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Title :   STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE IN COMPLEX WITH HEXASACCHARIDE HYALURONAN SUBSTRATE

Authors :   M. J. Jedrzejas, L. V. Mello, B. L. De Groot, S. Li

Date :   06 May 02 (Deposition) - 07 Aug 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A

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

Reference :   M. J. Jedrzejas, L. V. Mello, B. L. De Groot, S. Li
Mechanism Of Hyaluronan Degradation By Streptococcus Pneumoniae Hyaluronate Lyase. Structures Of Complexes With The Substrate.
J. Biol. Chem. V. 277 28287 2002
PubMed-ID: 11991948 | Reference-DOI: 10.1074/JBC.M112009200

Molecule 1 - HYALURONATE LYASE
	Chains	:	A
	EC Number	:	4.2.2.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Scientific	:	STREPTOCOCCUS PNEUMONIAE
	Organism Taxid	:	1313
	Synonym	:	HYALURONIDASE

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 6)

No.	Name	Count	Type	Full Name
1	BDP	3	Ligand/Ion	BETA-D-GLUCOPYRANURONIC ACID
2	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:291 , ARG A:336 , PHE A:343 , HIS A:399 , GLN A:808 , GLU A:812 , HOH A:1200 , BDP A:2001	BINDING SITE FOR RESIDUE NAG A 2000
2	AC2	SOFTWARE	ASN A:290 , TRP A:291 , TRP A:292 , ASN A:349 , HIS A:399 , PHE A:408 , ARG A:462 , ASN A:580 , HOH A:1558 , NAG A:2000 , NAG A:2002	BINDING SITE FOR RESIDUE BDP A 2001
3	AC3	SOFTWARE	TRP A:292 , PHE A:408 , ARG A:462 , ARG A:466 , HOH A:1108 , HOH A:1110 , HOH A:1121 , HOH A:1122 , HOH A:1558 , BDP A:2001 , BDP A:2003	BINDING SITE FOR RESIDUE NAG A 2002
4	AC4	SOFTWARE	ARG A:243 , TRP A:292 , GLU A:477 , HOH A:1108 , HOH A:1119 , NAG A:2002 , NAG A:2004	BINDING SITE FOR RESIDUE BDP A 2003
5	AC5	SOFTWARE	ARG A:243 , ARG A:300 , ARG A:355 , ASP A:414 , GLN A:418 , ARG A:480 , HOH A:1099 , HOH A:1104 , HOH A:1106 , BDP A:2003 , BDP A:2005	BINDING SITE FOR RESIDUE NAG A 2004
6	AC6	SOFTWARE	ILE A:185 , GLU A:246 , LYS A:250 , ASN A:304 , GLN A:418 , THR A:519 , HOH A:1101 , HOH A:1539 , NAG A:2004	BINDING SITE FOR RESIDUE BDP A 2005

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

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

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

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

(no "Exon" information available for 1LOH)

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
	(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:721
 aligned with HYSA_STRPN | Q54873 from UniProtKB/Swiss-Prot  Length:1066

    Alignment length:721
                                   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 VKDAYTDRLDDWNGIIAGNQYYDSKNEQMAKLNQELEGKVADSLSSISSQADRTYLWEKFSNYKTSANLTATYRKLEEMAKQVTNPSSRYYQDETVVRTVRDSMEWMHKHVYNSEKSIVGNWWDYEIGTPRAINNTLSLMKEYFSDEEIKKYTDVIEKFVPDPEHFRKTTDNPFKALGGNLVDMGRVKVIAGLLRKDDQEISSTIRSIEQVFKLVDQGEGFYQDGSYIDHTNVAYTGAYGNVLIDGLSQLLPVIQKTKNPIDKDKMQTMYHWIDKSFAPLLVNGELMDMSRGRSISRANSEGHVAAVEVLRGIHRIADMSEGETKQCLQSLVKTIVQSDSYYDVFKNLKTYKDISLMQSLLSDAGVASVPRPSYLSAFNKMDKTAMYNAEKGFGFGLSLFSSRTLNYEHMNKENKRGWYTSDGMFYLYNGDLSHYSDGYWPTVNPYKMPGTTETDAKRADSDTGKVLPSAFVGTSKLDDANATATMDFTNWNQTLTAHKSWFMLKDKIAFLGSNIQNTSTDTAATTIDQRKLESGNPYKVYVNDKEASLTEQEKDYPETQSVFLESFDSKKNIGYFFFKKSSISMSKALQKGAWKDINEGQSDKEVENEFLTISQAHKQNRDSYGYMLIPNVDRATFNQMIKELESSLIENNETLQSVYDAKQGVWGIVKYDDSVSTISNQFQVLKRGVYTIRKEGDEYKIAYYNPETQESAPDQEVFKKL 1007
               SCOP domains d1loha1 A:170-540 Hyaluronate lyase                                                                                                                                                                                                                                                                                                                                                d1loha3 A:541-814 Hyaluronate lyase                                                                                                                                                                                                                                               d1loha2 A:815-890 Hyaluronate lyase                                          SCOP domains
               CATH domains -1lohA02 A:171-542  [code=1.50.10.100, no name defined]                                                                                                                                                                                                                                                                                                                              -----1lohA01 A:548-804  [code=2.70.98.10, no name defined]                                                                                                                                                                                                            1lohA03 A:805-890 Chondroitinase Ac; Chain A, domain 3                                 CATH domains
               Pfam domains -----------Lyase_8_N-1lohA02 A:181-503                                                                                                                                                                                                                                                                                                        ---------------------------------Lyase_8-1lohA01 A:537-807                                                                                                                                                                                                                                                      -------Lyase_8_C-1lohA03 A:815-887                                              --- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.........hhhhh...hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh....ee.......ee.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh......ee.....eee...ee...hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.ee..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhhhhhh..........eeeee....eeeeee....eeeeee.........................eeeee.........hhhhhh........eee.................eeeee....eeeeeeeee.....eeeeeeeeee...eeeeeeeeee.....eeeeeeeee.......eeee..eee......eeeeeeeeeeee..hhhh.eeeeeeeeeeeeeeeeeeeee.hhh.......eeeeeeeeeeeee....eeeeeeeee..hhhhhhhhhhhh...eeee...eeeeee....eeeeee.....eee...eee...eeeeeeee..eeeeeee........hhhhheee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1loh A  170 VKDTYTDRLDDWNGIIAGNQYYDSKNDQMAKLNQELEGKVADSLSSISSQADRIYLWEKFSNYKTSANLTATYRKLEEMAKQVTNPSSRYYQDETVVRTVRDSMEWMHKHVYNSEKSIVGNWWDYEIGTPRAINNTLSLMKEYFSDEEIKKYTDVIEKFVPDPEHFRKTTDNPFKALGGNLVDMGRVKVIAGLLRKDDQEISSTIRSIEQVFKLVDQGEGFYQDGSYIDHTNVAYTGAFGNVLIDGLSQLLPVIQKTKNPIDKDKMQTMYHWIDKSFAPLLVNGELMDMSRGRSISRANSEGHVAAVEVLRGIHRIADMSEGETKQRLQSLVKTIVQSDSYYDVFKNLKTYKDISLMQSLLSDAGVASVPRTSYLSAFNKMDKTAMYNAEKGFGFGLSLFSSRTLNYEHMNKENKRGWYTSDGMFYLYNGDLSHYSDGYWPTVNPYKMPGTTETDAKRADSDTGKVLPSAFVGTSKLDDANATATMDFTNWNQTLTAHKSWFMLKDKIAFLGSNIQNTSTDTAATTIDQRKLESSNPYKVYVNDKEASLTEQEKDYPETQSVFLESSDSKKNIGYFFFKKSSISMSKALQKGAWKDINEGQSDKEVENEFLTISQAHKQNGDSYGYMLIPNVDRATFNQMIKELESSLIENNETLQSVYDAKQGVWGIVKYDDSVSTISNQFQVLKRGVYTIRKEGDEYKIAYYNPETQESAPDQEVFKKL  890
                                   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_8-1lohA01

A:537-807

Clan: Hy-ly_N (15)

Family: Lyase_8_N (15)

Streptococcus pneumoniae (11)

Lyase_8_N-1lohA02

A:181-503

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

Family: Lyase_8_C (15)

Streptococcus pneumoniae (11)

Lyase_8_C-1lohA03

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	1C82 IS THE MECHANISM OF HYALURONAN BINDING AND DEGRADATION: STRUCTURE OF STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE IN COMPLEX WITH HYALURONIC ACID DISACCHARIDE AT 1.7 A RESOLUTION
1egu	1EGU IS THE CRYSTAL STRUCTURE OF STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE AT 1.56 A RESOLUTION

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

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Cis Peptide Bonds (0, 0)

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