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Title :   CRYSTAL STRUCTURES OF CATALYTIC SITE MUTANTS OF ACTIVE DOMAIN 2 OF CHITINASE FROM PYROCOCCUS FURIOSUS

Authors :   H. Tsuji

Date :   25 Feb 10 (Deposition) - 09 Jun 10 (Release) - 29 Dec 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.76

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

Keywords :   (Beta/Alpha)8-Barrel, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Tsuji, S. Nishimura, T. Inui, Y. Kado, K. Ishikawa, T. Nakamura, K. Uegaki
Kinetic And Crystallographic Analyses Of The Catalytic Domain Of Chitinase From Pyrococcus Furiosus- The Role Of Conserved Residues In The Active Site
Febs J. V. 277 2683 2010
PubMed-ID: 20553502 | Reference-DOI: 10.1111/J.1742-464X.2010.07685.X

Molecule 1 - PUTATIVE CHITINASE
	Chains	:	A, B
	EC Number	:	3.2.1.14
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	CATALYTIC DOMAIN (AD2), UNP RESIDUES 409-717
	Gene	:	PF1233
	Mutation	:	YES
	Organism Scientific	:	PYROCOCCUS FURIOSUS
	Organism Taxid	:	2261

		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, 7)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL
2	MG	2	Ligand/Ion	MAGNESIUM ION
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	GOL	3	Ligand/Ion	GLYCEROL
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:49 , LEU A:495 , CYS A:496 , TYR A:509	BINDING SITE FOR RESIDUE MG A 1
2	AC2	SOFTWARE	HOH A:51 , HOH A:308 , HOH A:323 , TRP A:664 , VAL A:677 , SER A:678	BINDING SITE FOR RESIDUE GOL A 718
3	AC3	SOFTWARE	HOH A:308 , HOH A:323 , PHE A:448 , ALA A:490 , GLU A:526 , HOH A:728	BINDING SITE FOR RESIDUE GOL A 2
4	AC4	SOFTWARE	HOH A:152 , LYS A:617 , GLU A:621 , HOH B:199 , ASP B:530	BINDING SITE FOR RESIDUE GOL A 3
5	AC5	SOFTWARE	HOH B:8 , LEU B:495 , CYS B:496 , TYR B:509	BINDING SITE FOR RESIDUE MG B 2
6	AC6	SOFTWARE	HOH B:370 , PHE B:448 , ALA B:490 , GLU B:526 , TRP B:664	BINDING SITE FOR RESIDUE GOL B 4
7	AC7	SOFTWARE	GLU A:616 , GLU A:621 , ASP B:530 , ASP B:532 , HOH B:740	BINDING SITE FOR RESIDUE SO4 B 1

(no "SS Bond" information available for 3AFB)

Asymmetric Unit

No.	Residues
1	Ala A:447	-	Phe A:448
2	Gly A:492	-	Pro A:493
3	Trp A:664	-	Ser A:665
4	Ala B:447	-	Phe B:448
5	Gly B:492	-	Pro B:493
6	Trp B:664	-	Ser B:665

(no "SAP(SNP)/Variant" information available for 3AFB)

(no "PROSITE Motif" information available for 3AFB)

(no "Exon" information available for 3AFB)

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:300
 aligned with Q8U1H5_PYRFU | Q8U1H5 from UniProtKB/TrEMBL  Length:717

    Alignment length:367
                                   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       
         Q8U1H5_PYRFU   340 GPQGDKVEEITLEINGQVIDIWTPTGGTTPTPTTTTTSTPTPSQTPTPTPTPTPTPTPTPTLTPTPLPGNANPIPEHFFAPYIDMSLSVHKPLVEYAKLTGTKYFTLAFILYSSVYNGPAWAGSIPLEKFVDEVRELREIGGEVIIAFGGAVGPYLCQQASTPEQLAEWYIKVIDTYNATYLDFDIEAGIDADKLADALLIVQRERPWVKFSFTLPSDPGIGLAGGYGIIETMAKKGVRVDRVNPMTMDYYWTPSNAENAIKVAENVFRQLKQIYPEKSDEEIWKMIGLTPMIGVNDDKSVFTLEDAQQLVDWAIQHKIGSLAFWSVDRDHPGPTGEVSPLHRGTNDPDWAFSHVFVKFMEAFGYTF 706
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..-------------------------------------------------------------------........ee..eee.......hhhhhhhhhh..eeeeeeeeee....eeee....hhhhhhhhhhhhhhh..eeeeeeee....hhhhhh.hhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhh...eeeeeeeee...ee.hhhhhhhhhhhhh....eeeee.........hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhee....ee.....eehhhhhhhhhhhhhhhh..ee...hhhhh...................hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3afb A 407 GP-------------------------------------------------------------------NANPIPEHFFAPYIDMSLSVHKPLVEYAKLTGTKYFTLAFILYSSVYNGPAWAGSIPLEKFVDEVRELREIGGEVIIAFGGAVGPYLCQQASTPEQLAEWYIKVIDTYNATYLDFAIEAGIDADKLADALLIVQRERPWVKFSFTLPSDPGIGLAGGYGIIETMAKKGVRVDRVNPMTMDYYWTPSNAENAIKVAENVFRQLKQIYPEKSDEEIWKMIGLTPMIGVNDDKSVFTLEDAQQLVDWAIQHKIGSLAFWSVDRDHPGPTGEVSPLHRGTNDPDWAFSHVFVKFMEAFGYTF 706
                             |       -         -         -         -         -         -       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       
                             |                                                                 409                                                                                                                                                                                                                                                                                                         
                           408

Chain B from PDB  Type:PROTEIN  Length:300
 aligned with Q8U1H5_PYRFU | Q8U1H5 from UniProtKB/TrEMBL  Length:717

    Alignment length:367
                                   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       
         Q8U1H5_PYRFU   340 GPQGDKVEEITLEINGQVIDIWTPTGGTTPTPTTTTTSTPTPSQTPTPTPTPTPTPTPTPTLTPTPLPGNANPIPEHFFAPYIDMSLSVHKPLVEYAKLTGTKYFTLAFILYSSVYNGPAWAGSIPLEKFVDEVRELREIGGEVIIAFGGAVGPYLCQQASTPEQLAEWYIKVIDTYNATYLDFDIEAGIDADKLADALLIVQRERPWVKFSFTLPSDPGIGLAGGYGIIETMAKKGVRVDRVNPMTMDYYWTPSNAENAIKVAENVFRQLKQIYPEKSDEEIWKMIGLTPMIGVNDDKSVFTLEDAQQLVDWAIQHKIGSLAFWSVDRDHPGPTGEVSPLHRGTNDPDWAFSHVFVKFMEAFGYTF 706
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..-------------------------------------------------------------------........ee..eee.......hhhhhhhhhh..eeeeeeeeee....eeee...ee...hhhhhhhhhh...eeeeeeee....hhhhhh.hhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhh...eeeeeeeee...ee..hhhhhhhhhhhh....eeeee.........hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhee....ee.....eehhhhhhhhhhhhhhhh..ee...hhhhh...................hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3afb B 407 GP-------------------------------------------------------------------NANPIPEHFFAPYIDMSLSVHKPLVEYAKLTGTKYFTLAFILYSSVYNGPAWAGSIPLEKFVDEVRELREIGGEVIIAFGGAVGPYLCQQASTPEQLAEWYIKVIDTYNATYLDFAIEAGIDADKLADALLIVQRERPWVKFSFTLPSDPGIGLAGGYGIIETMAKKGVRVDRVNPMTMDYYWTPSNAENAIKVAENVFRQLKQIYPEKSDEEIWKMIGLTPMIGVNDDKSVFTLEDAQQLVDWAIQHKIGSLAFWSVDRDHPGPTGEVSPLHRGTNDPDWAFSHVFVKFMEAFGYTF 706
                             |       -         -         -         -         -         -       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       
                           408                                                                 409

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 '\|'

(no "SCOP Domain" information available for 3AFB)

(no "CATH Domain" information available for 3AFB)

(no "Pfam Domain" information available for 3AFB)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q8U1H5_PYRFU | Q8U1H5)

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:0004568	chitinase activity	Catalysis of the hydrolysis of (1->4)-beta linkages of N-acetyl-D-glucosamine (GlcNAc) polymers of chitin and chitodextrins.
	GO:0004553	hydrolase activity, hydrolyzing O-glycosyl compounds	Catalysis of the hydrolysis of any O-glycosyl bond.
	GO:0030247	polysaccharide binding	Interacting selectively and non-covalently with any polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
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.
	GO:0006032	chitin catabolic process	The chemical reactions and pathways resulting in the breakdown of chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues.

Asymmetric Unit
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	Cis Peptide Bonds
		Ala A:447 - Phe A:448	[ RasMol ]
		Ala B:447 - Phe B:448	[ RasMol ]
		Gly A:492 - Pro A:493	[ RasMol ]
		Gly B:492 - Pro B:493	[ RasMol ]
		Trp A:664 - Ser A:665	[ RasMol ]
		Trp B:664 - Ser B:665	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	Q8U1H5_PYRFU \| Q8U1H5	:	2cwr 2czn 2dsk 3a4w 3a4x

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

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