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(-) Description

Title :  E. CLOACAE MURA R120A COMPLEX WITH UNAG AND COVALENT ADDUCT OF PEP WITH CYS115
 
Authors :  H. Han, J. -Y. Zhu, E. Schonbrunn
Date :  13 Jul 11  (Deposition) - 07 Mar 12  (Release) - 02 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Mura, Close Enzyme State, Cell Wall, Biogenesis/Degradation, Peptidoglycan Synthesis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Y. Zhu, Y. Yang, H. Han, S. Betzi, S. H. Olesen, F. Marsilio, E. Schonbrunn
Functional Consequence Of Covalent Reaction Of Phosphoenolpyruvate With Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase (Mura).
J. Biol. Chem. V. 287 12657 2012
PubMed-ID: 22378791  |  Reference-DOI: 10.1074/JBC.M112.342725

(-) Compounds

Molecule 1 - UDP-N-ACETYLGLUCOSAMINE 1-CARBOXYVINYLTRANSFERASE
    Chains: A, B
    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: MURA, MURZ, ECL_04571
    Mutation: YES
    Organism Scientific: ENTEROBACTER CLOACAE
    Organism Taxid: 716541
    Strain: ATCC 13047 / DSM 30054 / NBRC 13535 / NCDC 279-56
    Synonym: ENOYLPYRUVATE TRANSFERASE, UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYL TRANSFERASE, EPT

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 17)

Asymmetric Unit (4, 17)
No.NameCountTypeFull Name
1EDO11Ligand/Ion1,2-ETHANEDIOL
2IAS2Mod. Amino AcidBETA-L-ASPARTIC ACID
3QPA2Mod. Amino AcidS-[(1S)-1-CARBOXY-1-(PHOSPHONOOXY)ETHYL]-L-CYSTEINE
4UD12Ligand/IonURIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE
Biological Unit 1 (4, 8)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2IAS1Mod. Amino AcidBETA-L-ASPARTIC ACID
3QPA1Mod. Amino AcidS-[(1S)-1-CARBOXY-1-(PHOSPHONOOXY)ETHYL]-L-CYSTEINE
4UD11Ligand/IonURIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE
Biological Unit 2 (4, 9)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2IAS1Mod. Amino AcidBETA-L-ASPARTIC ACID
3QPA1Mod. Amino AcidS-[(1S)-1-CARBOXY-1-(PHOSPHONOOXY)ETHYL]-L-CYSTEINE
4UD11Ligand/IonURIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:400 , ARG A:401 , LYS A:405 , HOH A:660 , HOH A:709 , HOH A:792BINDING SITE FOR RESIDUE EDO A 420
02AC2SOFTWAREGLU A:325 , PHE A:328 , GLU A:329 , ASN A:330 , ARG A:331 , PHE A:332 , SER A:349BINDING SITE FOR RESIDUE EDO A 421
03AC3SOFTWAREGLU A:348 , SER A:349 , ASN A:350 , THR A:351 , HOH A:525 , PRO B:121 , VAL B:122 , ASP B:123 , LEU B:138BINDING SITE FOR RESIDUE EDO A 422
04AC4SOFTWAREARG A:91 , ALA A:92 , ILE A:94 , TRP A:95 , UD1 A:425 , HOH A:557 , HOH A:810BINDING SITE FOR RESIDUE EDO A 423
05AC5SOFTWAREGLU A:37 , PRO A:38 , HOH A:766BINDING SITE FOR RESIDUE EDO A 424
06AC6SOFTWAREASN A:23 , TRP A:95 , ALA A:119 , PRO A:121 , VAL A:122 , ASP A:123 , LEU A:124 , HIS A:125 , SER A:162 , VAL A:163 , GLY A:164 , THR A:304 , ASP A:305 , ILE A:327 , PHE A:328 , ARG A:331 , EDO A:423 , HOH A:426 , HOH A:434 , HOH A:436 , HOH A:444 , HOH A:450 , HOH A:493 , HOH A:557 , HOH A:566 , HOH A:568 , HOH A:661 , HOH A:720 , HOH A:721 , HOH A:728 , HOH A:734BINDING SITE FOR RESIDUE UD1 A 425
07AC7SOFTWAREPRO A:121 , VAL A:122 , ASP A:123 , LEU A:138 , GLU B:348 , SER B:349 , ASN B:350 , THR B:351 , HOH B:683BINDING SITE FOR RESIDUE EDO B 420
08AC8SOFTWAREGLU B:325 , PHE B:328 , GLU B:329 , ASN B:330 , ARG B:331 , PHE B:332 , SER B:349BINDING SITE FOR RESIDUE EDO B 421
09AC9SOFTWAREGLN B:7 , ASN B:412 , ILE B:413 , HOH B:572BINDING SITE FOR RESIDUE EDO B 422
10BC1SOFTWAREARG B:91 , ALA B:92 , ILE B:94 , UD1 B:426 , HOH B:466 , HOH B:570 , HOH B:606BINDING SITE FOR RESIDUE EDO B 423
11BC2SOFTWAREASP B:2 , TYR B:393 , ARG B:415BINDING SITE FOR RESIDUE EDO B 424
12BC3SOFTWARETHR B:10 , ARG B:11 , SER B:245 , ILE B:382 , HOH B:658BINDING SITE FOR RESIDUE EDO B 425
13BC4SOFTWAREASN B:23 , TRP B:95 , ALA B:119 , PRO B:121 , VAL B:122 , ASP B:123 , LEU B:124 , HIS B:125 , SER B:162 , VAL B:163 , GLY B:164 , THR B:304 , ASP B:305 , ILE B:327 , PHE B:328 , ARG B:331 , EDO B:423 , HOH B:429 , HOH B:437 , HOH B:455 , HOH B:458 , HOH B:466 , HOH B:494 , HOH B:583 , HOH B:591 , HOH B:606 , HOH B:641 , HOH B:661 , HOH B:668BINDING SITE FOR RESIDUE UD1 B 426

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3SWA)

(-) Exons   (0, 0)

(no "Exon" information available for 3SWA)

(-) Sequences/Alignments

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 d3swaa_ 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........eee....hhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhh..eee.....eeeee.......eeee...hhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhh..eeee...eeeee.........eee.......hhhhhhhhhhhhhh...eeeee........hhhhhhhhh..eeeee..eeeee........eee..hhhhhhhhhhhhhhh.eeeeee.hhhhhhhh.hhhhhhhhh..eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3swa A   1 MDKFRVQGPTRLQGEVTISGAKNAALPILFAALLAEEPVEIQNVPKLKDIDTTMKLLTQLGTKVERxGSVWIDASNVNNFSAPYDLVKTMRASIWALGPLVARFGQGQVSLPGGcAIGAAPVDLHIFGLEKLGAEIKLEEGYVKASVNGRLKGAHIVMDKVSVGATVTIMSAATLAEGTTIIENAAREPEIVDTANFLVALGAKISGQGTDRITIEGVERLGGGVYRVLPDRIETGTFLVAAAISGGKIVCRNAQPDTLDAVLAKLREAGADIETGEDWISLDMHGKRPKAVTVRTAPHPAFPTDMQAQFTLLNLVAEGTGVITETIFENRFMHVPELIRMGAHAEIESNTVICHGVEKLSGAQVMATDLRASASLVLAGCIAEGTTVVDRIYHIDRGYERIEDKLRALGANIERVKGE 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                                         115-QPA                                                                                                                                                                                                                                                                                                            


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 d3swab_ B: 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........eee....hhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhh.eee.....eeeee.......eeee...hhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhh..eeee...eeeee.........eee.......hhhhhhhhhhhhhh...eeeee........hhhhhhhhh..eeeee..eeeee........eee..hhhhhhhhhhhhhhh.eeeeee.hhhhhhhh.hhhhhhhh....eeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3swa B   1 MDKFRVQGPTRLQGEVTISGAKNAALPILFAALLAEEPVEIQNVPKLKDIDTTMKLLTQLGTKVERxGSVWIDASNVNNFSAPYDLVKTMRASIWALGPLVARFGQGQVSLPGGcAIGAAPVDLHIFGLEKLGAEIKLEEGYVKASVNGRLKGAHIVMDKVSVGATVTIMSAATLAEGTTIIENAAREPEIVDTANFLVALGAKISGQGTDRITIEGVERLGGGVYRVLPDRIETGTFLVAAAISGGKIVCRNAQPDTLDAVLAKLREAGADIETGEDWISLDMHGKRPKAVTVRTAPHPAFPTDMQAQFTLLNLVAEGTGVITETIFENRFMHVPELIRMGAHAEIESNTVICHGVEKLSGAQVMATDLRASASLVLAGCIAEGTTVVDRIYHIDRGYERIEDKLRALGANIERVKGE 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                                         115-QPA
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3SWA)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        MURA_ENTCC | P33038: 1dlg 1ejc 1ejd 1eyn 1naw 1q3g 1ryw 1ybg 3kqa 3lth 3spb 3su9 3swi 3swq 3upk 3v4t 3v5v 4e7b 4e7c 4e7d 4e7e 4e7f 4e7g 4eii

(-) Related Entries Specified in the PDB File

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