhhhhhhhhhhhhhhheeeee...........hhhhhhhhhhh..eeeee..eeeee........eee....hhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhh..eee.....eeeee.......eeee...hhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhh..eeee...eeeee..........eee......hhhhhhhhhhhhhh...eeeeee........hhhhhhhh..eeeee..eeeee........eee..hhhhhhhhhhhhhhh.eeeeee.hhhhhhhh.hhhhhhhh...eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ejd B   1 MDKFRVQGPTRLQGEVTISGAKNAALPILFAALLAEEPVEIQNVPKLKDIDTTMKLLTQLGTKVERxGSVWIDASNVNNFSAPYDLVKTMRASIWALGPLVARFGQGQVSLPGGCAIGARPVDLHIFGLEKLGAEIKLEEGYVKASVNGRLKGAHIVMDKVSVGATVTIMSAATLAEGTTIIENAAREPEIVDTANFLVALGAKISGQGTDRITIEGVERLGGGVYRVLPDRIETGTFLVAAAISGGKIVCRNAQPDTLDAVLAKLREAGADIETGEDWISLDMHGKRPKAVTVRTAPHPAFPTDMQAQFTLLNLVAEGTGVITETIFENRFMHVPELIRMGAHAEIESNTVICHGVEKLSGAQVMATDLRASASLVLAGCIAEGTTVVDRIYHIDRGYERIEDKLRALGANIERVKGE 419
                                    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       410         
                                                                                             67-IAS

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	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) (23004)

Fold: IF3-like (127)

Superfamily: EPT/RTPC-like (82)

Family: Enolpyruvate transferase, EPT (68)

Protein domain: UDP-N-acetylglucosamine enolpyruvyl transferase (EPT, MurA, MurZ) (27)

Enterobacter cloacae [TaxId: 550] (12)

1a	d1ejda_	A:
1b	d1ejdb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-beta prism (50)

Topology: UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain (50)

Homologous Superfamily: [code=3.65.10.10, no name defined] (47)

Enterobacter cloacae. Organism_taxid: 550. (5)

1a	1ejdA01	A:1-18,A:230-418
1b	1ejdB01	B:1-18,B:230-418
1c	1ejdA02	A:21-228
1d	1ejdB02	B:21-228

(no "Pfam Domain" information available for 1EJD)

Asymmetric Unit(hide GO term definitions)

Chain A,B (MURA_ENTCC | P33038)

molecular function
	GO:0008760	UDP-N-acetylglucosamine 1-carboxyvinyltransferase activity	Catalysis of the reaction: phosphoenolpyruvate + UDP-N-acetyl-alpha-D-glucosamine = phosphate + UDP-N-acetyl-3-O-(1-carboxyvinyl)-D-glucosamine.
	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:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0016765	transferase activity, transferring alkyl or aryl (other than methyl) groups	Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor).
biological process
	GO:0019277	UDP-N-acetylgalactosamine biosynthetic process	The chemical reactions and pathways resulting in the formation of UDP-N-acetylgalactosamine, a substance composed of N-acetylgalactosamine, a common structural unit of oligosaccharides, in glycosidic linkage with uridine diphosphate.
	GO:0007049	cell cycle	The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
	GO:0051301	cell division	The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
	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: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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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	Cis Peptide Bonds
		Gly A:8 - Pro A:9	[ RasMol ]
		Gly B:8 - Pro B:9	[ RasMol ]
		His A:299 - Pro A:300	[ RasMol ]
		His B:299 - Pro B:300	[ RasMol ]

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		Biological Unit 5	[ Jena3D ]

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	1ejd
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	2.5.1.7
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1dgl	1DLG CONTAINS UNLIGANDED MURA MUTANT CYS115SER
1ejc	1EJC CONTAINS UNLIGANDED MURA (TYPE2) REFINED TO 1.8 A RESOLUTION
1naw	1NAW CONTAINS UNLIGANDED MURA (TYPE1) REFINED TO 2.0 A RESOLUTION

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 22)

Sites (19, 19)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (1, 2)

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Gene Ontology (11, 11)

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