2DFV - JenaLib

Title :   HYPERTHERMOPHILIC THREONINE DEHYDROGENASE FROM PYROCOCCUS HORIKOSHII

Authors :   K. Ishikawa, N. Higashi, T. Nakamura, T. Matsuura, A. Nakagawa

Date :   03 Mar 06 (Deposition) - 16 Jan 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.05

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

Keywords :   Threonine Dehydrogenase, Pyrococcus Horikoshii, Archaea, Alchol Dehydrogenase, Ph0655, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Ishikawa, N. Higashi, T. Nakamura, T. Matsuura, A. Nakagawa
The First Crystal Structure Of L-Threonine Dehydrogenase.
J. Mol. Biol. V. 366 857 2007
PubMed-ID: 17188300 | Reference-DOI: 10.1016/J.JMB.2006.11.060

Compounds

Molecule 1 - PROBABLE L-THREONINE 3-DEHYDROGENASE
	Chains	:	A, B, C
	EC Number	:	1.1.1.103
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	PYROCOCCUS HORIKOSHII
	Organism Taxid	:	70601
	Strain	:	OT3
	Synonym	:	THREONINE DEHYDROGENASE

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (4, 27)

Asymmetric Unit (4, 27)

No.	Name	Count	Type	Full Name
1	MSE	18	Mod. Amino Acid	SELENOMETHIONINE
2	NAD	3	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
3	SO4	3	Ligand/Ion	SULFATE ION
4	ZN	3	Ligand/Ion	ZINC ION

Biological Unit 1 (3, 8)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
2	NAD	1	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
3	SO4	1	Ligand/Ion	SULFATE ION
4	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (3, 8)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
2	NAD	1	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
3	SO4	1	Ligand/Ion	SULFATE ION
4	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (3, 8)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
2	NAD	1	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
3	SO4	1	Ligand/Ion	SULFATE ION
4	ZN	-1	Ligand/Ion	ZINC ION

Sites (9, 9)

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:97 , CYS A:100 , CYS A:103 , CYS A:111	BINDING SITE FOR RESIDUE ZN A 1001
2	AC2	SOFTWARE	CYS B:97 , CYS B:100 , CYS B:103 , CYS B:111	BINDING SITE FOR RESIDUE ZN B 1002
3	AC3	SOFTWARE	CYS C:97 , CYS C:100 , CYS C:103 , CYS C:111	BINDING SITE FOR RESIDUE ZN C 1003
4	AC4	SOFTWARE	HIS A:94 , ASN A:156 , GLY A:293 , ARG A:294 , NAD A:1401 , HOH A:2186	BINDING SITE FOR RESIDUE SO4 A 2001
5	AC5	SOFTWARE	HIS B:94 , ASN B:156 , GLY B:293 , ARG B:294 , NAD B:2401 , HOH B:2403	BINDING SITE FOR RESIDUE SO4 B 2002
6	AC6	SOFTWARE	HIS C:94 , ASN C:156 , GLY C:293 , ARG C:294 , NAD C:3401 , HOH C:3403	BINDING SITE FOR RESIDUE SO4 C 2003
7	AC7	SOFTWARE	CYS A:42 , ASN A:156 , GLY A:175 , GLY A:177 , PRO A:178 , LEU A:179 , SER A:198 , GLU A:199 , PRO A:200 , ARG A:204 , PHE A:243 , SER A:244 , ALA A:246 , ALA A:249 , LEU A:266 , GLY A:267 , LEU A:268 , ILE A:282 , ILE A:291 , THR A:292 , SO4 A:2001 , HOH A:2010 , HOH A:2028 , HOH A:2029 , HOH A:2038 , HOH A:2053 , HOH A:2137 , HOH A:2152 , HOH A:2153 , HOH A:2154 , HOH A:2166	BINDING SITE FOR RESIDUE NAD A 1401
8	AC8	SOFTWARE	CYS B:42 , ASN B:156 , GLY B:175 , GLY B:177 , PRO B:178 , LEU B:179 , SER B:198 , GLU B:199 , PRO B:200 , ARG B:204 , PHE B:243 , SER B:244 , ALA B:246 , LEU B:266 , GLY B:267 , LEU B:268 , ILE B:291 , THR B:292 , SO4 B:2002 , HOH B:2413 , HOH B:2423 , HOH B:2426 , HOH B:2443 , HOH B:2493 , HOH B:2521 , HOH B:2537 , HOH B:2560 , ILE C:282	BINDING SITE FOR RESIDUE NAD B 2401
9	AC9	SOFTWARE	ILE B:282 , CYS C:42 , ASN C:156 , GLY C:175 , GLY C:177 , PRO C:178 , LEU C:179 , SER C:198 , GLU C:199 , PRO C:200 , ARG C:204 , PHE C:243 , SER C:244 , ALA C:246 , LEU C:266 , GLY C:267 , LEU C:268 , ILE C:291 , THR C:292 , SO4 C:2003 , HOH C:3407 , HOH C:3420 , HOH C:3451 , HOH C:3484 , HOH C:3495 , HOH C:3513 , HOH C:3536	BINDING SITE FOR RESIDUE NAD C 3401

SS Bonds (0, 0)

Cis Peptide Bonds (9, 9)

Asymmetric Unit

No.	Residues
1	Pro A:61	-	Pro A:62
2	Tyr A:193	-	Pro A:194
3	Leu A:296	-	Trp A:297
4	Pro B:61	-	Pro B:62
5	Tyr B:193	-	Pro B:194
6	Leu B:296	-	Trp B:297
7	Pro C:61	-	Pro C:62
8	Tyr C:193	-	Pro C:194
9	Leu C:296	-	Trp C:297

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 3)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_ZINC	PS00059	Zinc-containing alcohol dehydrogenases signature.	TDH_PYRHO	66-80	3	A:66-80 B:66-80 C:66-80

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_ZINC	PS00059	Zinc-containing alcohol dehydrogenases signature.	TDH_PYRHO	66-80	1	A:66-80 - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_ZINC	PS00059	Zinc-containing alcohol dehydrogenases signature.	TDH_PYRHO	66-80	1	- B:66-80 -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_ZINC	PS00059	Zinc-containing alcohol dehydrogenases signature.	TDH_PYRHO	66-80	1	- - C:66-80

Exons (0, 0)

Sequences/Alignments

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:346
 aligned with TDH_PYRHO | O58389 from UniProtKB/Swiss-Prot  Length:348

    Alignment length:346
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342      
            TDH_PYRHO     3 EKMVAIMKTKPGYGAELVEVDVPKPGPGEVLIKVLATSICGTDLHIYEWNEWAQSRIKPPQIMGHEVAGEVVEIGPGVEGIEVGDYVSVETHIVCGKCYACRRGQYHVCQNTKIFGVDTDGVFAEYAVVPAQNIWKNPKSIPPEYATLQEPLGNAVDTVLAGPISGKSVLITGAGPLGLLGIAVAKASGAYPVIVSEPSDFRRELAKKVGADYVINPFEEDVVKEVMDITDGNGVDVFLEFSGAPKALEQGLQAVTPAGRVSLLGLYPGKVTIDFNNLIIFKALTIYGITGRHLWETWYTVSRLLQSGKLNLDPIITHKYKGFDKYEEAFELMRAGKTGKVVFMLK 348
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.......eeeeee.......eeeeeeeeee.hhhhhhhhhhhhhhhhhh...ee...eeeeeeeee...........eeee..ee....hhhhhh.hhhhh...ee...........eeeee...eee.....hhhhhhhhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhh....eeee..hhhhhhhhhhhh..eee.....hhhhhhhhhh....eeeeee...hhhhhhhhhhheeeeeeeee..........hhhhhh.....eeee......hhhhhhhhhhhhh........eeeeee...hhhhhhhhhhh....eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------ADH_ZINC       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dfv A   3 EKmVAImKTKPGYGAELVEVDVPKPGPGEVLIKVLATSICGTDLHIYEWNEWAQSRIKPPQImGHEVAGEVVEIGPGVEGIEVGDYVSVETHIVCGKCYACRRGQYHVCQNTKIFGVDTDGVFAEYAVVPAQNIWKNPKSIPPEYATLQEPLGNAVDTVLAGPISGKSVLITGAGPLGLLGIAVAKASGAYPVIVSEPSDFRRELAKKVGADYVINPFEEDVVKEVmDITDGNGVDVFLEFSGAPKALEQGLQAVTPAGRVSLLGLYPGKVTIDFNNLIIFKALTIYGITGRHLWETWYTVSRLLQSGKLNLDPIITHKYKGFDKYEEAFELmRAGKTGKVVFmLK 348
                              |   | 12        22        32        42        52        62  |     72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222      |232       242       252       262       272       282       292       302       312       322       332  |    342   |  
                              |   |                                                      65-MSE                                                                                                                                                             229-MSE                                                                                                   335-MSE    346-MSE
                              5-MSE                                                                                                                                                                                                                                                                                                                                                   
                                  9-MSE

Chain B from PDB  Type:PROTEIN  Length:346
 aligned with TDH_PYRHO | O58389 from UniProtKB/Swiss-Prot  Length:348

    Alignment length:346
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342      
            TDH_PYRHO     3 EKMVAIMKTKPGYGAELVEVDVPKPGPGEVLIKVLATSICGTDLHIYEWNEWAQSRIKPPQIMGHEVAGEVVEIGPGVEGIEVGDYVSVETHIVCGKCYACRRGQYHVCQNTKIFGVDTDGVFAEYAVVPAQNIWKNPKSIPPEYATLQEPLGNAVDTVLAGPISGKSVLITGAGPLGLLGIAVAKASGAYPVIVSEPSDFRRELAKKVGADYVINPFEEDVVKEVMDITDGNGVDVFLEFSGAPKALEQGLQAVTPAGRVSLLGLYPGKVTIDFNNLIIFKALTIYGITGRHLWETWYTVSRLLQSGKLNLDPIITHKYKGFDKYEEAFELMRAGKTGKVVFMLK 348
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.......eeeeee.......eeeeeeeeee.hhhhhhhhhhhhhhhhhh...ee...eeeeeeeee...........eeee..ee....hhhhhh.hhhhh...ee...........eeeee...eee.....hhhhhhhhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhh....eeee..hhhhhhhhhhhh..eee.....hhhhhhhhhh....eeeeee...hhhhhhhhhhheeeeeeeee..........hhhhhh.....eeee......hhhhhhhhhhhhh....hhh.eeeeee...hhhhhhhhhhh....eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------ADH_ZINC       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dfv B   3 EKmVAImKTKPGYGAELVEVDVPKPGPGEVLIKVLATSICGTDLHIYEWNEWAQSRIKPPQImGHEVAGEVVEIGPGVEGIEVGDYVSVETHIVCGKCYACRRGQYHVCQNTKIFGVDTDGVFAEYAVVPAQNIWKNPKSIPPEYATLQEPLGNAVDTVLAGPISGKSVLITGAGPLGLLGIAVAKASGAYPVIVSEPSDFRRELAKKVGADYVINPFEEDVVKEVmDITDGNGVDVFLEFSGAPKALEQGLQAVTPAGRVSLLGLYPGKVTIDFNNLIIFKALTIYGITGRHLWETWYTVSRLLQSGKLNLDPIITHKYKGFDKYEEAFELmRAGKTGKVVFmLK 348
                              |   | 12        22        32        42        52        62  |     72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222      |232       242       252       262       272       282       292       302       312       322       332  |    342   |  
                              |   |                                                      65-MSE                                                                                                                                                             229-MSE                                                                                                   335-MSE    346-MSE
                              5-MSE                                                                                                                                                                                                                                                                                                                                                   
                                  9-MSE

Chain C from PDB  Type:PROTEIN  Length:346
 aligned with TDH_PYRHO | O58389 from UniProtKB/Swiss-Prot  Length:348

    Alignment length:346
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342      
            TDH_PYRHO     3 EKMVAIMKTKPGYGAELVEVDVPKPGPGEVLIKVLATSICGTDLHIYEWNEWAQSRIKPPQIMGHEVAGEVVEIGPGVEGIEVGDYVSVETHIVCGKCYACRRGQYHVCQNTKIFGVDTDGVFAEYAVVPAQNIWKNPKSIPPEYATLQEPLGNAVDTVLAGPISGKSVLITGAGPLGLLGIAVAKASGAYPVIVSEPSDFRRELAKKVGADYVINPFEEDVVKEVMDITDGNGVDVFLEFSGAPKALEQGLQAVTPAGRVSLLGLYPGKVTIDFNNLIIFKALTIYGITGRHLWETWYTVSRLLQSGKLNLDPIITHKYKGFDKYEEAFELMRAGKTGKVVFMLK 348
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.......eeeeee.......eeeeeeeeee.hhhhhhhhhhhhhhhhhh...ee...eeeeeeeee...........eeee..ee....hhhhhhhhhhhh...ee...........eeeee...eee.....hhhhhhhhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhh....eeee..hhhhhhhhhhhh..eee.....hhhhhhhhhh....eeeeee...hhhhhhhhhhheeeeeeeee..........hhhhhh.....eeee......hhhhhhhhhhhhh....hhh.eeeeee...hhhhhhhhhhhh...eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------ADH_ZINC       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dfv C   3 EKmVAImKTKPGYGAELVEVDVPKPGPGEVLIKVLATSICGTDLHIYEWNEWAQSRIKPPQImGHEVAGEVVEIGPGVEGIEVGDYVSVETHIVCGKCYACRRGQYHVCQNTKIFGVDTDGVFAEYAVVPAQNIWKNPKSIPPEYATLQEPLGNAVDTVLAGPISGKSVLITGAGPLGLLGIAVAKASGAYPVIVSEPSDFRRELAKKVGADYVINPFEEDVVKEVmDITDGNGVDVFLEFSGAPKALEQGLQAVTPAGRVSLLGLYPGKVTIDFNNLIIFKALTIYGITGRHLWETWYTVSRLLQSGKLNLDPIITHKYKGFDKYEEAFELmRAGKTGKVVFmLK 348
                              |   | 12        22        32        42        52        62  |     72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222      |232       242       252       262       272       282       292       302       312       322       332  |    342   |  
                              |   |                                                      65-MSE                                                                                                                                                             229-MSE                                                                                                   335-MSE    346-MSE
                              5-MSE                                                                                                                                                                                                                                                                                                                                                   
                                  9-MSE

Legend:		→ Mismatch	(orange background)
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	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 (13, 13)

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