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(-) Description

Title :  STRUCTURE OF ACTIVATED ACONITASE. FORMATION OF THE (4FE-4S) CLUSTER IN THE CRYSTAL
 
Authors :  A. H. Robbins, C. D. Stout
Date :  16 Jan 90  (Deposition) - 15 Jul 90  (Release) - 24 Mar 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Lyase(Carbon-Oxygen) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. H. Robbins, C. D. Stout
Structure Of Activated Aconitase: Formation Of The [4Fe-4S] Cluster In The Crystal.
Proc. Natl. Acad. Sci. Usa V. 86 3639 1989
PubMed-ID: 2726740  |  Reference-DOI: 10.1073/PNAS.86.10.3639
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ACONITASE
    Chains: A
    EC Number: 4.2.1.3
    Engineered: YES
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 4)

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
1PCA1Mod. Amino AcidPYROGLUTAMIC ACID
2SF41Ligand/IonIRON/SULFUR CLUSTER
3SO41Ligand/IonSULFATE ION
4TRC1Ligand/IonTRICARBALLYLIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:72 , ARG A:580 , SER A:642 , SER A:643 , ARG A:644 , HOH A:807BINDING SITE FOR RESIDUE SO4 A 998
2AC2SOFTWAREILE A:145 , HIS A:147 , HIS A:167 , CYS A:358 , CYS A:421 , CYS A:424 , ILE A:425 , ASN A:446 , HOH A:806BINDING SITE FOR RESIDUE SF4 A 999
3AC3SOFTWARELYS A:198 , GLY A:235 , ARG A:666 , THR A:730 , HOH A:770 , HOH A:824 , HOH A:849 , HOH A:978 , HOH A:979 , HOH A:1029BINDING SITE FOR RESIDUE TRC A 899
4ACTAUTHORSF4 A:999 , SO4 A:998 , GLN 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:644THE ACTIVE SITE HAS BEEN SHOWN, BY MOSSBAUER AND ENDOR SPECTROSCOPY, TO BE AT FE4 OF THE IRON-SULFUR CLUSTER. RESIDUES LINING THE ACTIVE SITE ARE LISTED IN HERE. THE ACTIVE SITE IS OCCUPIED BY A TIGHTLY BOUND SULFATE ION AND SOLVENT MOLECULES. THE DENSITY THAT HAS BEEN MODELLED AS TRICARBALLYLATE INHIBITOR LIES AT THE ENTRANCE TO THE CLEFT, WITH ITS CENTRAL CARBOXYL POINTING OUT INTO BULK SOLVENT. LYSINES 198 AND 673 AND ARG 666 ARE POTENTIAL CHARGE BALANCING SIDE CHAINS NEARBY. THIS INHIBITOR LOCATION IS APPROXIMATELY 20 ANGSTROMS FROM THE LOCATION OF ATOM FE4 OF FS4 999 IN PROTEIN DATA BANK ENTRY 6ACN.

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 6ACN)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 6ACN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 6ACN)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 6ACN)

(-) Exons   (0, 0)

(no "Exon" information available for 6ACN)

(-) 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:754
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d6acna2 A:1-528 Aconitase A, N-terminal domain                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  d6acna1 A:529-754 Aconitase A, C-terminal domain                                                                                                                                                                                   SCOP domains
               CATH domains -6acnA01 A:2-202 Aconitase, domain 3                                                                                                                                                                      6acnA02 A:203-315 Aconitase, Domain 2                                                                            6acnA03 A:316-490 Aconitase, domain 3                                                                                                                                          -------------------------------------------6acnA04 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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 6acn A   1 xRAKVAMSHFEPHEYIRYDLLEKNIDIVRKRLNRPLTLSEKIVYGHLDDPANQEIERGKTYLRLRPDRVAMQDATAQMAMLQFISSGLPKVAVPSTIHCDHLIEAQLGGEKDLRRAKDINQEVYNFLATAGAKYGVGFWRPGSGIIHQIILENYAYPGVLLIGTDSHTPNGGGLGGICIGVGGADAVDVMAGIPWELKCPKVIGVKLTGSLSGWTSPKDVILKVAGILTVKGGTGAIVEYHGPGVDSISCTGMATICNMGAEIGATTSVFPYNHRMKKYLSKTGRADIANLADEFKDHLVPDPGCHYDQVIEINLSELKPHINGPFTPDLAHPVAEVGSVAEKEGWPLDIRVGLIGSCTNSSYEDMGRSAAVAKQALAHGLKCKSQFTITPGSEQIRATIERDGYAQVLRDVGGIVLANACGPCIGQWDRKDIKKGEKNTIVTSYNRNFTGRNDANPETHAFVTSPEIVTALAIAGTLKFNPETDFLTGKDGKKFKLEAPDADELPRAEFDPGQDTYQHPPKDSSGQRVDVSPTSQRLQLLEPFDKWDGKDLEDLQILIKVKGKCTTDHISAAGPWLKFRGHLDNISNNLLIGAINIENRKANSVRNAVTQEFGPVPDTARYYKQHGIRWVVIGDENYGEGSSREHSALEPRHLGGRAIITKSFARIHETNLKKQGLLPLTFADPADYNKIHPVDKLTIQGLKDFAPGKPLKCIIKHPNGTQETILLNHTFNETQIEWFRAGSALNRMKELQQK 754
                            |       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       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750    
                            |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
                            1-PCA
   Legend:   → Mismatch (orange background)
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  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 6ACN)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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        ACON_PIG | P16276: 1b0j 1b0k 1b0m 5acn 7acn

(-) Related Entries Specified in the PDB File

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