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Title :   SPECIFICITY AND MECHANISM OF STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE: COMPLEX OF THE TYR408PHE MUTANT WITH 4-SULPHATED CHONDROITIN DISACCHARIDE

Authors :   D. J. Rigden, M. J. Jedrzejas

Date :   11 Jul 03 (Deposition) - 30 Oct 03 (Release) - 23 Jan 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

Chains :   Asym./Biol. Unit : A

Keywords :   Lyase, Protein-Carbohydrate Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. J. Rigden, M. J. Jedrzejas
Structures Of Streptococcus Pneumoniae Hyaluronate Lyase In Complex With Chondroitin And Chondroitin Sulfate Disaccharides: Insights Into Specificity And Mechanism Of Action
J. Biol. Chem. V. 278 50596 2003
PubMed-ID: 14523022 | Reference-DOI: 10.1074/JBC.M307596200
(for further references see the PDB file header)

Molecule 1 - HYALURONATE LYASE
	Chains	:	A
	EC Number	:	4.2.2.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Fragment	:	HYALURONATE LYASE, RESIDUES 285-1009
	Mutation	:	YES
	Organism Scientific	:	STREPTOCOCCUS PNEUMONIAE
	Organism Taxid	:	1313
	Synonym	:	HYALURONIDASE, HYASE

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 6)

No.	Name	Count	Type	Full Name
1	ASG	1	Ligand/Ion	2-DEOXY-2-ACETAMIDO-BETA-D-GALACTOSE-4-SULFATE
2	GCD	1	Ligand/Ion	4,5-DEHYDRO-D-GLUCURONIC ACID
3	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:578 , LYS A:581 , LYS A:584 , SER A:630 , HOH A:2535	BINDING SITE FOR RESIDUE SO4 A1200
2	AC2	SOFTWARE	ALA A:628 , ASP A:629 , SER A:630 , HOH A:2536	BINDING SITE FOR RESIDUE SO4 A1201
3	AC3	SOFTWARE	GLN A:729 , LYS A:748 , LYS A:749	BINDING SITE FOR RESIDUE SO4 A1202
4	AC4	SOFTWARE	HIS A:334 , LYS A:344 , LYS A:811	BINDING SITE FOR RESIDUE SO4 A1203
5	AC5	SOFTWARE	ARG A:243 , TRP A:292 , ARG A:300 , ALA A:407 , PHE A:408 , ARG A:462 , SER A:463 , ARG A:466 , GLU A:477 , GLU A:582 , HOH A:2095 , HOH A:2227 , HOH A:2228 , HOH A:2240 , HOH A:2326 , HOH A:2528 , HOH A:2529 , HOH A:2530 , HOH A:2531 , HOH A:2533	BINDING SITE FOR RESIDUES GCD A 900 AND ASG A 901

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

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

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

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

(no "Exon" information available for 1OJO)

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:722
 aligned with HYSA_STRPN | Q54873 from UniProtKB/Swiss-Prot  Length:1066

    Alignment length:722
                                   296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876       886       896       906       916       926       936       946       956       966       976       986       996      1006  
          HYSA_STRPN    287 VKDAYTDRLDDWNGIIAGNQYYDSKNEQMAKLNQELEGKVADSLSSISSQADRTYLWEKFSNYKTSANLTATYRKLEEMAKQVTNPSSRYYQDETVVRTVRDSMEWMHKHVYNSEKSIVGNWWDYEIGTPRAINNTLSLMKEYFSDEEIKKYTDVIEKFVPDPEHFRKTTDNPFKALGGNLVDMGRVKVIAGLLRKDDQEISSTIRSIEQVFKLVDQGEGFYQDGSYIDHTNVAYTGAYGNVLIDGLSQLLPVIQKTKNPIDKDKMQTMYHWIDKSFAPLLVNGELMDMSRGRSISRANSEGHVAAVEVLRGIHRIADMSEGETKQCLQSLVKTIVQSDSYYDVFKNLKTYKDISLMQSLLSDAGVASVPRPSYLSAFNKMDKTAMYNAEKGFGFGLSLFSSRTLNYEHMNKENKRGWYTSDGMFYLYNGDLSHYSDGYWPTVNPYKMPGTTETDAKRADSDTGKVLPSAFVGTSKLDDANATATMDFTNWNQTLTAHKSWFMLKDKIAFLGSNIQNTSTDTAATTIDQRKLESGNPYKVYVNDKEASLTEQEKDYPETQSVFLESFDSKKNIGYFFFKKSSISMSKALQKGAWKDINEGQSDKEVENEFLTISQAHKQNRDSYGYMLIPNVDRATFNQMIKELESSLIENNETLQSVYDAKQGVWGIVKYDDSVSTISNQFQVLKRGVYTIRKEGDEYKIAYYNPETQESAPDQEVFKKLE 1008
               SCOP domains d1ojoa1 A:170-540 Hyaluronate lyase                                                                                                                                                                                                                                                                                                                                                d1ojoa3 A:541-814 Hyaluronate lyase                                                                                                                                                                                                                                               d1ojoa2 A:815-891 Hyaluronate lyase                                           SCOP domains
               CATH domains 1ojoA02 A:170-542  [code=1.50.10.100, no name defined]                                                                                                                                                                                                                                                                                                                               -----1ojoA01 A:548-804  [code=2.70.98.10, no name defined]                                                                                                                                                                                                            1ojoA03 A:805-890 Chondroitinase Ac; Chain A, domain 3                                - CATH domains
               Pfam domains -----------Lyase_8_N-1ojoA02 A:181-503                                                                                                                                                                                                                                                                                                        ---------------------------------Lyase_8-1ojoA01 A:537-807                                                                                                                                                                                                                                                      -------Lyase_8_C-1ojoA03 A:815-887                                              ---- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.........hhhhh....hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh....ee.......ee.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh......ee.....eee...ee...hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.ee..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhhhhhh..........eeeeehhh.eeeeee....eeeeee.........................eeeee.........hhhhhhhhhhh...eee.................eeeee....eeeeeeeee.....eeeeeeeeee...eeeeeeeeee.....eeeeeeeee.......eeee..eee......eeeeeeeeeeee..hhhh.eeeeeeeeeeeeeeeeeeeehhhhhh.......eeeeeeeeeee.....eeeeeeeee..hhhhhhhhhhhh...eeee...eeeeee....eeeeee.....eee...eee...eeeeeeee..eeeeeee........hhhhheee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ojo A  170 VKDTYTDRLDDWNGIIAGNQYYDSKNDQMAKLNQELEGKVADSLSSISSQADRIYLWEKFSNYKTSANLTATYRKLEEMAKQVTNPSSRYYQDETVVRTVRDSMEWMHKHVYNSEKSIVGNWWDYEIGTPRAINNTLSLMKEYFSDEEIKKYTDVIEKFVPDPEHFRKTTDNPFKALGGNLVDMGRVKVIAGLLRKDDQEISSTIRSIEQVFKLVDQGEGFYQDGSYIDHTNVAYTGAFGNVLIDGLSQLLPVIQKTKNPIDKDKMQTMYHWIDKSFAPLLVNGELMDMSRGRSISRANSEGHVAAVEVLRGIHRIADMSEGETKQRLQSLVKTIVQSDSYYDVFKNLKTYKDISLMQSLLSDAGVASVPRTSYLSAFNKMDKTAMYNAEKGFGFGLSLFSSRTLNYEHMNKENKRGWYTSDGMFYLYNGDLSHYSDGYWPTVNPYKMPGTTETDAKRADSDTGKVLPSAFVGTSKLDDANATATMDFTNWNQTLTAHKSWFMLKDKIAFLGSNIQNTSTDTAATTIDQRKLESSNPYKVYVNDKEASLTEQEKDYPETQSVFLESSDSKKNIGYFFFKKSSISMSKALQKGAWKDINEGQSDKEVENEFLTISQAHKQNRDSYGYMLIPNVDRATFNQMIKELESSLIENNETLQSVYDAKQGVWGIVKYDDSVSTISNQFQVLKRGVYTIRKEGDEYKIAYYNPETQESAPDQEVFKKLE  891
                                   179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859       869       879       889

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/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Gal_mutarotase (81)

Family: Lyase_8 (15)

Streptococcus pneumoniae (11)

Lyase_8-1ojoA01

A:537-807

Clan: Hy-ly_N (15)

Family: Lyase_8_N (15)

Streptococcus pneumoniae (11)

Lyase_8_N-1ojoA02

A:181-503

Clan: no clan defined [family: Lyase_8_C] (15)

Family: Lyase_8_C (15)

Streptococcus pneumoniae (11)

Lyase_8_C-1ojoA03

A:815-887

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.

Asymmetric/Biological Unit
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1c82	MECHANISM OF HYALURONAN BINDING AND DEGRADATION: STRUCTURE OF STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE IN COMPLEX WITH HYALURONIC ACID DISACCHARIDE AT 1.7 A RESOLUTION
1egu	CRYSTAL STRUCTURE OF STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE AT 1.56 A RESOLUTION
1f9g	CRYSTAL STRUCTURE OF STREPTOCOCCUS PNEUMONIAE HYALURONATELYASE COCRYSTALLIZED WITH ASCORBIC ACID
1loh	STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE IN COMPLEX WITHHEXASACCHARIDE HYALURONAN SUBSTRATE
1lxk	STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE IN COMPLEX WITHTETRASACCHARIDE HYALURONAN SUBSTRATE
1n7n	STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE W292A MUTANT
1n7o	STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE F343V MUTANT
1n7p	STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE W292A /F343VDOUBLE MUTANT
1n7q	STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE W291A /W292ADOUBLE MUTANT COMPLEX WITH HYALURONAN HEXASACCHRIDE
1n7r	STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASEW291A/ W292A/F343V MUTANT COMPLEX WITH HEXASACCHARIDE HYALURONAN
1ojm	SPECIFICITY AND MECHANISM OF STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE: COMPLEX WITH UNSULPHATED CHONDROITIN DISACCHARIDE
1ojn	SPECIFICITY AND MECHANISM OF STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE: COMPLEX OF THE TYR408PHE MUTANT WITH 6-SULPHATED CHONDROITIN DISACCHARIDE
1ojp	SPECIFICITY AND MECHANISM OF STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE: COMPLEX WITH 6-SULPHATED CHONDROITIN DISACCHARIDE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (3, 3)

CATH Domains (3, 3)

Pfam Domains (3, 3)

Gene Ontology (8, 8)

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