1P31 - JenaLib

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Title :   CRYSTAL STRUCTURE OF UDP-N-ACETYLMURAMIC ACID:L-ALANINE LIGASE (MURC) FROM HAEMOPHILUS INFLUENZAE

Authors :   C. D. Mol, A. Brooun, D. R. Dougan, M. T. Hilgers, L. W. Tari, R. A. Wijnand M. W. Knuth, D. E. Mcree, R. V. Swanson

Date :   16 Apr 03 (Deposition) - 15 Jul 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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

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

Reference :   C. D. Mol, A. Brooun, D. R. Dougan, M. T. Hilgers, L. W. Tari, R. A. Wijnands, M. W. Knuth, D. E. Mcree, R. V. Swanson
Crystal Structures Of Active Fully Assembled Substrate- And Product-Bound Complexes Of Udp-N-Acetylmuramic Acid:L-Alanine Ligase (Murc) From Haemophilus Influenzae.
J. Bacteriol. V. 185 4152 2003
PubMed-ID: 12837790 | Reference-DOI: 10.1128/JB.185.14.4152-4162.2003

Molecule 1 - UDP-N-ACETYLMURAMATE--ALANINE LIGASE
	Chains	:	A, B
	EC Number	:	6.3.2.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PSX29
	Expression System Strain	:	DL41
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	MURC
	Organism Scientific	:	HAEMOPHILUS INFLUENZAE
	Organism Taxid	:	727
	Synonym	:	UDP-N-ACETYLMURAMOYL-L-ALANINE 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 (3, 34)

No.	Name	Count	Type	Full Name
1	EPU	2	Ligand/Ion	URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRICACID
2	MG	4	Ligand/Ion	MAGNESIUM ION
3	MSE	28	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 15)

No.	Name	Count	Type	Full Name
1	EPU	1	Ligand/Ion	URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRICACID
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	14	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (2, 15)

No.	Name	Count	Type	Full Name
1	EPU	1	Ligand/Ion	URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRICACID
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	14	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:198 , EPU A:598 , HOH A:1014 , HOH A:1089 , HOH A:1090	BINDING SITE FOR RESIDUE MG A 776
2	AC2	SOFTWARE	HOH B:1148 , HOH B:1149 , HOH B:1150 , HOH B:1151 , HOH B:1152	BINDING SITE FOR RESIDUE MG B 710
3	AC3	SOFTWARE	HIS B:198 , EPU B:602 , HOH B:732 , HOH B:735 , HOH B:736 , HOH B:737	BINDING SITE FOR RESIDUE MG B 601
4	AC4	SOFTWARE	HOH A:962 , HOH A:1058 , HOH A:1059 , HOH A:1060 , HOH A:1061	BINDING SITE FOR RESIDUE MG A 611
5	AC5	SOFTWARE	GLY A:25 , GLY A:27 , GLY A:28 , ALA A:29 , GLY A:30 , MSE A:31 , ASP A:49 , ILE A:50 , HIS A:70 , SER A:84 , SER A:85 , ILE A:87 , ARG A:107 , GLU A:173 , ASP A:175 , SER A:177 , HIS A:198 , MG A:776 , HOH A:812 , HOH A:905 , HOH A:914 , HOH A:935 , HOH A:986 , HOH A:987 , HOH A:988 , HOH A:992 , HOH A:999 , HOH A:1014 , HOH A:1090	BINDING SITE FOR RESIDUE EPU A 598
6	AC6	SOFTWARE	GLY B:25 , GLY B:27 , GLY B:28 , ALA B:29 , GLY B:30 , MSE B:31 , ASP B:49 , ILE B:50 , HIS B:70 , SER B:84 , SER B:85 , ALA B:86 , ILE B:87 , ARG B:107 , GLU B:173 , ASP B:175 , SER B:177 , HIS B:198 , MG B:601 , HOH B:614 , HOH B:619 , HOH B:626 , HOH B:653 , HOH B:654 , HOH B:735 , HOH B:737 , HOH B:746 , HOH B:863 , HOH B:915 , HOH B:955 , HOH B:956 , HOH B:1071 , HOH B:1158 , HOH B:1160	BINDING SITE FOR RESIDUE EPU B 602

(no "SS Bond" information available for 1P31)

(no "Cis Peptide Bond" information available for 1P31)

(no "SAP(SNP)/Variant" information available for 1P31)

(no "PROSITE Motif" information available for 1P31)

(no "Exon" information available for 1P31)

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:463
 aligned with MURC_HAEIN | P45066 from UniProtKB/Swiss-Prot  Length:475

    Alignment length:463
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471   
           MURC_HAEIN    12 IPEMRRVQQIHFIGIGGAGMSGIAEILLNEGYQISGSDIADGVVTQRLAQAGAKIYIGHAEEHIEGASVVVVSSAIKDDNPELVTSKQKRIPVIQRAQMLAEIMRFRHGIAVAGTHGKTTTTAMISMIYTQAKLDPTFVNGGLVKSAGKNAHLGASRYLIAEADESDASFLHLQPMVSVVTNMEPDHMDTYEGDFEKMKATYVKFLHNLPFYGLAVMCADDPVLMELVPKVGRQVITYGFSEQADYRIEDYEQTGFQGHYTVICPNNERINVLLNVPGKHNALNATAALAVAKEEGIANEAILEALADFQGAGRRFDQLGEFIRPNGKVRLVDDYGHHPTEVGVTIKAAREGWGDKRIVMIFQPHRYSRTRDLFDDFVQVLSQVDALIMLDVYAAGEAPIVGADSKSLCRSIRNLGKVDPILVSDTSQLGDVLDQIIQDGDLILAQGAGSVSKISRGLAESWK 474
               SCOP domains d1p31a1 A:12-106 UDP-N-acetylmuramate-alanine ligase MurC                                      d1p31a3 A:107-321 UDP-N-acetylmuramate-alanine ligase MurC                                                                                                                                                             d1p31a2 A:322-474 UDP-N-acetylmuramate-alanine ligase MurC                                                                                                SCOP domains
               CATH domains -------1p31A01 A:19-106 NAD(P)-binding Rossmann-like Domain                                    1p31A02 A:107-323  [code=3.40.1190.10, no name defined]                                                                                                                                                                  1p31A03 A:324-474  [code=3.90.190.20, no name defined]                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee...hhhhhhhhhhhhhhh.eeeeee...hhhhhhhhhhh.eeee..hhhhhh...eeee.......hhhhhhhhhh...eeehhhhhhhhhhh.eeeeee...hhhhhhhhhhhhhhhh....eee...........ee.....eeeee.....hhhhhh...eeee......hhhhhh.hhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhh.eeeeee......eeeeeeeee..eeeeeee.....eeeeee...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.......eeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhh...eeeee.............hhhhhhhhhhhhh....eee.hhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p31 A  12 IPEmRRVQQIHFIGIGGAGmSGIAEILLNEGYQISGSDIADGVVTQRLAQAGAKIYIGHAEEHIEGASVVVVSSAIKDDNPELVTSKQKRIPVIQRAQmLAEImRFRHGIAVAGTHGKTTTTAmISmIYTQAKLDPTFVNGGLVKSAGKNAHLGASRYLIAEADESDASFLHLQPmVSVVTNmEPDHmDTYEGDFEKmKATYVKFLHNLPFYGLAVmCADDPVLmELVPKVGRQVITYGFSEQADYRIEDYEQTGFQGHYTVICPNNERINVLLNVPGKHNALNATAALAVAKEEGIANEAILEALADFQGAGRRFDQLGEFIRPNGKVRLVDDYGHHPTEVGVTIKAAREGWGDKRIVmIFQPHRYSRTRDLFDDFVQVLSQVDALImLDVYAAGEAPIVGADSKSLCRSIRNLGKVDPILVSDTSQLGDVLDQIIQDGDLILAQGAGSVSKISRGLAESWK 474
                               |    21        31        41        51        61        71        81        91       101       111   |   121       131   |  |141       151       161       171       181     | 191  |    201       211       221      |231    |  241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471   
                               |              31-MSE                                                                        110-MSE|                 135-MSE                                             187-MSE  |    |       209-MSE            228-MSE 236-MSE                                                                                                                                371-MSE                      400-MSE                                                                      
                              15-MSE                                                                                             115-MSE                138-MSE                                                 194-MSE|                                                                                                                                                                                                                                                                                   
                                                                                                                                                                                                                     199-MSE

Chain B from PDB  Type:PROTEIN  Length:465
 aligned with MURC_HAEIN | P45066 from UniProtKB/Swiss-Prot  Length:475

    Alignment length:465
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468     
           MURC_HAEIN     9 RKIIPEMRRVQQIHFIGIGGAGMSGIAEILLNEGYQISGSDIADGVVTQRLAQAGAKIYIGHAEEHIEGASVVVVSSAIKDDNPELVTSKQKRIPVIQRAQMLAEIMRFRHGIAVAGTHGKTTTTAMISMIYTQAKLDPTFVNGGLVKSAGKNAHLGASRYLIAEADESDASFLHLQPMVSVVTNMEPDHMDTYEGDFEKMKATYVKFLHNLPFYGLAVMCADDPVLMELVPKVGRQVITYGFSEQADYRIEDYEQTGFQGHYTVICPNNERINVLLNVPGKHNALNATAALAVAKEEGIANEAILEALADFQGAGRRFDQLGEFIRPNGKVRLVDDYGHHPTEVGVTIKAAREGWGDKRIVMIFQPHRYSRTRDLFDDFVQVLSQVDALIMLDVYAAGEAPIVGADSKSLCRSIRNLGKVDPILVSDTSQLGDVLDQIIQDGDLILAQGAGSVSKISRGLAESW 473
               SCOP domains d1p31b1 B:9-106 UDP-N-acetylmuramate-alanine ligase MurC                                          d1p31b3 B:107-321 UDP-N-acetylmuramate-alanine ligase MurC                                                                                                                                                             d1p31b2 B:322-473 UDP-N-acetylmuramate-alanine ligase MurC                                                                                               SCOP domains
               CATH domains ----------1p31B01 B:19-106 NAD(P)-binding Rossmann-like Domain                                    1p31B02 B:107-323  [code=3.40.1190.10, no name defined]                                                                                                                                                                  1p31B03 B:324-473  [code=3.90.190.20, no name defined]                                                                                                 CATH domains
           Pfam domains (1) -----------Mur_ligase-1p31B01 B:20-119                                                                         ---Mur_ligase_M-1p31B05 B:123-303                                                                                                                                                       -------------------Mur_ligase_C-1p31B03 B:323-414                                                              ----------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------Mur_ligase-1p31B02 B:20-119                                                                         ---Mur_ligase_M-1p31B06 B:123-303                                                                                                                                                       -------------------Mur_ligase_C-1p31B04 B:323-414                                                              ----------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...........eeeee...hhhhhhhhhhhhhhh.eeeeee...hhhhhhhhhh..eeee..hhhhhh...eeee.......hhhhhhhhhh...eeehhhhhhhhhhh.eeeeee...hhhhhhhhhhhhhhhh....eeeeeeee....eeee.....eeeee.....hhhhhh...eeee.............hhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhh.eeeeee......eeeeeeeee..eeeeeee.....eeeeee...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh........eeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhh...eeeee.............hhhhhhhhhhhhh....eee.hhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p31 B   9 RKIIPEmRRVQQIHFIGIGGAGmSGIAEILLNEGYQISGSDIADGVVTQRLAQAGAKIYIGHAEEHIEGASVVVVSSAIKDDNPELVTSKQKRIPVIQRAQmLAEImRFRHGIAVAGTHGKTTTTAmISmIYTQAKLDPTFVNGGLVKSAGKNAHLGASRYLIAEADESDASFLHLQPmVSVVTNmEPDHmDTYEGDFEKmKATYVKFLHNLPFYGLAVmCADDPVLmELVPKVGRQVITYGFSEQADYRIEDYEQTGFQGHYTVICPNNERINVLLNVPGKHNALNATAALAVAKEEGIANEAILEALADFQGAGRRFDQLGEFIRPNGKVRLVDDYGHHPTEVGVTIKAAREGWGDKRIVmIFQPHRYSRTRDLFDDFVQVLSQVDALImLDVYAAGEAPIVGADSKSLCRSIRNLGKVDPILVSDTSQLGDVLDQIIQDGDLILAQGAGSVSKISRGLAESW 473
                                  | 18        28  |     38        48        58        68        78        88        98       108 |    |118       128      |138       148       158       168       178       188     | 198|      208|      218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368  |    378       388       398 |     408       418       428       438       448       458       468     
                                 15-MSE          31-MSE                                                                        110-MSE|                 135-MSE                                             187-MSE  |    |       209-MSE            228-MSE 236-MSE                                                                                                                                371-MSE                      400-MSE                                                                     
                                                                                                                                    115-MSE                138-MSE                                                 194-MSE|                                                                                                                                                                                                                                                                                  
                                                                                                                                                                                                                        199-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 '\|'

Asymmetric Unit(hide GO term definitions)

Chain A,B (MURC_HAEIN | P45066)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0008763	UDP-N-acetylmuramate-L-alanine ligase activity	Catalysis of the reaction: L-alanine + ATP + UDP-N-acetylmuramate = ADP + 2 H(+) + phosphate + UDP-N-acetylmuramoyl-L-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.

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	MURC_HAEIN \| P45066	:	1gqq 1gqy 1p3d

1p3d	CRYSTAL STRUCTURE OF UDP-N-ACETYLMURAMIC ACID:L-ALANINE LIGASE (MURC) IN COMPLEX WITH UMA AND ANP

Description

Compounds

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Ligands, Modified Residues, Ions (3, 34)

Sites (6, 6)

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