4D0Q - JenaLib

Title :   HYALURONAN BINDING MODULE OF THE STREPTOCOCCAL PNEUMONIAE HYALURONATE LYASE

Authors :   M. D. L. Suits, B. Pluvinage, A. Law, Y. Liu, A. S. Palma, W. Chai, T. Feizi A. B. Boraston

Date :   29 Apr 14 (Deposition) - 06 Aug 14 (Release) - 08 Oct 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.20

Chains :   Asym./Biol. Unit : A

Keywords :   Lyase, Hyaluronan Binding Carbohydrate Binding Module, Cbm, Pl Family 8, Pl8, Hyl (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. D. L. Suits, B. Pluvinage, A. Law, Y. Liu, A. S. Palma, W. Chai, T. Feizi, A. B. Boraston
Conformational Analysis Of The Streptococcus Pneumoniae Hyaluronate Lyase And Characterization Of Its Hyaluronan- Specific Carbohydrate-Binding Module.
J. Biol. Chem. V. 289 27264 2014
PubMed-ID: 25100731 | Reference-DOI: 10.1074/JBC.M114.578435

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 9)

Sites (9, 9)

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:147 , GLU A:148 , GLU A:149 , LYS A:183 , LYS A:185 , HOH A:2137	BINDING SITE FOR RESIDUE EDO A1213
2	AC2	SOFTWARE	GLU A:148 , ARG A:155 , SER A:176 , THR A:178 , HOH A:2028	BINDING SITE FOR RESIDUE EDO A1214
3	AC3	SOFTWARE	PRO A:120 , ILE A:121 , ILE A:139 , GLY A:140 , SER A:163 , ASP A:182 , HOH A:2213 , HOH A:2214	BINDING SITE FOR RESIDUE EDO A1215
4	AC4	SOFTWARE	GLU A:65 , ASP A:66 , LYS A:152 , LYS A:154 , HOH A:2036 , HOH A:2038 , HOH A:2143 , HOH A:2145 , HOH A:2215 , HOH A:2216	BINDING SITE FOR RESIDUE EDO A1216
5	AC5	SOFTWARE	GLU A:122 , TYR A:127 , SER A:163 , GLY A:164 , GLU A:206	BINDING SITE FOR RESIDUE EDO A1217
6	AC6	SOFTWARE	MET A:118 , ILE A:139 , LYS A:183 , THR A:194 , HOH A:2198 , HOH A:2217	BINDING SITE FOR RESIDUE EDO A1218
7	AC7	SOFTWARE	GLU A:57 , ASN A:58 , HOH A:2015 , HOH A:2018 , HOH A:2020 , HOH A:2026 , HOH A:2128 , HOH A:2152	BINDING SITE FOR RESIDUE EDO A1219
8	AC8	SOFTWARE	LYS A:124 , SER A:176 , PRO A:177 , THR A:178 , HOH A:2192	BINDING SITE FOR RESIDUE EDO A1220
9	AC9	SOFTWARE	GLY A:73 , SER A:74 , GLU A:97 , ALA A:98	BINDING SITE FOR RESIDUE EDO A1221

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

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

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Chain A from PDB  Type:PROTEIN  Length:161
 aligned with HYSA_STRPN | Q54873 from UniProtKB/Swiss-Prot  Length:1066

    Alignment length:161
                                    61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211 
           HYSA_STRPN    52 TKNLVENGDFGQTEDGSSPWTGSKAQGWSAWVDQKNSADASTRVIEAKDGAITISSHEKLRAALHRMVPIEAKKKYKLRFKIKTDNKIGIAKVRIIEESGKDKRLWNSATTSGTKDWQTIEADYSPTLDVDKIKLELFYETGTGTVSFKDIELVEVADQLS 212
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............ee.........ee...eeee.hhhh......eeeee..eeeeeeeeeeeeeeeeeee......eeeeeeeeeeeeeeeeeeeeeeee..eeeeee...eeeeeeeeeeeeee..................................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d0q A  52 MQNLVENGDFGQTEDGSSPWTGSKAQGWSAWVDQKNSADASTRVIEAKDGAITISSHEKLRAALHRMVPIEAKKKYKLRFKIKTDNKIGIAKVRIIEESGKDKRLWNSATTSGTKDWQTIEADYSPTLDVDKIKLELFYETGTGTVSFKDIELVEVADQLS 212
                                    61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211

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 (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (HYSA_STRPN | Q54873)

molecular function
	GO:0030246	carbohydrate binding	Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
	GO:0016837	carbon-oxygen lyase activity, acting on polysaccharides	Catalysis of the cleavage of a carbon-oxygen bond by the elimination of an alcohol from a polysaccharide.
	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:0030340	hyaluronate lyase activity	Catalysis of the reaction: hyaluronate = n 3-(4-deoxy-beta-D-gluc-4-enuronosyl)-N-acetyl-D-glucosamine.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
cellular component
	GO:0005618	cell wall	The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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