1NXG - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   THE F383A VARIANT OF TYPE II CITRATE SYNTHASE COMPLEXED WITH NADH

Authors :   R. Maurus, N. T. Nguyen, D. J. Stokell, A. Ayed, P. G. Hultin, H. W. Duckwo G. D. Brayer

Date :   10 Feb 03 (Deposition) - 08 Apr 03 (Release) - 06 Nov 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Nadh, Citrate Synthase, F383A, Allosteric, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Maurus, N. T. Nguyen, D. J. Stokell, A. Ayed, P. G. Hultin, H. W. Duckworth, G. D. Brayer
Insights Into The Evolution Of Allosteric Properties. The Nadh Binding Site Of Hexameric Type Ii Citrate Synthases.
Biochemistry V. 42 5555 2003
PubMed-ID: 12741811 | Reference-DOI: 10.1021/BI020622S

Molecule 1 - CITRATE SYNTHASE
	Chains	:	A, B
	EC Number	:	2.3.3.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	GLTA OR GLUT OR ICDB OR B0720
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	NAI	2	Ligand/Ion	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 18)

No.	Name	Count	Type	Full Name
1	NAI	6	Ligand/Ion	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
2	SO4	12	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:407 , HOH B:54 , ASN B:1232 , ALA B:1233 , ARG B:1299 , ARG B:1306	BINDING SITE FOR RESIDUE SO4 B 2001
2	AC2	SOFTWARE	HOH B:54 , HOH B:406 , HIS B:1229 , ASN B:1232 , HIS B:1305 , ARG B:1314 , ARG B:1387	BINDING SITE FOR RESIDUE SO4 B 2003
3	AC3	SOFTWARE	ASN A:232 , ALA A:233 , ARG A:299 , ARG A:306 , HOH A:3021 , HOH A:3052 , HOH A:3188 , ARG B:1407	BINDING SITE FOR RESIDUE SO4 A 2004
4	AC4	SOFTWARE	HIS A:229 , ASN A:232 , ARG A:299 , HIS A:305 , ARG A:314 , ARG A:387 , HOH A:3021	BINDING SITE FOR RESIDUE SO4 A 2006
5	AC5	SOFTWARE	THR A:106 , THR A:108 , ARG A:109 , HIS A:110 , THR A:111 , MET A:112 , ILE A:113 , HIS A:114 , TYR A:145 , PHE A:162 , ARG A:163 , LYS A:167 , ILE A:180 , ASN A:189 , CYS A:206 , HOH A:3008 , HOH A:3010 , HOH A:3027 , HOH A:3042 , HOH A:3162	BINDING SITE FOR RESIDUE NAI A 3000
6	AC6	SOFTWARE	HOH B:27 , HOH B:49 , HOH B:81 , HOH B:95 , HOH B:133 , THR B:1106 , THR B:1108 , ARG B:1109 , HIS B:1110 , THR B:1111 , MET B:1112 , TYR B:1145 , ILE B:1159 , ARG B:1163 , LYS B:1167 , GLN B:1182 , ASN B:1189 , CYS B:1206	BINDING SITE FOR RESIDUE NAI B 3001

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

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

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CITRATE_SYNTHASE	PS00480	Citrate synthase signature.	CISY_ECOLI	303-315	2	A:302-314 B:1302-1314

Biological Unit 1 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CITRATE_SYNTHASE	PS00480	Citrate synthase signature.	CISY_ECOLI	303-315	6	A:302-314 B:1302-1314

(no "Exon" information available for 1NXG)

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:426
 aligned with CISY_ECOLI | P0ABH7 from UniProtKB/Swiss-Prot  Length:427

    Alignment length:426
                                    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      
          CISY_ECOLI      2 ADTKAKLTLNGDTAVELDVLKGTLGQDVIDIRTLGSKGVFTFDPGFTSTASCESKITFIDGDEGILLHRGFPIDQLATDSNYLEVCYILLNGEKPTQEQYDEFKTTVTRHTMIHEQITRLFHAFRRDSHPMAVMCGITGALAAFYHDSLDVNNPRHREIAAFRLLSKMPTMAAMCYKYSIGQPFVYPRNDLSYAGNFLNMMFSTPCEPYEVNPILERAMDRILILHADHEQNASTSTVRTAGSSGANPFACIAAGIASLWGPAHGGANEAALKMLEEISSVKHIPEFVRRAKDKNDSFRLMGFGHRVYKNYDPRATVMRETCHEVLKELGTKDDLLEVAMELENIALNDPYFIEKKLYPNVDFYSGIILKAMGIPSSMFTVIFAMARTVGWIAHWSEMHSDGMKIARPRQLYTGYEKRDFKSDIKR  427
               SCOP domains d1nxga_ A: Citrate synthase                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains -------------------------------------------------1nxgA02 A:50-266,A:376-412 Citrate Synthase, domain 1                                                                                                                                                                    1nxgA03 A:267-375 Cytochrome P450-Terp, domain 2                                                             1nxgA02 A:50-266,A:376-412           -------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeee...eeeeeee.......eee..........ee......eeeeee..eeee....eeee..eehhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh....hhhhhhhhh......hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhh........hhhhhhhhhhhhhh......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh................................................hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CITRATE_SYNTH---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1nxg A    1 ADTKAKLTLNGDTAVELDVLKGTLGQDVIDIRTLGSKGVFTFDPGFTSTASCESKITFIDGDEGILLHRGFPIDQLATDSNYLEVCYILLNGEKPTQEQYDEFKTTVTRHTMIHEQITRLFHAFRRDSHPMAVMCGITGALAAFYHDSLDVNNPRHREIAAFRLLSKMPTMAAMCYKYSIGQPFVYPRNDLSYAGNFLNMMFSTPCEPYEVNPILERAMDRILILHADHEQNASTSTVRTAGSSGANPFACIAAGIASLWGPAHGGANEAALKMLEEISSVKHIPEFFRRAKDKNDSFRLMGFGHRVYKNYDPRATVMRETCHEVLKELGTKDDLLEVAMELENIALNDPYFIEKKLYPNVDFYSGIILKAMGIPSSMFTVIAAMARTVGWIAHWSEMHSDGMKIARPRQLYTGYEKRDFKSDIKR  426
                                    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       320       330       340       350       360       370       380       390       400       410       420

Chain B from PDB  Type:PROTEIN  Length:426
 aligned with CISY_ECOLI | P0ABH7 from UniProtKB/Swiss-Prot  Length:427

    Alignment length:426
                                    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      
          CISY_ECOLI      2 ADTKAKLTLNGDTAVELDVLKGTLGQDVIDIRTLGSKGVFTFDPGFTSTASCESKITFIDGDEGILLHRGFPIDQLATDSNYLEVCYILLNGEKPTQEQYDEFKTTVTRHTMIHEQITRLFHAFRRDSHPMAVMCGITGALAAFYHDSLDVNNPRHREIAAFRLLSKMPTMAAMCYKYSIGQPFVYPRNDLSYAGNFLNMMFSTPCEPYEVNPILERAMDRILILHADHEQNASTSTVRTAGSSGANPFACIAAGIASLWGPAHGGANEAALKMLEEISSVKHIPEFVRRAKDKNDSFRLMGFGHRVYKNYDPRATVMRETCHEVLKELGTKDDLLEVAMELENIALNDPYFIEKKLYPNVDFYSGIILKAMGIPSSMFTVIFAMARTVGWIAHWSEMHSDGMKIARPRQLYTGYEKRDFKSDIKR  427
               SCOP domains d1nxgb_ B: Citrate synthase                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains -------------------------------------------------1nxgB02 B:1050-1266,B:1376-1412 Citrate Synthase, domain 1                                                                                                                                                               1nxgB03 B:1267-1375 Cytochrome P450-Terp, domain 2                                                           1nxgB02 B:1050-1266,B:1376-1412      -------------- CATH domains
           Pfam domains (1) --------------------------------------------Citrate_synt-1nxgB01 B:1045-1408                                                                                                                                                                                                                                                                                                                                            ------------------ Pfam domains (1)
           Pfam domains (2) --------------------------------------------Citrate_synt-1nxgB02 B:1045-1408                                                                                                                                                                                                                                                                                                                                            ------------------ Pfam domains (2)
         Sec.struct. author ......eeee...eeee...........ee.hhhhhhh.eee......eeeeee..eeee....eeee..eehhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh....hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh........hhhhhhhhhhhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.......hhhhh....................................hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CITRATE_SYNTH---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1nxg B 1001 ADTKAKLTLNGDTAVELDVLKGTLGQDVIDIRTLGSKGVFTFDPGFTSTASCESKITFIDGDEGILLHRGFPIDQLATDSNYLEVCYILLNGEKPTQEQYDEFKTTVTRHTMIHEQITRLFHAFRRDSHPMAVMCGITGALAAFYHDSLDVNNPRHREIAAFRLLSKMPTMAAMCYKYSIGQPFVYPRNDLSYAGNFLNMMFSTPCEPYEVNPILERAMDRILILHADHEQNASTSTVRTAGSSGANPFACIAAGIASLWGPAHGGANEAALKMLEEISSVKHIPEFFRRAKDKNDSFRLMGFGHRVYKNYDPRATVMRETCHEVLKELGTKDDLLEVAMELENIALNDPYFIEKKLYPNVDFYSGIILKAMGIPSSMFTVIAAMARTVGWIAHWSEMHSDGMKIARPRQLYTGYEKRDFKSDIKR 1426
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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 Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All alpha proteins (14657)

Fold: Citrate synthase (43)

Superfamily: Citrate synthase (43)

Family: Citrate synthase (38)

Protein domain: Citrate synthase (32)

Escherichia coli [TaxId: 562] (9)

1a	d1nxga_	A:
1b	d1nxgb_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Citrate Synthase; domain 1 (32)

Homologous Superfamily: Citrate Synthase, domain 1 (32)

Escherichia coli. Organism_taxid: 562. (4)

1a	1nxgA02	A:50-266,A:376-412
1b	1nxgB02	B:1050-1266,B:1376-1412

Topology: Cytochrome p450-Terp; domain 2 (32)

Homologous Superfamily: Cytochrome P450-Terp, domain 2 (32)

Escherichia coli. Organism_taxid: 562. (4)

2a	1nxgA03	A:267-375
2b	1nxgB03	B:1267-1375

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Citrate_synt] (9)

Family: Citrate_synt (9)

Escherichia coli (strain K12) (3)

1a	Citrate_synt-1nxgB01	B:1045-1408
1b	Citrate_synt-1nxgB02	B:1045-1408

Asymmetric Unit(hide GO term definitions)

Chain A,B (CISY_ECOLI | P0ABH7)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0004108	citrate (Si)-synthase activity	Catalysis of the reaction: acetyl-CoA + H2O + oxaloacetate = citrate + CoA, where the acetyl group is added to the si-face of oxaloacetate; acetyl-CoA thus provides the two carbon atoms of the pro-S carboxymethyl group.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0046912	transferase activity, transferring acyl groups, acyl groups converted into alkyl on transfer	Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor), with the acyl group being converted into alkyl on transfer.
biological process
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0006099	tricarboxylic acid cycle	A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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Ligands, Modified Residues, Ions (2, 6)

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