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Title :   CRYSTAL STRUCTURE OF GLUTAMYL-TRNA REDUCTASE FROM THERMOPLASMA VOLCANIUM (NUCLEOTIDE BINDING DOMAIN)

Authors :   K. Michalska, N. Marshall, S. Clancy, R. Puttagunta, A. Joachimiak, Mi Center For Structural Genomics (Mcsg)

Date :   20 Aug 10 (Deposition) - 01 Sep 10 (Release) - 01 Sep 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

Chains :   Asym./Biol. Unit : A

Keywords :   Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Reductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Michalska, N. Marshall, S. Clancy, R. Puttagunta, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Crystal Structure Of Glutamyl-Trna Reductase From Thermoplasma Volcanium (Nucleotide Binding Domain)
To Be Published
PubMed: search

Compounds

Molecule 1 - GLUTAMYL-TRNA REDUCTASE
	Chains	:	A
	EC Number	:	1.2.1.70
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG7
	Expression System Strain	:	BL21 MAGIC
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	NUCLEOTIDE BINDING DOMAIN
	Gene	:	HEMA, TV0590, TVG0579613
	Organism Scientific	:	THERMOPLASMA VOLCANIUM
	Organism Taxid	:	273116
	Strain	:	GSS1
	Synonym	:	GLUTR

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 12)

Sites (9, 9)

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:126 , LYS A:130 , MSE A:133 , LEU A:134 , GLU A:137	BINDING SITE FOR RESIDUE GOL A 142
2	AC2	SOFTWARE	SER A:4 , ILE A:5 , LYS A:101 , HOH A:151 , HOH A:187 , HOH A:203 , HOH A:210 , HOH A:211	BINDING SITE FOR RESIDUE GOL A 143
3	AC3	SOFTWARE	TYR A:39 , GLU A:62 , VAL A:66 , LEU A:67 , GOL A:145 , HOH A:170	BINDING SITE FOR RESIDUE GOL A 144
4	AC4	SOFTWARE	TYR A:39 , LYS A:43 , VAL A:44 , GLU A:62 , TYR A:63 , GLU A:64 , GOL A:144	BINDING SITE FOR RESIDUE GOL A 145
5	AC5	SOFTWARE	LEU A:29 , THR A:85 , LEU A:106 , GLY A:107 , ASN A:108 , LEU A:121	BINDING SITE FOR RESIDUE GOL A 146
6	AC6	SOFTWARE	ARG A:49 , SER A:87 , LYS A:88 , THR A:89 , HOH A:196 , HOH A:206 , HOH A:231	BINDING SITE FOR RESIDUE GOL A 147
7	AC7	SOFTWARE	LYS A:2 , VAL A:3 , SER A:4 , SER A:7 , ARG A:135 , HOH A:210 , HOH A:227	BINDING SITE FOR RESIDUE SO4 A 148
8	AC8	SOFTWARE	ASN A:26 , GLY A:48 , ARG A:49 , ASN A:50 , THR A:85 , HOH A:218 , HOH A:226	BINDING SITE FOR RESIDUE SO4 A 149
9	AC9	SOFTWARE	GLY A:27 , MSE A:28	BINDING SITE FOR RESIDUE SO4 A 150

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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

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Chain A from PDB  Type:PROTEIN  Length:138
 aligned with HEM1_THEVO | Q97B68 from UniProtKB/Swiss-Prot  Length:409

    Alignment length:138
                                   150       160       170       180       190       200       210       220       230       240       250       260       270        
           HEM1_THEVO   141 GKVSIPSIVYDIVRKNGGNKILLVGNGMLASEIAPYFSYPQYKVTVAGRNIDHVRAFAEKYEYEYVLINDIDSLIKNNDVIITATSSKTPIVEERSLMPGKLFIDLGNPPNIERGNNVITLDEIYEISKKNEMLREEK 278
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -------Shikimate_DH-3oj0A01 A:8-133                                                                                                  ----- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhh.eeee..hhhhhhhh..eeee.........hhhhh....eeee.............eehhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3oj0 A   1 GKVSIPSIVYDIVRKNGGNKILLVGNGmLASEIAPYFSYPQYKVTVAGRNIDHVRAFAEKYEYEYVLINDIDSLIKNNDVIITATSSKTPIVEERSLmPGKLFIDLGNPPNIERGNNVITLDEIYEISKKNEmLREEK 138
                                    10        20       |30        40        50        60        70        80        90       100       110       120       130  |     
                                                      28-MSE                                                                98-MSE                            133-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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (HEM1_THEVO | Q97B68)

molecular function
	GO:0050661	NADP binding	Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
	GO:0008883	glutamyl-tRNA reductase activity	Catalysis of the reaction: (S)-4-amino-5-oxopentanoate + NADP(+) + tRNA(Glu) = L-glutamyl-tRNA(Glu) + H(+) + NADPH.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0006779	porphyrin-containing compound biosynthetic process	The chemical reactions and pathways resulting in the formation of any member of a large group of derivatives or analogs of porphyrin. Porphyrin consists of a ring of four pyrrole nuclei linked each to the next at their alpha positions through a methine group.
	GO:0006782	protoporphyrinogen IX biosynthetic process	The chemical reactions and pathways resulting in the formation of protoporphyrinogen IX.
	GO:0033014	tetrapyrrole biosynthetic process	The chemical reactions and pathways leading to the formation of tetrapyrroles, natural pigments containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next.

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