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Title :   CRYSTAL STRUCTURE OF GH63 MANNOSYLGLYCERATE HYDROLASE FROM THERMUS THERMOPHILUS HB8 IN COMPLEX WITH TRIS

Authors :   T. Miyazaki, M. Ichikawa, A. Nishikawa, T. Tonozuka

Date :   05 Nov 14 (Deposition) - 11 Mar 15 (Release) - 22 Apr 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.67

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (3x)
Biol. Unit 2: B  (3x)

Keywords :   Hydrolase, Gh63, (Alpha/Alpha)6-Barrel (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Miyazaki, M. Ichikawa, H. Iino, A. Nishikawa, T. Tonozuka
Crystal Structure And Substrate-Binding Mode Of Gh63 Mannosylglycerate Hydrolase From Thermus Thermophilus Hb8.
J. Struct. Biol. V. 190 21 2015
PubMed-ID: 25712767 | Reference-DOI: 10.1016/J.JSB.2015.02.006

Molecule 1 - UNCHARACTERIZED PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-11A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	TTHA0978
	Organism Scientific	:	THERMUS THERMOPHILUS HB8
	Organism Taxid	:	300852

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (3x)	:	A
Biological Unit 2 (3x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 9)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	MPD	5	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	TRS	2	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 1 (2, 12)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MPD	9	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	TRS	3	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 2 (2, 9)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MPD	6	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	TRS	3	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:312 , GLN A:313 , HOH A:735	binding site for residue CL A 500
2	AC2	SOFTWARE	TYR A:28 , TRP A:32 , TRP A:34 , ASP A:35 , GLN A:103 , GLY A:163 , ASP A:165 , TYR A:349 , TRP A:350 , GLU A:393 , PHE A:408 , TRP A:410 , HOH A:679 , HOH A:700	binding site for residue TRS A 501
3	AC3	SOFTWARE	GLU A:10 , VAL A:190 , LYS A:191 , HIS A:192 , PRO A:195 , HOH A:659 , HOH A:819	binding site for residue MPD A 502
4	AC4	SOFTWARE	GLY A:64 , PRO A:133 , LYS A:134 , HOH A:814 , HOH A:823 , HOH A:919 , PRO B:65	binding site for residue MPD A 503
5	AC5	SOFTWARE	ARG A:243 , ARG A:279 , TRP A:360 , GLU A:364 , HOH A:619 , HOH A:767	binding site for residue MPD A 504
6	AC6	SOFTWARE	HIS B:312 , GLN B:313 , HOH B:687	binding site for residue CL B 500
7	AC7	SOFTWARE	TYR B:28 , TRP B:32 , TRP B:34 , ASP B:35 , GLN B:103 , GLY B:163 , ASP B:165 , TYR B:349 , TRP B:350 , GLU B:393 , PHE B:408 , TRP B:410 , HOH B:745	binding site for residue TRS B 501
8	AC8	SOFTWARE	PRO A:65 , GLY B:64 , GLY B:67 , PRO B:133 , HOH B:860	binding site for residue MPD B 502
9	AC9	SOFTWARE	THR B:109 , ARG B:243 , TRP B:360 , GLU B:364 , HOH B:773	binding site for residue MPD B 503

(no "SS Bond" information available for 4WVA)

Asymmetric Unit

No.	Residues
1	Phe A:82	-	Pro A:83
2	Leu A:333	-	Leu A:334
3	Phe B:82	-	Pro B:83
4	Leu B:333	-	Leu B:334

(no "SAP(SNP)/Variant" information available for 4WVA)

(no "PROSITE Motif" information available for 4WVA)

(no "Exon" information available for 4WVA)

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:413
                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh..............eehhhhhhhhhhhh..hhhhhhhhhhhhhhhhh........eee.........hhhhhh..ee.......hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhh...hhhhhhhhhh...........hhhhh.hhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhee....ee..ee....ee....hhhhhhhhhhh..hhhhhhhhhhhhhhhhh..........................hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.eeee......eeeee.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wva A   3 PLRTKAVEVLQRNSRGAFTVPAHGLYPYQWLWDSAFIALGWTQVDWERAWQELLCLFDYGQGPDGMLPHIVFHEQSRDYFPGPDVWGQPATSGITQPPVVATVVRYLYEKDPDRDRARERARYLFPKLLAFHRWLYHARDPYRTGLVVIVHPWESGMDNSPAWDKPLSRVPVENLPPYERRDVKHVNPEERPRKEDYDRYLSLLYLFRRLEYDPREIYRQSPFKVVDVGFNAILQRANRDLYALAVLLQEDPYEIEEWIVRGEVGLEALWDREAGFYFSWDLVAGEPIAVKTSAGFLPLFAGTPHQGRASLLAQEAERWGEKARYLLPSVDPTSPFFEPGRYWRGPVWINVNWMVAEGFRDYGFAALAARLKADALALMEREGFREYYDPLTGQGRGGEGFSWSAALALFWTR 420
                                    12        22        32        42        52        62        72        82      ||97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417   
                                                                                                                 89|                                                                                                                                                                                                                                                                                                                                     
                                                                                                                  95

Chain B from PDB  Type:PROTEIN  Length:414
                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..............eehhhhhhhhhhhh..hhhhhhhhhhhhhhhhh........ee..........hhhhhh............hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhh...hhhhhhhhhh...........hhhhh.hhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhee....ee..ee....ee....hhhhhhhhhhh..hhhhhhhhhhhhhhhh...........................hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.eeee......eeeee.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4wva B   3 PLRTKAVEVLQRNSRGAFTVPAHGLYPYQWLWDSAFIALGWTQVDWERAWQELLCLFDYGQGPDGMLPHIVFHEQSRDYFPGPDVWGRQPATSGITQPPVVATVVRYLYEKDPDRDRARERARYLFPKLLAFHRWLYHARDPYRTGLVVIVHPWESGMDNSPAWDKPLSRVPVENLPPYERRDVKHVNPEERPRKEDYDRYLSLLYLFRRLEYDPREIYRQSPFKVVDVGFNAILQRANRDLYALAVLLQEDPYEIEEWIVRGEVGLEALWDREAGFYFSWDLVAGEPIAVKTSAGFLPLFAGTPHQGRASLLAQEAERWGEKARYLLPSVDPTSPFFEPGRYWRGPVWINVNWMVAEGFRDYGFAALAARLKADALALMEREGFREYYDPLTGQGRGGEGFSWSAALALFWTR 420
                                    12        22        32        42        52        62        72        82       |96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416    
                                                                                                                  90|                                                                                                                                                                                                                                                                                                                                     
                                                                                                                   95

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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 '\|'

(no "SCOP Domain" information available for 4WVA)

(no "CATH Domain" information available for 4WVA)

(no "Pfam Domain" information available for 4WVA)

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	Cis Peptide Bonds
		Leu A:333 - Leu A:334	[ RasMol ]
		Leu B:333 - Leu B:334	[ RasMol ]
		Phe A:82 - Pro A:83	[ RasMol ]
		Phe B:82 - Pro B:83	[ RasMol ]

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	Q5SJN0_THET8 \| Q5SJN0	:	2z07 4wvb 4wvc

2z07	THE SAME PROTEIN AT 2.1-A RESOLUTION
4wvb
4wvc

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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