4E7F - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   E. CLOACAE C115D MURA IN COMPLEX WITH UDP

Authors :   J. -Y. Zhu, S. Betzi, Y. Yang, E. Schonbrunn

Date :   16 Mar 12 (Deposition) - 20 Mar 13 (Release) - 20 Mar 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

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

Keywords :   Open Enzyme State, Cell Wall, Biogenesis/Degradation, Peptidoglycan Synthesis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. -Y. Zhu, Y. Yang, S. Betzi, E. Schonbrunn
Open-Close Transition Of Mura
To Be Published
PubMed: search

Molecule 1 - UDP-N-ACETYLGLUCOSAMINE 1-CARBOXYVINYLTRANSFERASE
	Chains	:	A, B, C, D
	EC Number	:	2.5.1.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET9D
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	ECL_04571, MURA, MURZ
	Mutation	:	YES
	Organism Scientific	:	ENTEROBACTER CLOACAE SUBSP. CLOACAE
	Organism Taxid	:	716541
	Strain	:	ATCC 13047 / DSM 30054 / NBRC 13535 / NCDC 279-56
	Synonym	:	MURA, ENOYLPYRUVATE TRANSFERASE, UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYL TRANSFERASE, EPT

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 21)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	EDO	15	Ligand/Ion	1,2-ETHANEDIOL
3	IAS	4	Mod. Amino Acid	BETA-L-ASPARTIC ACID
4	UDP	1	Ligand/Ion	URIDINE-5'-DIPHOSPHATE

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	ACT	-1	Ligand/Ion	ACETATE ION
2	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
3	IAS	1	Mod. Amino Acid	BETA-L-ASPARTIC ACID
4	UDP	1	Ligand/Ion	URIDINE-5'-DIPHOSPHATE

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	ACT	-1	Ligand/Ion	ACETATE ION
2	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
3	IAS	1	Mod. Amino Acid	BETA-L-ASPARTIC ACID
4	UDP	-1	Ligand/Ion	URIDINE-5'-DIPHOSPHATE

Biological Unit 3 (3, 8)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	EDO	6	Ligand/Ion	1,2-ETHANEDIOL
3	IAS	1	Mod. Amino Acid	BETA-L-ASPARTIC ACID
4	UDP	-1	Ligand/Ion	URIDINE-5'-DIPHOSPHATE

Biological Unit 4 (2, 4)

No.	Name	Count	Type	Full Name
1	ACT	-1	Ligand/Ion	ACETATE ION
2	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
3	IAS	1	Mod. Amino Acid	BETA-L-ASPARTIC ACID
4	UDP	-1	Ligand/Ion	URIDINE-5'-DIPHOSPHATE

Asymmetric Unit (17, 17)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:344 , GLU A:346 , HIS A:355 , HOH A:811 , LYS D:63	BINDING SITE FOR RESIDUE EDO A 501
02	AC2	SOFTWARE	ARG A:187 , THR A:210 , ASP A:211 , LYS B:265 , GLU B:268 , HOH B:605	BINDING SITE FOR RESIDUE EDO A 502
03	AC3	SOFTWARE	ARG A:91 , TRP A:95 , HIS A:125 , GLY A:164 , UDP A:505 , HOH A:649 , HOH A:680	BINDING SITE FOR RESIDUE EDO A 503
04	AC4	SOFTWARE	PRO A:38 , VAL A:39 , TRP A:71 , ILE A:72 , ASP A:73 , HOH A:766	BINDING SITE FOR RESIDUE EDO A 504
05	AC5	SOFTWARE	ARG A:91 , PRO A:121 , VAL A:122 , ASP A:123 , LEU A:124 , HIS A:125 , LYS A:160 , SER A:162 , VAL A:163 , GLY A:164 , EDO A:503 , HOH A:649 , HOH A:680 , HOH A:781	BINDING SITE FOR RESIDUE UDP A 505
06	AC6	SOFTWARE	GLY B:164 , HOH B:771	BINDING SITE FOR RESIDUE EDO B 501
07	AC7	SOFTWARE	LEU B:111 , GLY B:141 , GLU C:130	BINDING SITE FOR RESIDUE EDO B 502
08	AC8	SOFTWARE	GLN C:42 , ASN C:43 , GLY C:68 , SER C:69 , HOH C:784	BINDING SITE FOR RESIDUE EDO C 501
09	AC9	SOFTWARE	ASP C:211 , HOH C:728 , HOH C:792 , ALA D:264 , LYS D:265 , GLU D:268 , HOH D:696 , HOH D:772	BINDING SITE FOR RESIDUE EDO C 502
10	BC1	SOFTWARE	TYR B:393 , ARG B:397 , HOH B:735 , HOH B:833 , GLU C:37 , PRO C:38 , GLY C:223 , GLY C:224 , HOH C:808	BINDING SITE FOR RESIDUE EDO C 503
11	BC2	SOFTWARE	SER C:162 , VAL C:163 , GLY C:164 , EDO C:506	BINDING SITE FOR RESIDUE EDO C 504
12	BC3	SOFTWARE	LYS C:46 , ASP C:51 , ACT C:507 , HOH C:646 , GLU D:358 , HOH D:674	BINDING SITE FOR RESIDUE EDO C 505
13	BC4	SOFTWARE	ALA C:92 , TRP C:95 , GLY C:164 , EDO C:504 , HOH C:636	BINDING SITE FOR RESIDUE EDO C 506
14	BC5	SOFTWARE	LYS C:46 , LEU C:47 , LYS C:48 , ASP C:51 , EDO C:505	BINDING SITE FOR RESIDUE ACT C 507
15	BC6	SOFTWARE	ARG D:252 , TRP D:279	BINDING SITE FOR RESIDUE EDO D 501
16	BC7	SOFTWARE	SER C:110 , LEU C:111 , GLY C:141 , GLU D:65 , ARG D:66	BINDING SITE FOR RESIDUE EDO D 502
17	BC8	SOFTWARE	ARG D:187 , GLY D:209 , HIS D:299	BINDING SITE FOR RESIDUE EDO D 503

(no "SS Bond" information available for 4E7F)

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
5	Gly C:8	-	Pro C:9
6	His C:299	-	Pro C:300
7	Gly D:8	-	Pro D:9
8	His D:299	-	Pro D:300

(no "SAP(SNP)/Variant" information available for 4E7F)

(no "PROSITE Motif" information available for 4E7F)

(no "Exon" information available for 4E7F)

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
                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains d4e7fa_ A: UDP-N-acetylglucosamine enolpyruvyl transferase (EPT, MurA, MurZ)                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....eeee...hhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhh..eeee...eeee.......eehhhhhh.hhhhhhhhhhhhhhhheeeee...........hhhhhhhhhhh..eeeee..eeeee........eeee...hhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhh..eee.....eeeee.......eeee...hhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhh..eeee...eeeee..........eee......hhhhhhhhhhhhhh...eeeeee........hhhhhhhh..eeeee..eeeee........eee..hhhhhhhhhhhhhhh.eeeeee.hhhhhhhh.hhhhhhhhh..eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e7f A   1 MDKFRVQGPTRLQGEVTISGAKNAALPILFAALLAEEPVEIQNVPKLKDIDTTMKLLTQLGTKVERxGSVWIDASNVNNFSAPYDLVKTMRASIWALGPLVARFGQGQVSLPGGDAIGARPVDLHIFGLEKLGAEIKLEEGYVKASVNGRLKGAHIVMDKVSVGATVTIMSAATLAEGTTIIENAAREPEIVDTANFLVALGAKISGQGTDRITIEGVERLGGGVYRVLPDRIETGTFLVAAAISGGKIVCRNAQPDTLDAVLAKLREAGADIETGEDWISLDMHGKRPKAVTVRTAPHPAFPTDMQAQFTLLNLVAEGTGVITETIFENRFMHVPELIRMGAHAEIESNTVICHGVEKLSGAQVMATDLRASASLVLAGCIAEGTTVVDRIYHIDRGYERIEDKLRALGANIERVKGE 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
                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains d4e7fb_ B: UDP-N-acetylglucosamine enolpyruvyl transferase (EPT, MurA, MurZ)                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....eeee...hhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhh..eeee...eeee.......eehhhhhh.hhhhhhhhhhhhhhhheeeee...........hhhhhhhhhhh..eeee...eeeee........eee....hhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhh..eee.....eeeee.......eeee...hhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhh..eeee...eeeee..........eee......hhhhhhhhhhhhhh...eeeeee........hhhhhhhh..eeeee..eeeee........ee...hhhhhhhhhhhhhhh.eeeeee.hhhhhh...hhhhhhhh...eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e7f B   1 MDKFRVQGPTRLQGEVTISGAKNAALPILFAALLAEEPVEIQNVPKLKDIDTTMKLLTQLGTKVERxGSVWIDASNVNNFSAPYDLVKTMRASIWALGPLVARFGQGQVSLPGGDAIGARPVDLHIFGLEKLGAEIKLEEGYVKASVNGRLKGAHIVMDKVSVGATVTIMSAATLAEGTTIIENAAREPEIVDTANFLVALGAKISGQGTDRITIEGVERLGGGVYRVLPDRIETGTFLVAAAISGGKIVCRNAQPDTLDAVLAKLREAGADIETGEDWISLDMHGKRPKAVTVRTAPHPAFPTDMQAQFTLLNLVAEGTGVITETIFENRFMHVPELIRMGAHAEIESNTVICHGVEKLSGAQVMATDLRASASLVLAGCIAEGTTVVDRIYHIDRGYERIEDKLRALGANIERVKGE 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 C from PDB  Type:PROTEIN  Length:419
                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains d4e7fc_ C: UDP-N-acetylglucosamine enolpyruvyl transferase (EPT, MurA, MurZ)                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....eeee...hhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh...eeee...eeeehhhh...eehhhhhhhhhhhhhhhhhhhhhhheeeee..........hhhhhhhhhhhh..eeeee..eeeee........eee....hhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhh..eee.....eeeee.......eeee...hhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhh..eeee...eeeee..........ee.......hhhhhhhhhhhhhh...eeeee........hhhhhhhh...eeeee..eeeee........eee..hhhhhhhhhhhhhhh.eeeeee.hhhhhh...hhhhhhhhh..eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e7f C   1 MDKFRVQGPTRLQGEVTISGAKNAALPILFAALLAEEPVEIQNVPKLKDIDTTMKLLTQLGTKVERxGSVWIDASNVNNFSAPYDLVKTMRASIWALGPLVARFGQGQVSLPGGDAIGARPVDLHIFGLEKLGAEIKLEEGYVKASVNGRLKGAHIVMDKVSVGATVTIMSAATLAEGTTIIENAAREPEIVDTANFLVALGAKISGQGTDRITIEGVERLGGGVYRVLPDRIETGTFLVAAAISGGKIVCRNAQPDTLDAVLAKLREAGADIETGEDWISLDMHGKRPKAVTVRTAPHPAFPTDMQAQFTLLNLVAEGTGVITETIFENRFMHVPELIRMGAHAEIESNTVICHGVEKLSGAQVMATDLRASASLVLAGCIAEGTTVVDRIYHIDRGYERIEDKLRALGANIERVKGE 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 D from PDB  Type:PROTEIN  Length:419
                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains d4e7fd_ D: UDP-N-acetylglucosamine enolpyruvyl transferase (EPT, MurA, MurZ)                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....eeee...hhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhh..eeee...eeee.......eehhhhhh.hhhhhhhhhhhhhhhheeeee.....ee...hhhhhhhhhhhh..eeeee..eeeee........eee....hhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhh..eee.....eeeee.......eeee...hhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhh..eeee...eeeee.........eee.......hhhhhhhhhhhhhh...eeeee........hhhhhhhhh..eeeee..eeeee........eee..hhhhhhhhhhhhhhh.eeeeee.hhhhhhhh.hhhhhhhh...eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e7f D   1 MDKFRVQGPTRLQGEVTISGAKNAALPILFAALLAEEPVEIQNVPKLKDIDTTMKLLTQLGTKVERxGSVWIDASNVNNFSAPYDLVKTMRASIWALGPLVARFGQGQVSLPGGDAIGARPVDLHIFGLEKLGAEIKLEEGYVKASVNGRLKGAHIVMDKVSVGATVTIMSAATLAEGTTIIENAAREPEIVDTANFLVALGAKISGQGTDRITIEGVERLGGGVYRVLPDRIETGTFLVAAAISGGKIVCRNAQPDTLDAVLAKLREAGADIETGEDWISLDMHGKRPKAVTVRTAPHPAFPTDMQAQFTLLNLVAEGTGVITETIFENRFMHVPELIRMGAHAEIESNTVICHGVEKLSGAQVMATDLRASASLVLAGCIAEGTTVVDRIYHIDRGYERIEDKLRALGANIERVKGE 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

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 '\|'

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: 716541] (12)

1a	d4e7fa_	A:
1b	d4e7fb_	B:
1c	d4e7fc_	C:
1d	d4e7fd_	D:

(no "CATH Domain" information available for 4E7F)

(no "Pfam Domain" information available for 4E7F)

Asymmetric Unit(hide GO term definitions)

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

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	4e7f
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 21)

Sites (17, 17)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (1, 4)

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Gene Ontology (11, 11)

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