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Title :   CRYSTAL STRUCTURE OF ESCHERICHIA COLI UDPMURNAC-TRIPEPTIDE D-ALANYL-D-ALANINE-ADDING ENZYME (MURF) AT 2.3 ANGSTROM RESOLUTION

Authors :   Y. Yan, S. Munshi, Z. Chen

Date :   12 Jul 00 (Deposition) - 20 Dec 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Alpha/Beta Sheet, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Yan, S. Munshi, B. Leiting, M. S. Anderson, J. Chrzas, Z. Chen
Crystal Structure Of Escherichia Coli Udpmurnac-Tripeptide D-Alanyl-D-Alanine-Adding Enzyme (Murf) At 2. 3 A Resolution.
J. Mol. Biol. V. 304 435 2000
PubMed-ID: 11090285 | Reference-DOI: 10.1006/JMBI.2000.4215
(for further references see the PDB file header)

Molecule 1 - UDP-N-ACETYLMURAMOYLALANYL-D-GLUTAMYL-2,6- DIAMINOPIMELATE-D-ALANYL-D-ALANYL LIGASE
	Chains	:	A, B
	EC Number	:	6.3.2.15
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET30A(+)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	D-ALANYL-D-ALANINE-ADDING ENZYME, UDP-MURNAC- PENTAPEPTIDE SYNTHETASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 18)

No.	Name	Count	Type	Full Name
1	MSE	18	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 9)

No.	Name	Count	Type	Full Name
1	MSE	9	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 9)

No.	Name	Count	Type	Full Name
1	MSE	9	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 1GG4)

(no "SS Bond" information available for 1GG4)

(no "Cis Peptide Bond" information available for 1GG4)

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_MURF_ECOLI_001 *	A	288	T	MURF_ECOLI	---	---	A B	A	288 788	T
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_MURF_ECOLI_001 *	A	288	T	MURF_ECOLI	---	---	A A	A	288 788	T
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_MURF_ECOLI_001 *	A	288	T	MURF_ECOLI	---	---	A B	A	288 788	T
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 1GG4)

(no "Exon" information available for 1GG4)

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:439
 aligned with MURF_ECOLI | P11880 from UniProtKB/Swiss-Prot  Length:452

    Alignment length:447
                                    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       420       430       440       
           MURF_ECOLI     1 MISVTLSQLTDILNGELQGADITLDAVTTDTRKLTPGCLFVALKGERFDAHDFADQAKAGGAGALLVSRPLDIDLPQLIVKDTRLAFGELAAWVRQQVPARVVALTGSSGKTSVKEMTAAILSQCGNTLYTAGNLNNDIGVPMTLLRLTPEYDYAVIELGANHQGEIAWTVSLTRPEAALVNNLAAAHLEGFGSLAGVAKAKGEIFSGLPENGIAIMNADNNDWLNWQSVIGSRKVWRFSPNAANSDFTATNIHVTSHGTEFTLQTPTGSVDVLLPLPGRHNIANALAAAALSMSVGATLDAIKAGLANLKAVPGRLFPIQLAENQLLLDDSYNANVGSMTAAVQVLAEMPGYRVLVVGDMAELGAESEACHVQVGEAAKAAGIDRVLSVGKQSHAISTASGVGEHFADKTALITRLKLLIAEQQVITILVKGSRSAAMEEVVRALQ 447
               SCOP domains d1gg4a3 A:1-98 UDP-murNac-tripeptide D-alanyl-D-alanine-adding enzyme MurF                        d1gg4a4 A:99-312 UDP-murNac-tripeptide D-alanyl-D-alanine-adding enzyme MurF                                                                                                                                          d1gg4a1 A:313-447 UDP-murNac-tripeptide D-alanyl-D-alanine-adding enzyme MurF                                                           SCOP domains
               CATH domains -1gg4A03 A:2-80  [code=3.40.1390.10, no name defined]                           1gg4A02 A:81-311  [code=3.40.1190.10, no name defined]                                                                                                                                                                                 1gg4A01 A:312-447  [code=3.90.190.20, no name defined]                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eehhhhhhhh..eee....ee..ee.hhhhh....eee...........hhhhhhhh...eeee.........eee..hhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhh....eee........hhhhhhhh.......eeeee......hhhhhhhhhhh..eeee....--------hhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhh..eeeee.........eeeeeee....eeeeeee..eeeeeee....hhhhhhhhhhhhhhhhh..hhhhhhhhhh.........eeeeee..eeeee.....hhhhhhhhhhhhhhh..eeeeee.......hhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhh...eee.hhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gg4 A   1 mISVTLSQLTDILNGELQGADITLDAVTTDTRKLTPGCLFVALKGERFDAHDFADQAKAGGAGALLVSRPLDIDLPQLIVKDTRLAFGELAAWVRQQVPARVVALTGSSGKTSVKEmTAAILSQCGNTLYTAGNLNNDIGVPmTLLRLTPEYDYAVIELGANHQGEIAWTVSLTRPEAALVNNLA--------SLAGVAKAKGEIFSGLPENGIAImNADNNDWLNWQSVIGSRKVWRFSPNAANSDFTATNIHVTSHGTEFTLQTPTGSVDVLLPLPGRHNIANALAAAALSmSVGATLDAIKAGLANLKAVPGRLFPIQLAENQLLLDDSYNANVGSmTAAVQVLAEmPGYRVLVVGDmAELGAESEACHVQVGEAAKAAGIDRVLSVGKQSHAISTASGVGEHFADKTALITRLKLLIAEQQVITILVKGSRSAAmEEVVRALQ 447
                            |       10        20        30        40        50        60        70        80        90       100       110      |120       130       140  |    150       160       170       180    |    -   |   200       210      |220       230       240       250       260       270       280       290   |   300       310       320       330       340       350       360|      370       380       390       400       410       420       430       440       
                            |                                                                                                                 117-MSE                   143-MSE                                   185      194                    217-MSE                                                                      294-MSE                                       340-MSE   350-MSE    361-MSE                                                                       439-MSE    
                            1-MSE

Chain B from PDB  Type:PROTEIN  Length:439
 aligned with MURF_ECOLI | P11880 from UniProtKB/Swiss-Prot  Length:452

    Alignment length:447
                                    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       420       430       440       
           MURF_ECOLI     1 MISVTLSQLTDILNGELQGADITLDAVTTDTRKLTPGCLFVALKGERFDAHDFADQAKAGGAGALLVSRPLDIDLPQLIVKDTRLAFGELAAWVRQQVPARVVALTGSSGKTSVKEMTAAILSQCGNTLYTAGNLNNDIGVPMTLLRLTPEYDYAVIELGANHQGEIAWTVSLTRPEAALVNNLAAAHLEGFGSLAGVAKAKGEIFSGLPENGIAIMNADNNDWLNWQSVIGSRKVWRFSPNAANSDFTATNIHVTSHGTEFTLQTPTGSVDVLLPLPGRHNIANALAAAALSMSVGATLDAIKAGLANLKAVPGRLFPIQLAENQLLLDDSYNANVGSMTAAVQVLAEMPGYRVLVVGDMAELGAESEACHVQVGEAAKAAGIDRVLSVGKQSHAISTASGVGEHFADKTALITRLKLLIAEQQVITILVKGSRSAAMEEVVRALQ 447
               SCOP domains d1gg4b3 B:501-598 UDP-murNac-tripeptide D-alanyl-D-alanine-adding enzyme MurF                     d1gg4b4 B:599-812 UDP-murNac-tripeptide D-alanyl-D-alanine-adding enzyme MurF                                                                                                                                         d1gg4b1 B:813-947 UDP-murNac-tripeptide D-alanyl-D-alanine-adding enzyme MurF                                                           SCOP domains
               CATH domains -1gg4B03 B:502-580  [code=3.40.1390.10, no name defined]                        1gg4B02 B:581-811  [code=3.40.1190.10, no name defined]                                                                                                                                                                                1gg4B01 B:812-938  [code=3.90.190.20, no name defined]                                                                         --------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eehhhhhhhhh.eee....ee..ee.hhhhh....eee..ee..ee...hhhhhhhhh..eeee.........eee..hhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhh.eee........hhhhhhhh.......eeeee......hhhhhhhhhhh..eeee....--------hhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhh..eeeee.........eeeeee.....eeeeeee..eeeeeee....hhhhhhhhhhhhhhhh...hhhhhhhhhh.........eeeeee..eeeee.....hhhhhhhhhhhhhhh..eeeeee.......hhhhhhhhhhhhhhhhh......ee...hhhhhhhh....ee.hhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T--------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gg4 B 501 mISVTLSQLTDILNGELQGADITLDAVTTDTRKLTPGCLFVALKGERFDAHDFADQAKAGGAGALLVSRPLDIDLPQLIVKDTRLAFGELAAWVRQQVPARVVALTGSSGKTSVKEmTAAILSQCGNTLYTAGNLNNDIGVPmTLLRLTPEYDYAVIELGANHQGEIAWTVSLTRPEAALVNNLA--------SLAGVAKAKGEIFSGLPENGIAImNADNNDWLNWQSVIGSRKVWRFSPNAANSDFTATNIHVTSHGTEFTLQTPTGSVDVLLPLPGRHNIANALAAAALSmSVGATLDAIKAGLANLKAVPGRLFPIQLAENQLLLDDSYNANVGSmTAAVQVLAEmPGYRVLVVGDmAELGAESEACHVQVGEAAKAAGIDRVLSVGKQSHAISTASGVGEHFADKTALITRLKLLIAEQQVITILVKGSRSAAmEEVVRALQ 947
                            |      510       520       530       540       550       560       570       580       590       600       610      |620       630       640  |    650       660       670       680    |    -   |   700       710      |720       730       740       750       760       770       780       790   |   800       810       820       830       840       850       860|      870       880       890       900       910       920       930       940       
                          501-MSE                                                                                                             617-MSE                   643-MSE                                   685      694                    717-MSE                                                                      794-MSE                                       840-MSE   850-MSE    861-MSE                                                                       939-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 "Pfam Domain" information available for 1GG4)

Asymmetric Unit(hide GO term definitions)

Chain A,B (MURF_ECOLI | P11880)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0047480	UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase activity	Catalysis of the reaction: UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-L-lysine + ATP + D-alanyl-D-alanine = phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-L-lysyl-D-alanyl-D-alanine + ADP.
	GO:0008766	UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate-D-alanyl-D-alanine ligase activity	Catalysis of the reaction: ATP + UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate + D-alanyl-D-alanine = ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-6-carboxy-L-lysyl-D-alanyl-D-alanine.
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
	GO:0009058	biosynthetic process	The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
	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.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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Description

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Ligands, Modified Residues, Ions (1, 18)

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