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(-) Description

Title :  THE X-RAY STRUCTURE OF OCTAMERIC HUMAN NATIVE 5-AMINOLAEVULINIC ACID DEHYDRATASE.
 
Authors :  N. L. Mills-Davies, D. Thompson, P. M. Shoolingin-Jordan, P. T. Erskin J. B. Cooper
Date :  18 Jan 16  (Deposition) - 27 Jan 16  (Release) - 25 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.83
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (4x)
Keywords :  Tetrapyrrole Biosynthesis Enzyme, Tim Barrel, Substrate Complex. , Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Mills-Davies, D. Butler, E. Norton, D. Thompson, M. Sarwar, J. Guo, R. Gill, N. Azim, A. Coker, S. P. Wood, P. T. Erskine, L. Coates, J. B. Cooper, N. Rashid, M. Akhtar, P. M. Shoolingin-Jordan
Structural Studies Of Substrate And Product Complexes Of 5-Aminolaevulinic Acid Dehydratase From Humans, Escherichia Coli And The Hyperthermophile Pyrobaculum Calidifontis.
Acta Crystallogr D Struct V. 73 9 2017 Biol
PubMed-ID: 28045381  |  Reference-DOI: 10.1107/S2059798316019525

(-) Compounds

Molecule 1 - DELTA-AMINOLEVULINIC ACID DEHYDRATASE
    Chains: A, B
    EC Number: 4.2.1.24
    Organ: BLOOD
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ALADH,PORPHOBILINOGEN SYNTHASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (4x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1DAV1Ligand/IonDELTA-AMINO VALERIC ACID
2SO42Ligand/IonSULFATE ION
3ZN1Ligand/IonZINC ION
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1DAV4Ligand/IonDELTA-AMINO VALERIC ACID
2SO48Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:122 , CYS A:124 , CYS A:132 , HOH A:662binding site for residue ZN A 501
2AC2SOFTWAREARG A:17 , ARG B:222binding site for residue SO4 A 502
3AC3SOFTWARELYS A:199 , TYR A:205 , PHE A:208 , LYS A:252 , TYR A:276 , SER A:279 , TYR A:318binding site for residue DAV A 503
4AC4SOFTWAREPRO B:14 , ARG B:17binding site for residue SO4 B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5HNR)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Lys A:252 -Pro A:253
2Lys B:252 -Pro B:253

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5HNR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5HNR)

(-) Exons   (0, 0)

(no "Exon" information available for 5HNR)

(-) Sequences/Alignments

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:326
                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh.hhhhhhhhh.....hhh.eeeeeeee.......ee.....eeeee..hhhhhhhhhhhh...eeeeeee.................hhhhhhhhhhhhhh...eeeeee..................hhhhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhh......ee....ee..hhhhhhhhhhhh................hhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...eeee.hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hnr A   1 MQPQSVLHSGYFHPLLRAWQTATTTLNASNLIYPIFVTDVPDDIQPITSLPGVARYGVKRLEEMLRPLVEEGLRCVLIFGVPSRVPKDERGSAADSEESPAIEAIHLLRKTFPNLLVACDVCLCPYTSHGHCGLLSGAFRAEESRQRLAEVALAYAKAGCQVVAPSDMMDGRVEAIKEALMAHGLGNRVSVMSYSAKFASCFYGPFRDAAKSSPAFGDRRCYQLPPGARGLALRAVDRDVREGADMLMVKPGMPYLDIVREVKDKHPDLPLAVYHVSGEFAMLWHGAQAGAFDLKAAVLEAMTAFRRAGADIIITYYTPQLLQWLK 328
                                    10        20        30        40        50        60        70        80        90       100       110       120       130     ||142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322      
                                                                                                                                                                 136|                                                                                                                                                                                             
                                                                                                                                                                  139                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:298
                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh.hhhhhhhhh.....hhh.eeeeeeee.......ee.....eeeehhhhhhhhhhhhhhh...eeeeeee...........hhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhh......ee....ee.....hhhhhhhh.........hhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...eeee.hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hnr B   1 MQPQSVLHSGYFHPLLRAWQTATTTLNASNLIYPIFVTDVPDDIQPITSLPGVARYGVKRLEEMLRPLVEEGLRCVLIFGVPSRVPKADSEESPAIEAIHLLRKTFPNLLVACDVCLCPYAEESRQRLAEVALAYAKAGCQVVAPSDMMDGRVEAIKEALMAHGLGNRVSVMSYSAKFASCFYGPFRDAARRCYQLPPGARGLALRAVDRDVREGADMLMVKPGMPYLDIVREVKDKHPDLPLAVYHVSGEFAMLWHGAQAGAFDLKAAVLEAMTAFRRAGADIIITYYTPQLLQWLK 328
                                    10        20        30        40        50        60        70        80      ||96       106       116       126|      152       162       172       182       192       202       212|      230       240       250       260       270       280       290       300       310       320        
                                                                                                                 87|                             126|                                                                  212|                                                                                                           
                                                                                                                  94                              143                                                                   221
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5HNR)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5HNR)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5HNR)

(-) Gene Ontology  (52, 52)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/Swiss-Prot
        HEM2_HUMAN | P13716: 1e51 1pv8 5hms

(-) Related Entries Specified in the PDB File

1e51 AN EARLIER STRUCTURAL INTERPRETATION OF THE SAME DATASET.