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(-) Description

Title :  STERIC AND CONFORMATIONAL FEATURES OF THE ACONITASE MECHANISM
 
Authors :  C. D. Stout
Date :  11 Nov 94  (Deposition) - 26 Jan 95  (Release) - 24 Mar 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Lyase(Carbon-Oxygen) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Lauble, C. D. Stout
Steric And Conformational Features Of The Aconitase Mechanism.
Proteins V. 22 1 1995
PubMed-ID: 7675781  |  Reference-DOI: 10.1002/PROT.340220102
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ACONITASE
    Chains: A
    EC Number: 4.2.1.3
    Engineered: YES
    Organism Common: CATTLE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1OH1Ligand/IonHYDROXIDE ION
2SF41Ligand/IonIRON/SULFUR CLUSTER
3SO41Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:165 , HIS A:167 , SF4 A:999 , HOH A:1336 , HOH A:1352BINDING SITE FOR RESIDUE OH A 998
2AC2SOFTWAREGLN A:72 , THR A:75 , ARG A:580 , SER A:642 , SER A:643 , ARG A:644 , HOH A:1266 , HOH A:1336BINDING SITE FOR RESIDUE SO4 A 997
3AC3SOFTWAREILE A:145 , HIS A:167 , CYS A:358 , CYS A:421 , CYS A:424 , ASN A:446 , OH A:998BINDING SITE FOR RESIDUE SF4 A 999
4ACTUNKNOWNGLN A:72 , ASP A:100 , HIS A:101 , HIS A:147 , ASP A:165 , SER A:166 , HIS A:167 , ASN A:170 , ASN A:258 , GLU A:262 , ASN A:446 , ARG A:447 , ARG A:452 , ARG A:580 , SER A:642 , SER A:643 , ARG A:644 , SF4 A:999NULL

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:324 -Pro A:325

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ACONITASE_1PS00450 Aconitase family signature 1.ACON_BOVIN377-393  1A:350-366
2ACONITASE_2PS01244 Aconitase family signature 2.ACON_BOVIN440-453  1A:413-426

(-) Exons   (17, 17)

Asymmetric/Biological Unit (17, 17)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSBTAT000000084311ENSBTAE00000314040chr5:119723315-11972337965ACON_BOVIN1-12120--
1.2ENSBTAT000000084312ENSBTAE00000314039chr5:119748644-119748780137ACON_BOVIN13-58461A:2-3130
1.3ENSBTAT000000084313ENSBTAE00000068175chr5:119754553-119754811259ACON_BOVIN58-144871A:31-11787
1.4ENSBTAT000000084314ENSBTAE00000068177chr5:119757942-11975803493ACON_BOVIN145-175311A:118-14831
1.5ENSBTAT000000084315ENSBTAE00000068178chr5:119761458-119761616159ACON_BOVIN176-228531A:149-20153
1.6ENSBTAT000000084316ENSBTAE00000068184chr5:119761847-119761997151ACON_BOVIN229-279511A:202-25251
1.7ENSBTAT000000084317ENSBTAE00000068188chr5:119763299-119763403105ACON_BOVIN279-314361A:252-28736
1.8ENSBTAT000000084318ENSBTAE00000068190chr5:119764314-11976440592ACON_BOVIN314-344311A:287-31731
1.9ENSBTAT000000084319ENSBTAE00000068193chr5:119765369-119765474106ACON_BOVIN345-380361A:318-35336
1.10ENSBTAT0000000843110ENSBTAE00000068197chr5:119766612-119766769158ACON_BOVIN380-432531A:353-40553
1.11ENSBTAT0000000843111ENSBTAE00000068199chr5:119766902-11976697574ACON_BOVIN433-457251A:406-43025
1.12ENSBTAT0000000843112ENSBTAE00000068200chr5:119767584-119767695112ACON_BOVIN457-494381A:430-46738
1.13ENSBTAT0000000843113ENSBTAE00000068201chr5:119768754-119768876123ACON_BOVIN495-535411A:468-50841
1.14ENSBTAT0000000843114ENSBTAE00000068202chr5:119769074-119769229156ACON_BOVIN536-587521A:509-56052
1.15ENSBTAT0000000843115ENSBTAE00000068203chr5:119770055-119770246192ACON_BOVIN588-651641A:561-62464
1.16ENSBTAT0000000843116ENSBTAE00000068204chr5:119770621-119770753133ACON_BOVIN652-696451A:625-66945
1.17ENSBTAT0000000843117ENSBTAE00000068205chr5:119771250-119771371122ACON_BOVIN696-736411A:669-70941
1.18ENSBTAT0000000843118ENSBTAE00000293773chr5:119771855-119772376522ACON_BOVIN737-780441A:710-75344

(-) 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    
   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:753
 aligned with ACON_BOVIN | P20004 from UniProtKB/Swiss-Prot  Length:780

    Alignment length:753
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         780 
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768       778 | 
           ACON_BOVIN    29 RAKVAMSHFEPNEYIRYDLLEKNINIVRKRLNRPLTLSEKIVYGHLDDPANQEIERGKTYLRLRPDRVAMQDATAQMAMLQFISSGLPKVAVPSTIHCDHLIEAQLGGEKDLRRAKDINQEVYNFLATAGAKYGVGFWRPGSGIIHQIILENYAYPGVLLIGTDSHTPNGGGLGGICIGVGGADAVDVMAGIPWELKCPKVIGVKLTGSLSGWTSPKDVILKVAGILTVKGGTGAIVEYHGPGVDSISCTGMATICNMGAEIGATTSVFPYNHRMKKYLSKTGRADIANLADEFKDHLVPDSGCHYDQLIEINLSELKPHINGPFTPDLAHPVAEVGSVAEKEGWPLDIRVGLIGSCTNSSYEDMGRSAAVAKQALAHGLQCKSQFTITPGSEQIRATIERDGYAQILRDVGGIVLANACGPCIGQWDRKDIKKGEKNTIVTSYNRNFTGRNDANPETHAFVTSPEIVTALAIAGTLKFNPETDFLTGKDGKKFKLEAPDADELPRAEFDPGQDTYQHPPKDSSGQQVDVSPTSQRLQLLEPFDKWDGRDLEDLQILIKVKGKCTTDHISAAGPWLKFRGHLDNISNNLLIGAINVENGKANSVRNAVTQEFGPVPDTARYYKKHGIRWVVIGDENYGEGSSREHAALEPRHLGGRAIITKSFARIHETNLKKQGLLPLTFADPADYNKIHPVDKLTIKGLKDFAPGKPLTCIIKHPNGTQETILLNHTFNETQIEWFRAGSALNRMKELQK-   -
               SCOP domains d1amja2 A:2-528 Aconitase A, N-terminal domain                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 d1amja1 A:529-754 Aconitase A, C-terminal domain                                                                                                                                                                                   SCOP domains
               CATH domains 1amjA01 A:2-202 Aconitase, domain 3                                                                                                                                                                      1amjA02 A:203-315 Aconitase, Domain 2                                                                            1amjA03 A:316-490 Aconitase, domain 3                                                                                                                                          -------------------------------------------1amjA04 A:534-754 Aconitase, domain 4                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) ................hhhhhhhhhhhhhhhh....hhhhhhhh....hhhh......eeeee..eeeeeee..hhhhhhhhhhh.......eeeee...........hhhhhhhhhh.hhhhhhhhhhhhhh.eeee.......hhhhhh......eeeee..hhhhhhhhh.eeeeee.hhhhhhhhh..eeeeee.eeeeeeeee.......hhhhhhhhhhhh.hhhhh--------hhhhh..hhhhhhhhhhhhhh..eeeee...hhhhhhhhh...hhhhhhhhhhhhh..........eeeeeee....eeee......eeee..hhhhhhhhh......eeeeeee.....hhhhhhhhhhhhhhhh.......eeeee...hhhhhhhhhh.hhhhhhhh..eee.....hhh.............eeeeee..............eeeeee.hhhhhhhhhh........................................eee.................................eeeeeeeeee.....hhhh....hhhhh...hhhhhhh..........................hhhhhhhhhh....eeeeee.........hhhhhhhhhh..eeeeee...hhhhhhhhhh.eeeeee...hhhhhh...eeeeee.........eeeeeeee...eeeeeeee....hhhhhhhhh..hhhhhhhh... Sec.struct. author (1)
     Sec.struct. author (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------eeeeeeeee------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACONITASE_1      ----------------------------------------------ACONITASE_2   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:2-31         --------------------------------------------------------------------------------------Exon 1.4  PDB: A:118-148       Exon 1.5  PDB: A:149-201 UniProt: 176-228            Exon 1.6  PDB: A:202-252 UniProt: 229-279          ----------------------------------Exon 1.8  PDB: A:287-317       -----------------------------------Exon 1.10  PDB: A:353-405 UniProt: 380-432           Exon 1.11  PDB: A:406-430-------------------------------------Exon 1.13  PDB: A:468-508                Exon 1.14  PDB: A:509-560 UniProt: 536-587          Exon 1.15  PDB: A:561-624 UniProt: 588-651                      Exon 1.16  PDB: A:625-669 UniProt: 652-696   ----------------------------------------Exon 1.18  PDB: A:710-753 UniProt: 737-780  - Transcript 1 (1)
           Transcript 1 (2) -----------------------------Exon 1.3  PDB: A:31-117 UniProt: 58-144                                                --------------------------------------------------------------------------------------------------------------------------------------Exon 1.7  PDB: A:252-287            ------------------------------Exon 1.9  PDB: A:318-353            ----------------------------------------------------------------------------Exon 1.12  PDB: A:430-467             ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.17  PDB: A:669-709                --------------------------------------------- Transcript 1 (2)
                 1amj A   2 RAKVAMSHFEPHEYIRYDLLEKNIDIVRKRLNRPLTLSEKIVYGHLDDPANQEIERGKTYLRLRPDRVAMQDATAQMAMLQFISSGLPKVAVPSTIHCDHLIEAQLGGEKDLRRAKDINQEVYNFLATAGAKYGVGFWRPGSGIIHQIILENYAYPGVLLIGTDSHTPNGGGLGGICIGVGGADAVDVMAGIPWELKCPKVIGVKLTGSLSGWTSPKDVILKVAGILTVKGGTGAIVEYHGPGVDSISCTGMATICNMGAEIGATTSVFPYNHRMKKYLSKTGRADIANLADEFKDHLVPDSGCHYDQLIEINLSELKPHINGPFTPDLAHPVAEVGSVAEKEGWPLDIRVGLIGSCTNSSYEDMGRSAAVAKQALAHGLKCKSQFTITPGSEQIRATIERDGYAQVLRDVGGIVLANACGPCIGQWDRKDIKKGEKNTIVTSYNRNFTGRNDANPETHAFVTSPEIVTALAIAGTLKFNPETDFLTGKDGKKFKLEAPDADELPRAEFDPGQDTYQHPPKDSSGQRVDVSPTSQRLQLLEPFDKWDGKDLEDLQILIKVKGKCTTDHISAAGPWLKFRGHLDNISNNLLIGAINSENRKANSVRNAVTQEFGPVPDTARYYKQHGIRWVVIGDENYGEGSSREHSALEPRFLGGRAIITKSFARIHETNLKKQGLLPLTFADPADYNKIHPVDKLTIQGLKDFAPGKPLTCIIKHPNGTQETILLNHTFNETQIEWFRAGSALNRMKELQQK 754
                                    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       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ACON_BOVIN | P20004)
molecular function
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0003994    aconitate hydratase activity    Catalysis of the reaction: citrate = isocitrate. The reaction occurs in two steps: (1) citrate = cis-aconitate + H2O, (2) cis-aconitate + H2O = isocitrate. This reaction is the interconversion of citrate and isocitrate via the labile, enzyme-bound intermediate cis-aconitate. Water is removed from one part of the citrate molecule and added back to a different atom to form isocitrate.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0006101    citrate metabolic process    The chemical reactions and pathways involving citrate, 2-hydroxy-1,2,3-propanetricarboyxlate. Citrate is widely distributed in nature and is an important intermediate in the TCA cycle and the glyoxylate cycle.
    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:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0043209    myelin sheath    An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ACON_BOVIN | P20004: 1aco 1ami 1c96 1c97 1fgh 1nis 1nit 8acn

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1AMJ)