1H4V - JenaLib

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Title :   HISTIDYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS (LIGAND FREE)

Authors :   S. Cusack, A. Yaremchuk, M. Tukalo

Date :   14 May 01 (Deposition) - 18 Jun 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Trna Synthetase, Class Iia Aminoacyl-Trna Synthetase, Atp + L-Histidine Trna(His)-> Amp + Ppi + L-Histidyl-Trna(His) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Yaremchuk, M. Tukalo, M. Grotli, S. Cusack
A Succession Of Substrate Induced Conformational Changes Ensures The Amino Acid Specificity Of Thermus Thermophilus Prolyl-Trna Synthetase: Comparison With Histidyl-Trna Synthetase
J. Mol. Biol. V. 309 989 2001
PubMed-ID: 11399074 | Reference-DOI: 10.1006/JMBI.2001.4712
(for further references see the PDB file header)

Molecule 1 - HISTIDYL-TRNA SYNTHETASE
	Chains	:	B
	EC Number	:	6.1.1.21
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	262724
	Other Details	:	LIGAND FREE FORM OF THE ENZYME
	Strain	:	HB27

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG B:18 , ARG B:22 , HOH B:2065	BINDING SITE FOR RESIDUE SO4 B1422

(no "SS Bond" information available for 1H4V)

Asymmetric Unit

No.	Residues
1	Gln B:100	-	Pro B:101
2	Arg B:352	-	Pro B:353

(no "SAP(SNP)/Variant" information available for 1H4V)

(no "PROSITE Motif" information available for 1H4V)

(no "Exon" information available for 1H4V)

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 B from PDB  Type:PROTEIN  Length:404
 aligned with SYH_THET2 | P62374 from UniProtKB/Swiss-Prot  Length:421

    Alignment length:420
                                    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       321       331       341       351       361       371       381       391       401       411       421
            SYH_THET2     2 TARAVRGTKDLFGKELRMHQRIVATARKVLEAAGALELVTPIFEETQVFEKGVGAATDIVRKEMFTFQDRGGRSLTLRPEGTAAMVRAYLEHGMKVWPQPVRLWMAGPMFRAERPQKGRYRQFHQVNYEALGSENPILDAEAVVLLYECLKELGLRRLKVKLSSVGDPEDRARYNAYLREVLSPHREALSEDSKERLELNPMRILDSKSERDQALLKELGVRPMLDFLGEEARAHLKEVERHLERLSVPYELEPALVRGLDYYVRTAFEVHHEEIGAQSALGGGGRYDGLSELLGGPRVPGVGFAFGVERVALALEAEGFGLPEEKGPDLYLIPLTEEAVAEAFYLAEALRPRLRAEYALAPRKPAKGLEEALKRGAAFAGFLGEDELRAGEVTLKRLATGEQVRLSREEVPGYLLQALG 421
               SCOP domains d1h4vb2 B:2-325 Histidyl-tRNA synthetase (HisRS)                                                                                                                                                                                                                                                                                    d1h4vb1 B:326-421 Histidyl-tRNA synthetase (HisRS), C-terminal domain                            SCOP domains
               CATH domains 1h4vB01 B:2-323 Bira Bifunctional Protein; Domain 2                                                                                                                                                                                                                                                                               1h4vB02 B:324-418  [code=3.40.50.800, no name defined]                                         --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhhhh..ee.....eee.hhhh.....------....eee.....eeee...hhhhhhhhhhhhhhhhh...eeeeeeeeee.....----..eeeeeeeeee...hhhhhhhhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh...eee...........eeeeeeee.------.eeeeeee..hhhhhh......eeeeeeehhhhhhhhhhh...........eeeee.hhhhhhhhhhhhhhhh....eee.....hhhhhhhhhhhh...eeeeehhhhhhhheeeeee.....eeeee..hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1h4v B   2 TARAVRGTKDLFGKELRMHQRIVATARKVLEAAGALELVTPIFEETQVFEKGVGA------KEMFTFQDRGGRSLTLRPEGTAAMVRAYLEHGMKVWPQPVRLWMAGPMFRAERP----YRQFHQVNYEALGSENPILDAEAVVLLYECLKELGLRRLKVKLSSVGDPEDRARYNAYLREVLSPHREALSEDSKERLEENPMRILDSKSERDQALLKELGVRPMLDFLGEEARAHLKEVERHLERLSVPYELEPALVRGLDYYVRTAFEVHH------SALGGGGRYDGLSELLGGPRVPGVGFAFGVERVALALEAEGFGLPEEKGPDLYLIPLTEEAVAEAFYLAEALRPRLRAEYALAPRKPAKGLEEALKRGAAFAGFLGEDELRAGEVTLKRLATGEQVRLSREEVPGYLLQALG 421
                                    11        21        31        41        51    |    - |      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       321       331       341       351       361       371       381       391       401       411       421
                                                                                 56     63                                                  116  121                                                                                                                                                     273    280

Chain B from PDB  Type:PROTEIN  Length:404
 aligned with SYH_THET8 | P56194 from UniProtKB/Swiss-Prot  Length:421

    Alignment length:420
                                    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       321       331       341       351       361       371       381       391       401       411       421
            SYH_THET8     2 TARAVRGTKDLFGKELRMHQRIVATARKVLEAAGALELVTPIFEETQVFEKGVGAATDIVRKEMFTFQDRGGRSLTLRPEGTAAMVRAYLEHGMKVWPQPVRLWMAGPMFRAERPQKGRYRQFHQVNYEALGSENPILDAEAVVLLYECLKELGLRRLKVKLSSVGDPEDRARYNAYLREVLSPHREALSEDSKERLELNPMRILDSKSERDQALLKELGVRPMLDFLGEEARAHLKEVERHLERLSVPYELEPALVRGLDYYVRTAFEVHHEEIGAQSALGGGGRYDGLSELLGGPRVPGVGFAFGVERVALALEAEGFGLPEEKGPDLYLIPLTEEAVAEAFYLAEALRPRLRAEYALAPRKPAKGLEEALKRGAAFAGFLGEDELRAGEVTLKRLATGEQVRLSREEVPGYLLQALG 421
               SCOP domains d1h4vb2 B:2-325 Histidyl-tRNA synthetase (HisRS)                                                                                                                                                                                                                                                                                    d1h4vb1 B:326-421 Histidyl-tRNA synthetase (HisRS), C-terminal domain                            SCOP domains
               CATH domains 1h4vB01 B:2-323 Bira Bifunctional Protein; Domain 2                                                                                                                                                                                                                                                                               1h4vB02 B:324-418  [code=3.40.50.800, no name defined]                                         --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhhhh..ee.....eee.hhhh.....------....eee.....eeee...hhhhhhhhhhhhhhhhh...eeeeeeeeee.....----..eeeeeeeeee...hhhhhhhhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh...eee...........eeeeeeee.------.eeeeeee..hhhhhh......eeeeeeehhhhhhhhhhh...........eeeee.hhhhhhhhhhhhhhhh....eee.....hhhhhhhhhhhh...eeeeehhhhhhhheeeeee.....eeeee..hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1h4v B   2 TARAVRGTKDLFGKELRMHQRIVATARKVLEAAGALELVTPIFEETQVFEKGVGA------KEMFTFQDRGGRSLTLRPEGTAAMVRAYLEHGMKVWPQPVRLWMAGPMFRAERP----YRQFHQVNYEALGSENPILDAEAVVLLYECLKELGLRRLKVKLSSVGDPEDRARYNAYLREVLSPHREALSEDSKERLEENPMRILDSKSERDQALLKELGVRPMLDFLGEEARAHLKEVERHLERLSVPYELEPALVRGLDYYVRTAFEVHH------SALGGGGRYDGLSELLGGPRVPGVGFAFGVERVALALEAEGFGLPEEKGPDLYLIPLTEEAVAEAFYLAEALRPRLRAEYALAPRKPAKGLEEALKRGAAFAGFLGEDELRAGEVTLKRLATGEQVRLSREEVPGYLLQALG 421
                                    11        21        31        41        51    |    - |      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       321       331       341       351       361       371       381       391       401       411       421
                                                                                 56     63                                                  116  121                                                                                                                                                     273    280

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 "Pfam Domain" information available for 1H4V)

Asymmetric Unit(hide GO term definitions)

Chain B (SYH_THET8 | P56194)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004812	aminoacyl-tRNA ligase activity	Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP.
	GO:0004821	histidine-tRNA ligase activity	Catalysis of the reaction: ATP + L-histidine + tRNA(His) = AMP + diphosphate + L-histidyl-tRNA(His).
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
	GO:0006427	histidyl-tRNA aminoacylation	The process of coupling histidine to histidyl-tRNA, catalyzed by histidyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA.
	GO:0006418	tRNA aminoacylation for protein translation	The synthesis of aminoacyl tRNA by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA, to be used in ribosome-mediated polypeptide synthesis.
	GO:0006412	translation	The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain B (SYH_THET2 | P62374)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004812	aminoacyl-tRNA ligase activity	Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP.
	GO:0004821	histidine-tRNA ligase activity	Catalysis of the reaction: ATP + L-histidine + tRNA(His) = AMP + diphosphate + L-histidyl-tRNA(His).
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
	GO:0006427	histidyl-tRNA aminoacylation	The process of coupling histidine to histidyl-tRNA, catalyzed by histidyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA.
	GO:0006418	tRNA aminoacylation for protein translation	The synthesis of aminoacyl tRNA by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA, to be used in ribosome-mediated polypeptide synthesis.
	GO:0006412	translation	The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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	Cis Peptide Bonds
		Arg B:352 - Pro B:353	[ RasMol ]
		Gln B:100 - Pro B:101	[ RasMol ]

Biological Unit
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	1h4v
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	SYH_THET8 \| P56194
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	6.1.1.21
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UniProtKB/Swiss-Prot
	SYH_THET2 \| P62374	:	4rdx
	SYH_THET8 \| P56194	:	1adj 1ady

1adj	HISTIDYL-TRNA SYNTHETASE IN COMPLEX WITH HISTIDINE
1ady	HISTIDYL-TRNA SYNTHETASE IN COMPLEX WITH HISTIDYL-ADENYLATE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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Exons (0, 0)

Sequences/Alignments

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SCOP Domains (2, 2)

CATH Domains (2, 2)

Pfam Domains (0, 0)

Gene Ontology (9, 18)

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