1IOW - JenaLib

Title :   COMPLEX OF Y216F D-ALA:D-ALA LIGASE WITH ADP AND A PHOSPHORYL PHOSPHINATE

Authors :   J. R. Knox, P. C. Moews, C. Fan

Date :   20 Sep 96 (Deposition) - 12 Feb 97 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A

Keywords :   Glycogen Phosphorylase, Ligase, Cell Wall, Peptidoglycan Synthesis, Vancomycin, Adp Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Fan, I. S. Park, C. T. Walsh, J. R. Knox
D-Alanine:D-Alanine Ligase: Phosphonate And Phosphinate Intermediates With Wild Type And The Y216F Mutant.
Biochemistry V. 36 2531 1997
PubMed-ID: 9054558 | Reference-DOI: 10.1021/BI962431T
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:270 , ASN A:272 , ADP A:310 , PHY A:320 , MG A:331 , HOH A:401	BINDING SITE FOR RESIDUE MG A 330
2	AC2	SOFTWARE	ASP A:257 , GLU A:270 , ADP A:310 , PHY A:320 , MG A:330 , HOH A:407	BINDING SITE FOR RESIDUE MG A 331
3	AC3	SOFTWARE	LYS A:97 , ILE A:142 , LYS A:144 , GLU A:148 , GLY A:149 , SER A:150 , SER A:151 , MET A:154 , GLU A:180 , LYS A:181 , TRP A:182 , LEU A:183 , GLU A:187 , PHE A:209 , TYR A:210 , LYS A:215 , ASP A:257 , MET A:259 , GLU A:270 , PHY A:320 , MG A:330 , MG A:331 , HOH A:401 , HOH A:407 , HOH A:443 , HOH A:449	BINDING SITE FOR RESIDUE ADP A 310
4	AC4	SOFTWARE	GLU A:15 , SER A:150 , LYS A:215 , ARG A:255 , ASP A:257 , GLU A:270 , ASN A:272 , PRO A:275 , GLY A:276 , SER A:281 , LEU A:282 , ADP A:310 , MG A:330 , MG A:331 , HOH A:405 , HOH A:407 , HOH A:410	BINDING SITE FOR RESIDUE PHY A 320
5	ADP	UNKNOWN	LYS A:97 , LYS A:144 , LYS A:215 , GLU A:270 , ASN A:272 , SER A:151 , GLU A:180 , GLU A:187 , TRP A:182 , ALA A:159 , ILE A:142 , PHE A:209	ADP BINDING SITE.
6	LIG	UNKNOWN	GLU A:15 , SER A:150 , PHE A:216 , VAL A:18 , HIS A:63 , SER A:281 , ARG A:255	LIGAND BINDING SITE.

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological 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
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Chain A from PDB  Type:PROTEIN  Length:306
 aligned with DDLB_ECOLI | P07862 from UniProtKB/Swiss-Prot  Length:306

    Alignment length:306
                                    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      
           DDLB_ECOLI     1 MTDKIAVLLGGTSAEREVSLNSGAAVLAGLREGGIDAYPVDPKEVDVTQLKSMGFQKVFIALHGRGGEDGTLQGMLELMGLPYTGSGVMASALSMDKLRSKLLWQGAGLPVAPWVALTRAEFEKGLSDKQLAEISALGLPVIVKPSREGSSVGMSKVVAENALQDALRLAFQHDEEVLIEKWLSGPEFTVAILGEEILPSIRIQPSGTFYDYEAKYLSDETQYFCPAGLEASQEANLQALVLKAWTTLGCKGWGRIDVMLDSDGQFYLLEANTSPGMTSHSLVPMAARQAGMSFSQLVVRILELAD 306
               SCOP domains d1iowa1 A:1-96 D-Ala-D-Ala ligase, N-domain                                                     d1iowa2 A:97-306 D-ala-D-ala ligase, C-domain                                                                                                                                                                      SCOP domains
               CATH domains 1iowA01 A:1-84  [code=3.40.50.20, no name defined]                                  1iowA02 A:85-110,A:184-3061iowA03 A:111-183 ATP-grasp fold, A domain                               1iowA02 A:85-110,A:184-306 ATP-grasp fold, B domain                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee......hhhhhhhhhhhhhhhhh...eeeeee.....hhh.....eeeeee..........hhhhhhhhh........hhhhhhhh.hhhhhhhhhh.......eeeeehhhhhh....hhhhhhhhh...eeeee.........eee..hhhhhhhhhhhhh...eeeeee.....eeeeeee.......eeee.......hhhhh.....eee......hhhhhhhhhhhhhhhhhh....eeeeeeee.....eeeeeee.........hhhhhhhh....hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------DALA_DALA_LI-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------DALA_DALA_LIGASE_2           ------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1iow A   1 MTDKIAVLLGGTSAEREVSLNSGAAVLAGLREGGIDAYPVDPKEVDVTQLKSMGFQKVFIALHGRGGEDGTLQGMLELMGLPYTGSGVMASALSMDKLRSKLLWQGAGLPVAPWVALTRAEFEKGLSDKQLAEISALGLPVIVKPSREGSSVGMSKVVAENALQDALRLAFQHDEEVLIEKWLSGPEFTVAILGEEILPSIRIQPSGTFYDYEAKFLSDETQYFCPAGLEASQEANLQALVLKAWTTLGCKGWGRIDVMLDSDGQFYLLEANTSPGMTSHSLVPMAARQAGMSFSQLVVRILELAD 306
                                    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

Legend:		→ Mismatch	(orange background)
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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 '\|'

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (3, 3)

Pfam Domains (0, 0)

Gene Ontology (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (DDLB_ECOLI | P07862)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0008716	D-alanine-D-alanine ligase activity	Catalysis of the reaction: 2 D-alanine + ATP = D-alanyl-D-alanine + ADP + 2 H(+) + phosphate.
	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: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:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0030145	manganese ion binding	Interacting selectively and non-covalently with manganese (Mn) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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: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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