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(-) Description

Title :  ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE FROM MYCOBACTERIUM TUBERCULOSIS COMPLEXED WITH A FRAGMENT FROM DSF SCREENING
 
Authors :  R. Dai, B. C. Finzel, T. W. Geders
Date :  17 Nov 14  (Deposition) - 15 Jul 15  (Release) - 22 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Keywords :  Transaminase Plp Complex Fragment, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Dai, T. W. Geders, F. Liu, S. W. Park, D. Schnappinger, C. C. Aldrich, B. C. Finzel
Fragment-Based Exploration Of Binding Site Flexibility In Mycobacterium Tuberculosis Bioa.
J. Med. Chem. V. 58 5208 2015
PubMed-ID: 26068403  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B00092

(-) Compounds

Molecule 1 - ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE
    Chains: A, B
    EC Number: 2.6.1.62
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: BIOA, RV1568, MTCY336.35C
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCC 25618 / H37RV)
    Organism Taxid: 83332
    Strain: ATCC 25618 / H37RV
    Synonym: 7,8-DIAMINO-PELARGONIC ACID AMINOTRANSFERASE,DAPA AMINOTRANSFERASE,8-DIAMINONONANOATE SYNTHASE,DANS,DIAMINOPELARGONIC ACID SYNTHASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 17)

Asymmetric Unit (4, 17)
No.NameCountTypeFull Name
13VR2Ligand/IonN-METHYL-1-[4-(1H-PYRAZOL-1-YLMETHYL)PHENYL]METHANAMINE
2EDO11Ligand/Ion1,2-ETHANEDIOL
3EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (4, 17)
No.NameCountTypeFull Name
13VR2Ligand/IonN-METHYL-1-[4-(1H-PYRAZOL-1-YLMETHYL)PHENYL]METHANAMINE
2EDO11Ligand/Ion1,2-ETHANEDIOL
3EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:65 , SER A:125 , TYR A:157 , HIS A:158 , GLU A:220 , ASP A:254 , ILE A:256 , ALA A:257 , LYS A:283 , 3VR A:502 , HOH A:622 , HOH A:737 , HOH A:741 , HOH A:784 , GLY B:316 , PRO B:317 , THR B:318binding site for residue PLP A 501
02AC2SOFTWARETYR A:25 , TRP A:64 , TRP A:65 , TYR A:157 , MET A:174 , ALA A:226 , PLP A:501 , EPE A:503 , HOH A:644 , GLY B:316 , THR B:318binding site for residue 3VR A 502
03AC3SOFTWARETYR A:25 , SER A:27 , GLU A:31 , TRP A:64 , ARG A:400 , 3VR A:502 , HOH A:676 , HOH A:707 , HOH A:714 , GLY B:93 , GLY B:94binding site for residue EPE A 503
04AC4SOFTWAREARG A:193 , ARG A:230 , PHE A:231 , ARG A:369 , HOH A:612 , HOH A:860 , HOH A:917binding site for residue EDO A 504
05AC5SOFTWAREPRO A:234 , CYS A:371 , HOH A:611 , HOH A:890binding site for residue EDO A 505
06AC6SOFTWAREARG A:142 , LEU A:144 , HOH A:615 , HOH A:641 , HOH A:812 , ARG B:154 , GLN B:185 , VAL B:186 , PHE B:187binding site for residue EDO A 506
07AC7SOFTWAREGLY A:355 , THR A:358 , THR A:423 , SER A:424 , HOH A:620 , ARG B:85 , HOH B:829 , HOH B:935binding site for residue EDO A 507
08AC8SOFTWAREARG A:241 , ARG A:245 , HOH A:638binding site for residue EDO A 508
09AC9SOFTWAREILE A:110 , THR A:111 , PRO A:112 , ALA A:113 , ASP A:270 , EDO A:510 , ARG B:235binding site for residue EDO A 509
10AD1SOFTWAREASP A:270 , EDO A:509 , ARG B:235 , HIS B:238binding site for residue EDO A 510
11AD2SOFTWAREGLY A:316 , THR A:318 , TYR B:25 , TRP B:64 , TRP B:65 , TYR B:157 , ALA B:226 , PHE B:402 , PLP B:501 , EPE B:503 , HOH B:634binding site for residue 3VR B 502
12AD3SOFTWAREGLY A:93 , GLY A:94 , TYR B:25 , SER B:27 , GLU B:31 , TRP B:64 , ARG B:400 , 3VR B:502 , HOH B:660 , HOH B:683 , HOH B:729binding site for residue EPE B 503
13AD4SOFTWAREARG A:403 , ASN A:404 , GLN B:53 , ILE B:55 , HOH B:687 , HOH B:734 , HOH B:809 , HOH B:851binding site for residue EDO B 504
14AD5SOFTWAREARG B:193 , ARG B:230 , PHE B:231 , ARG B:369 , HOH B:614 , HOH B:684binding site for residue EDO B 505
15AD6SOFTWARETRP B:45 , GLU B:56binding site for residue EDO B 506
16AD7SOFTWAREARG B:193 , ASP B:194binding site for residue EDO B 507
17AD8SOFTWAREGLY A:316 , PRO A:317 , THR A:318 , PHE A:319 , TRP B:64 , TRP B:65 , GLY B:124 , SER B:125 , TYR B:157 , HIS B:158 , GLU B:220 , ASP B:254 , ILE B:256 , ALA B:257 , GLY B:282 , ALA B:284 , LEU B:285 , THR B:286 , 3VR B:502 , HOH B:616 , HOH B:669 , HOH B:704 , HOH B:708 , HOH B:761 , HOH B:817binding site for Di-peptide PLP B 501 and LYS B 283

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4WYD)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser A:435 -Leu A:436
2Gly B:7 -Leu B:8

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4WYD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4WYD)

(-) Exons   (0, 0)

(no "Exon" information available for 4WYD)

(-) 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:430
                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..............eeeeeee..eeeeee..eeeeeee.hhhhhh......hhhhhhhhhhhhhhh.......eehhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhhhhhh......eeeee.......hhhhhh........hhhhhhhh...eee.......hhhhhhhhhhhhhhhh..eeeeee...ee.....ee..hhhhhhhhhhhhhhh.eeeee............hhhhhh.....eeeehhhhhh.....eeeeeehhhhhhhh...............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..eeeeee....eeeee....hhhhhhhhhhh..ee......eeee......hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wyd A   8 LTPEQIIAVDGAHLWHPYSSIGREAVSPVVAVAAHGAWLTLIRDGQPIEVLDAMSSWWTAIHGHGHPALDQALTTQLRVMNHVMFGGLTHEPAARLAKLLVDITPAGLDTVFFSDSGSVSVEVAAKMALQYWRGRGLPGKRRLMTWRGGYHGDTFLAMSICDPHGGMHSLWTDVLAAQVFAPQVPRDYDPAYSAAFEAQLAQHAGELAAVVVEPVVQGAGGMRFHDPRYLHDLRDICRRYEVLLIFDEIATGFGRTGALFAADHAGVSPDIMCVGKALTGGYLSLAATLCTADVAHTISAGAAGALMHGPTFMANPLACAVSVASVELLLGQDWRTRITELAAGLTAGLDTARALPAVTDVRVCGAIGVIECDRPVDLAVATPAALDRGVWLRPFRNLVYAMPPYICTPAEITQITSAMVEVARLVGSLP 437
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437


Chain B from PDB  Type:PROTEIN  Length:430
                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..............eeeeeee..eeeeee..eeeeeee.hhhhhh......hhhhhhhhhhhhhhh.......eehhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhhhhhh......eeeee.......hhhhhh........hhhhhhhh...eee.......hhhhhhhhhhhhhhhh..eeeeee...ee.....ee..hhhhhhhhhhhhhhh.eeeee............hhhhhh.....eeeehhhhhh.....eeeeeehhhhhhhhh..............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..eeeeee....eeeee....hhhhhhhhhhhh.ee......eeee......hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wyd B   7 GLTPEQIIAVDGAHLWHPYSSIGREAVSPVVAVAAHGAWLTLIRDGQPIEVLDAMSSWWTAIHGHGHPALDQALTTQLRVMNHVMFGGLTHEPAARLAKLLVDITPAGLDTVFFSDSGSVSVEVAAKMALQYWRGRGLPGKRRLMTWRGGYHGDTFLAMSICDPHGGMHSLWTDVLAAQVFAPQVPRDYDPAYSAAFEAQLAQHAGELAAVVVEPVVQGAGGMRFHDPRYLHDLRDICRRYEVLLIFDEIATGFGRTGALFAADHAGVSPDIMCVGKALTGGYLSLAATLCTADVAHTISAGAAGALMHGPTFMANPLACAVSVASVELLLGQDWRTRITELAAGLTAGLDTARALPAVTDVRVCGAIGVIECDRPVDLAVATPAALDRGVWLRPFRNLVYAMPPYICTPAEITQITSAMVEVARLVGSL 436
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436
   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  (0, 0)

(no "SCOP Domain" information available for 4WYD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4WYD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4WYD)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        BIOA_MYCTU | P9WQ81: 3bv0 3lv2 3tft 3tfu 4cxq 4cxr 4mqp 4mqq 4mqr 4w1v 4w1w 4w1x 4wya 4wyc 4wye 4wyf 4wyg 4xew 4xjl 4xjm 4xjo 4xjp

(-) Related Entries Specified in the PDB File

4wya 4wyc 4wye 4wyf 4wyg