2ZXH - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   STRUCTURE OF AQUIFEX AEOLICUS GIDA IN THE FORM I CRYSTAL

Authors :   T. Numata, T. Osawa

Date :   24 Dec 08 (Deposition) - 19 May 09 (Release) - 04 Apr 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.20

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

Keywords :   5-Carboxymethylaminomethyluridine, Modification, Trna, Wobble Uridine, Fad, Fad-Binding Protein, Trna Modification Enzyme (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Osawa, K. Ito, H. Inanaga, O. Nureki, K. Tomita, T. Numata
Conserved Cysteine Residues Of Gida Are Essential For Biogenesis Of 5-Carboxymethylaminomethyluridine At Trna Anticodon
Structure V. 17 713 2009
PubMed-ID: 19446527 | Reference-DOI: 10.1016/J.STR.2009.03.013

Molecule 1 - TRNA URIDINE 5-CARBOXYMETHYLAMINOMETHYL MODIFICATION ENZYME MNMG
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21-CODONPLUS (DE3)-RIL
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	AQ_761
	Organism Scientific	:	AQUIFEX AEOLICUS
	Organism Taxid	:	63363
	Synonym	:	GIDA, GLUCOSE-INHIBITED DIVISION PROTEIN A

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 5)

No.	Name	Count	Type	Full Name
1	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	PO4	3	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:13 , GLY A:14 , GLY A:15 , GLY A:16 , HIS A:17 , ALA A:18 , VAL A:37 , LEU A:38 , LYS A:57 , GLU A:125 , VAL A:126 , THR A:155 , THR A:156 , GLY A:157 , PHE A:159 , ARG A:175 , SER A:181 , THR A:200 , GLY A:201 , THR A:202 , TYR A:348 , ILE A:350 , GLY A:376 , ASN A:377 , THR A:382 , GLY A:383 , ALA A:387 , ARG A:434	BINDING SITE FOR RESIDUE FAD A 618
2	AC2	SOFTWARE	ILE B:13 , GLY B:14 , GLY B:15 , GLY B:16 , HIS B:17 , ALA B:18 , LEU B:38 , CYS B:48 , LYS B:57 , GLU B:124 , VAL B:126 , THR B:155 , THR B:156 , GLY B:157 , THR B:158 , PHE B:159 , SER B:181 , THR B:200 , GLY B:201 , TYR B:348 , ILE B:350 , GLY B:376 , ASN B:377 , THR B:382 , GLY B:383 , ALA B:387 , ARG B:434	BINDING SITE FOR RESIDUE FAD B 618
3	AC3	SOFTWARE	LYS A:89 , ARG A:439 , LYS B:277 , ASP B:296	BINDING SITE FOR RESIDUE PO4 A 619
4	AC4	SOFTWARE	LYS A:277 , ASP A:296 , ARG B:439	BINDING SITE FOR RESIDUE PO4 A 620
5	AC5	SOFTWARE	PRO B:281 , ARG B:282 , LYS B:297 , ARG B:299 , HIS B:300 , GLN B:301	BINDING SITE FOR RESIDUE PO4 B 619

(no "SS Bond" information available for 2ZXH)

Asymmetric/Biological Unit

No.	Residues
1	Asp A:223	-	Pro A:224
2	Glu A:233	-	Pro A:234
3	Asp B:223	-	Pro B:224
4	Glu B:233	-	Pro B:234

(no "SAP(SNP)/Variant" information available for 2ZXH)

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GIDA_1	PS01280	Glucose inhibited division protein A family signature 1.	MNMG_AQUAE	280-294	2	A:280-294 B:280-294
2	GIDA_2	PS01281	Glucose inhibited division protein A family signature 2.	MNMG_AQUAE	375-398	2	A:375-398 B:375-398

(no "Exon" information available for 2ZXH)

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:603
 aligned with MNMG_AQUAE | O66962 from UniProtKB/Swiss-Prot  Length:617

    Alignment length:611
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615 
           MNMG_AQUAE     6 DEFDVVVIGGGHAGIEAALAAARMGAKTAMFVLNADTIGQMSCNPAIGGIAKGIVVREIDALGGEMGKAIDQTGIQFKMLNTRKGKAVQSPRAQADKKRYREYMKKVCENQENLYIKQEEVVDIIVKNNQVVGVRTNLGVEYKTKAVVVTTGTFLNGVIYIGDKMIPGGRLGEPRSEGLSDFYRRFDFPLIRFKTGTPARLDKRTIDFSALEVAPGDDPPPKFSFWTEPVGSYWFPKGKEQVNCWITYTTPKTHEIIRKNLHRTALYGGLIKGIGPRYCPSIEDKIVKFPDKERHQIFLEPEGLDTIEIYPNGLSTSLPEEVQWEMYRSIPGLENVVLIRPAYAIEYDVVPPTELYPTLETKKIRGLFHAGNFNGTTGYEEAAGQGIVAGINAALRAFGKEPIYLRRDESYIGVMIDDLTTKGVTEPYRLFTSRSEYRLYIRQDNAILRLAKLGRELGLLSEEQYKLVKELEREIEKWKEFYKSERVSVAVGGDTRSYSVATLMTMNYTLDDVKEKFGYEVPQHPYVKEEVEIQLKYEPYIERERKLNEKLKKLEDTKIPPDIDYDKIPGLTKEAREKLKKFKPITVGQASRIDGITPAAITALLVYLGKL 616
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..hhhhhhhhhhhhhh...eeee..hhhhh.......eee..hhhhhhhhhhhhh.hhhhhhhhheee..ee.........eeeeeehhhhhhhhhhhhhhh...eeee...eeeeeee..eeeeeee....eeeeeeeee........eeee..eeee..........hhhhhhhhh....eeeeeee..eee.hhh.....eee.............................eeeee.hhhhhhhhhhhhhhh...............................eeeeee......eeeee......hhhhhhhhhh.........eee..eeeeeee.hhhhh...........eee.hhhhh..hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh.....................hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..--------....hhhhhhhh...hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhh...hhhhhhhh...hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GIDA_1         --------------------------------------------------------------------------------GIDA_2  PDB: A:375-398  -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zxh A   6 DEFDVVVIGGGHAGIEAALAAARMGAKTAMFVLNADTIGQMSCNPAIGGIAKGIVVREIDALGGEMGKAIDQTGIQFKMLNTRKGKAVQSPRAQADKKRYREYMKKVCENQENLYIKQEEVVDIIVKNNQVVGVRTNLGVEYKTKAVVVTTGTFLNGVIYIGDKMIPGGRLGEPRSEGLSDFYRRFDFPLIRFKTGTPARLDKRTIDFSALEVAPGDDPPPKFSFWTEPVGSYWFPKGKEQVNCWITYTTPKTHEIIRKNLHRTALYGGLIKGIGPRYCPSIEDKIVKFPDKERHQIFLEPEGLDTIEIYPNGLSTSLPEEVQWEMYRSIPGLENVVLIRPAYAIEYDVVPPTELYPTLETKKIRGLFHAGNFNGTTGYEEAAGQGIVAGINAALRAFGKEPIYLRRDESYIGVMIDDLTTKGVTEPYRLFTSRSEYRLYIRQDNAILRLAKLGRELGLLSEEQYKLVKELEREIEKWKEFYKSERV--------RSYSVATLMTMNYTLDDVKEKFGYEVPQHPYVKEEVEIQLKYEPYIERERKLNEKLKKLEDTKIPPDIDYDKIPGLTKEAREKLKKFKPITVGQASRIDGITPAAITALLVYLGKL 616
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485      |  -     | 505       515       525       535       545       555       565       575       585       595       605       615 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                492      501

Chain B from PDB  Type:PROTEIN  Length:601
 aligned with MNMG_AQUAE | O66962 from UniProtKB/Swiss-Prot  Length:617

    Alignment length:609
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605         
           MNMG_AQUAE     6 DEFDVVVIGGGHAGIEAALAAARMGAKTAMFVLNADTIGQMSCNPAIGGIAKGIVVREIDALGGEMGKAIDQTGIQFKMLNTRKGKAVQSPRAQADKKRYREYMKKVCENQENLYIKQEEVVDIIVKNNQVVGVRTNLGVEYKTKAVVVTTGTFLNGVIYIGDKMIPGGRLGEPRSEGLSDFYRRFDFPLIRFKTGTPARLDKRTIDFSALEVAPGDDPPPKFSFWTEPVGSYWFPKGKEQVNCWITYTTPKTHEIIRKNLHRTALYGGLIKGIGPRYCPSIEDKIVKFPDKERHQIFLEPEGLDTIEIYPNGLSTSLPEEVQWEMYRSIPGLENVVLIRPAYAIEYDVVPPTELYPTLETKKIRGLFHAGNFNGTTGYEEAAGQGIVAGINAALRAFGKEPIYLRRDESYIGVMIDDLTTKGVTEPYRLFTSRSEYRLYIRQDNAILRLAKLGRELGLLSEEQYKLVKELEREIEKWKEFYKSERVSVAVGGDTRSYSVATLMTMNYTLDDVKEKFGYEVPQHPYVKEEVEIQLKYEPYIERERKLNEKLKKLEDTKIPPDIDYDKIPGLTKEAREKLKKFKPITVGQASRIDGITPAAITALLVYLG 614
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---GIDA-2zxhB01 B:9-406                                                                                                                                                                                                                                                                                                                                                                                          -------------------------------------------------------------------------------------------------------------------------------------GIDA_assoc_3-2zxhB03 B:540-611                                          --- Pfam domains (1)
           Pfam domains (2) ---GIDA-2zxhB02 B:9-406                                                                                                                                                                                                                                                                                                                                                                                          -------------------------------------------------------------------------------------------------------------------------------------GIDA_assoc_3-2zxhB04 B:540-611                                          --- Pfam domains (2)
         Sec.struct. author .eeeeeee..hhhhhhhhhhhhhh...eeee..hhhhh.......eee..hhhhhhhhhhhhh.hhhhhhhhheee..ee.........eeeeeehhhhhhhhhhhhhhh...eeee...eeeeeee..eeeeeee....eeeeeeeee........eeee..eeee..........hhhhhhhhh....eeeeeee..eee.hhh.....eee.............................eeeee.hhhhhhhhhhhhhhh..........hhhhh................eeeeee......eeeee......hhhhhhhhhh.........eee..eeeeeee.hhhhh...........eee.hhhhh..hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh.....................hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..--------...hhhhhhhhh...hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhh...hhhhhhhh...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GIDA_1         --------------------------------------------------------------------------------GIDA_2  PDB: B:375-398  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zxh B   6 DEFDVVVIGGGHAGIEAALAAARMGAKTAMFVLNADTIGQMSCNPAIGGIAKGIVVREIDALGGEMGKAIDQTGIQFKMLNTRKGKAVQSPRAQADKKRYREYMKKVCENQENLYIKQEEVVDIIVKNNQVVGVRTNLGVEYKTKAVVVTTGTFLNGVIYIGDKMIPGGRLGEPRSEGLSDFYRRFDFPLIRFKTGTPARLDKRTIDFSALEVAPGDDPPPKFSFWTEPVGSYWFPKGKEQVNCWITYTTPKTHEIIRKNLHRTALYGGLIKGIGPRYCPSIEDKIVKFPDKERHQIFLEPEGLDTIEIYPNGLSTSLPEEVQWEMYRSIPGLENVVLIRPAYAIEYDVVPPTELYPTLETKKIRGLFHAGNFNGTTGYEEAAGQGIVAGINAALRAFGKEPIYLRRDESYIGVMIDDLTTKGVTEPYRLFTSRSEYRLYIRQDNAILRLAKLGRELGLLSEEQYKLVKELEREIEKWKEFYKSERV--------RSYSVATLMTMNYTLDDVKEKFGYEVPQHPYVKEEVEIQLKYEPYIERERKLNEKLKKLEDTKIPPDIDYDKIPGLTKEAREKLKKFKPITVGQASRIDGITPAAITALLVYLG 614
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485      |  -     | 505       515       525       535       545       555       565       575       585       595       605         
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                492      501

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 "SCOP Domain" information available for 2ZXH)

(no "CATH Domain" information available for 2ZXH)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: GIDA (2)

Aquifex aeolicus (2)

1a	GIDA-2zxhB01	B:9-406
1b	GIDA-2zxhB02	B:9-406

Clan: no clan defined [family: GIDA_assoc_3] (2)

Family: GIDA_assoc_3 (2)

Aquifex aeolicus (2)

2a	GIDA_assoc_3-2zxhB03	B:540-611
2b	GIDA_assoc_3-2zxhB04	B:540-611

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (MNMG_AQUAE | O66962)

molecular function
	GO:0050660	flavin adenine dinucleotide binding	Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
	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:0008033	tRNA processing	The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
	GO:0002098	tRNA wobble uridine modification	The process in which a uridine in position 34 of a tRNA is post-transcriptionally modified.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Asp A:223 - Pro A:224	[ RasMol ]
		Asp B:223 - Pro B:224	[ RasMol ]
		Glu A:233 - Pro A:234	[ RasMol ]
		Glu B:233 - Pro B:234	[ RasMol ]

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	2zxh
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	MNMG_AQUAE \| O66962	:	2zxi

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

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