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Title :   CRYSTAL STRUCTURE OF GLYCEROL-3-PHOSPHATE DEHYDROGENASE (TM0378) FROM THERMOTOGA MARITIMA AT 2.00 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   29 Mar 05 (Deposition) - 12 Apr 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A,B

Keywords :   Tm0378, Glycerol-3-Phosphate Dehydrogenase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Glycerol-3-Phosphate Dehydrogenase (Tm0378) From Thermotoga Maritima At 2. 00 A Resolution
To Be Published
PubMed: search

Molecule 1 - GLYCEROL-3-PHOSPHATE DEHYDROGENASE
	Chains	:	A, B
	EC Number	:	1.1.1.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TM0378
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	243274
	Strain	:	MSB8

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (6, 32)

No.	Name	Count	Type	Full Name
1	G3H	1	Ligand/Ion	GLYCERALDEHYDE-3-PHOSPHATE
2	G3P	1	Ligand/Ion	SN-GLYCEROL-3-PHOSPHATE
3	MPD	3	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
4	MRD	5	Ligand/Ion	(4R)-2-METHYLPENTANE-2,4-DIOL
5	MSE	20	Mod. Amino Acid	SELENOMETHIONINE
6	NDP	2	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ALA A:10 , GLY A:11 , SER A:12 , TRP A:13 , ARG A:33 , ARG A:34 , TYR A:49 , ALA A:75 , PRO A:77 , TYR A:80 , HIS A:84 , SER A:99 , LYS A:100 , SER A:129 , HIS A:130 , ALA A:131 , ARG A:243 , ASN A:265 , GLN A:266 , VAL A:267 , GLU A:269 , HOH A:621 , HOH A:626 , HOH A:629 , HOH A:634 , HOH A:641 , HOH A:648 , HOH A:651 , HOH A:663 , HOH A:664 , HOH A:687 , G3P B:600	BINDING SITE FOR RESIDUE NDP A 500
02	AC2	SOFTWARE	HOH A:613 , LYS B:100 , GLY B:127 , PRO B:128 , SER B:129 , HIS B:130 , LYS B:179 , ASN B:180 , ASP B:232 , THR B:236 , TYR B:241 , SER B:242 , ARG B:243 , ASN B:244 , NDP B:500 , HOH B:618 , HOH B:635	BINDING SITE FOR RESIDUE G3H A 600
03	AC3	SOFTWARE	ARG A:87 , G3H A:600 , ALA B:10 , GLY B:11 , SER B:12 , TRP B:13 , ARG B:33 , ARG B:34 , TYR B:49 , ALA B:75 , PRO B:77 , TYR B:80 , GLU B:83 , HIS B:84 , SER B:99 , LYS B:100 , SER B:129 , HIS B:130 , ALA B:131 , ARG B:243 , ASN B:265 , GLN B:266 , VAL B:267 , GLU B:269 , HOH B:618 , HOH B:620 , HOH B:621 , HOH B:633 , HOH B:635 , HOH B:636 , HOH B:638 , HOH B:652 , HOH B:653	BINDING SITE FOR RESIDUE NDP B 500
04	AC4	SOFTWARE	LYS A:100 , GLY A:127 , SER A:129 , HIS A:130 , LYS A:179 , ASP A:232 , THR A:236 , TYR A:241 , SER A:242 , ARG A:243 , ASN A:244 , NDP A:500 , HOH A:621 , HOH A:626 , HOH B:630	BINDING SITE FOR RESIDUE G3P B 600
05	AC5	SOFTWARE	ALA B:185 , ILE B:188 , GLU B:293 , SER B:307 , MSE B:308 , LEU B:311 , MRD B:602 , HOH B:684	BINDING SITE FOR RESIDUE MRD B 601
06	AC6	SOFTWARE	ALA A:185 , ILE A:188 , LEU A:189 , GLU A:293 , VAL A:294 , SER A:307 , MSE A:308 , LEU A:311 , HOH A:735	BINDING SITE FOR RESIDUE MRD A 601
07	AC7	SOFTWARE	THR A:140 , MSE B:312 , MRD B:601 , HOH B:684	BINDING SITE FOR RESIDUE MRD B 602
08	AC8	SOFTWARE	ARG B:243 , ARG B:246 , LEU B:260 , SER B:263 , SER B:264 , GLN B:266 , VAL B:268	BINDING SITE FOR RESIDUE MRD B 603
09	AC9	SOFTWARE	VAL A:43 , SER A:44 , MSE B:3 , GLU B:151	BINDING SITE FOR RESIDUE MRD B 604
10	BC1	SOFTWARE	ARG A:205 , LEU A:311 , HOH A:735	BINDING SITE FOR RESIDUE MPD A 602
11	BC2	SOFTWARE	ARG A:243 , ARG A:246 , LEU A:260 , SER A:263 , SER A:264 , GLN A:266	BINDING SITE FOR RESIDUE MPD A 603
12	BC3	SOFTWARE	GLY A:254 , PHE A:255	BINDING SITE FOR RESIDUE MPD A 604

(no "SS Bond" information available for 1Z82)

(no "Cis Peptide Bond" information available for 1Z82)

(no "SAP(SNP)/Variant" information available for 1Z82)

(no "PROSITE Motif" information available for 1Z82)

(no "Exon" information available for 1Z82)

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:312
 aligned with A0A0F6AK91_T | A0A0F6AK91 from UniProtKB/TrEMBL  Length:321

    Alignment length:312
                             1                                                                                                                                                                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309  
         A0A0F6AK91_T     - -MRFFVLGAGSWGTVFAQILHENGEEVVLWARRKEIVDLINVSHTSPYVEESKITVRATNDLEEIKKEDILVIAIPVQYIREHLLRLPVKPSMVLNLSKGIEIKTGKRVSEIVEEILGCPYAVLSGPSHAEEVAKKLPTAVTLAGENSKELQKRISTEYFRVYTCEDVVGVEIAGALKNVIAIAAGILDGFGGWDNAKAALETRGIYEIARFGMFFGADQKTFMGLAGIGDLMVTCNSRYSRNRRFGELIARGFNPLKLLESSNQVVEGAFTVKAVMKIAKENKIDMPISEEVYRVVYEGKPPLQSMRDLMR 311
               SCOP domains d1z82a1 A:2-166 automated matches                                                                                                                                    d1z82a2 A:167-313 automated matches                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1z82A02 A:177-313 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhh............eee.hhhhh...eeeee..hhhhhhhhhh.......eeee...........hhhhhhhhhh...eeeee...hhhhhhh...eeeeeee.hhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhh...hhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhhhh...hhhhhhhhhhhhh..hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1z82 A   2 EmRFFVLGAGSWGTVFAQmLHENGEEVILWARRKEIVDLINVSHTSPYVEESKITVRATNDLEEIKKEDILVIAIPVQYIREHLLRLPVKPSmVLNLSKGIEIKTGKRVSEIVEEILGCPYAVLSGPSHAEEVAKKLPTAVTLAGENSKELQKRISTEYFRVYTCEDVVGVEIAGALKNVIAIAAGILDGFGGWDNAKAALETRGIYEIARFGmFFGADQKTFmGLAGIGDLmVTCNSRYSRNRRFGELIARGFNPLKLLESSNQVVEGAFTVKAVmKIAKENKIDmPISEEVYRVVYEGKPPLQSmRDLmR 313
                             |      11        21        31        41        51        61        71        81        91  |    101       111       121       131       141       151       161       171       181       191       201       211   |   221   |   231  |    241       251       261       271      |281      |291       301      |311| 
                             |               20-MSE                                                                    94-MSE                                                                                                                  215-MSE   225-MSE  234-MSE                                     278-MSE   288-MSE             308-MSE 
                             3-MSE                                                                                                                                                                                                                                                                                                              312-MSE

Chain B from PDB  Type:PROTEIN  Length:312
 aligned with A0A0F6AK91_T | A0A0F6AK91 from UniProtKB/TrEMBL  Length:321

    Alignment length:312
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310  
         A0A0F6AK91_T     1 MRFFVLGAGSWGTVFAQILHENGEEVVLWARRKEIVDLINVSHTSPYVEESKITVRATNDLEEIKKEDILVIAIPVQYIREHLLRLPVKPSMVLNLSKGIEIKTGKRVSEIVEEILGCPYAVLSGPSHAEEVAKKLPTAVTLAGENSKELQKRISTEYFRVYTCEDVVGVEIAGALKNVIAIAAGILDGFGGWDNAKAALETRGIYEIARFGMFFGADQKTFMGLAGIGDLMVTCNSRYSRNRRFGELIARGFNPLKLLESSNQVVEGAFTVKAVMKIAKENKIDMPISEEVYRVVYEGKPPLQSMRDLMRR 312
               SCOP domains d1z82b1 B:3-166 automated matches                                                                                                                                   d1z82b2 B:167-314 automated matches                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1z82B02 B:177-314 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee..hhhhhhhhhhhhhh...eeee..hhhhhhhhhhh..............ee.hhhhh....eeee..hhhhhhhhhh.......eeee...........hhhhhhhhhh...eeeee...hhhhhhh...eeeeeee.hhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh..hhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhh....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1z82 B   3 mRFFVLGAGSWGTVFAQmLHENGEEVILWARRKEIVDLINVSHTSPYVEESKITVRATNDLEEIKKEDILVIAIPVQYIREHLLRLPVKPSmVLNLSKGIEIKTGKRVSEIVEEILGCPYAVLSGPSHAEEVAKKLPTAVTLAGENSKELQKRISTEYFRVYTCEDVVGVEIAGALKNVIAIAAGILDGFGGWDNAKAALETRGIYEIARFGmFFGADQKTFmGLAGIGDLmVTCNSRYSRNRRFGELIARGFNPLKLLESSNQVVEGAFTVKAVmKIAKENKIDmPISEEVYRVVYEGKPPLQSmRDLmRR 314
                            |       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  
                            |               20-MSE                                                                    94-MSE                                                                                                                  215-MSE   225-MSE  234-MSE                                     278-MSE   288-MSE             308-MSE  
                            3-MSE                                                                                                                                                                                                                                                                                                              312-MSE

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

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 (60)

Homologous Superfamily: N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 (59)

Thermotoga maritima msb8. Organism_taxid: 243274. Strain: msb8. (1)

1a	1z82B02	B:177-314
1b	1z82A02	A:177-313

(no "Pfam Domain" information available for 1Z82)

Asymmetric/Biological Unit(hide GO term definitions)

(no "Gene Ontology" information available for 1Z82)

Asymmetric/Biological Unit
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Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (6, 32)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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